From 81c5572f97da78e6230e21a50cb38864a7c3efee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20Mail=C3=A4nder?= Date: Fri, 27 Oct 2023 16:39:42 +0200 Subject: [PATCH] Add read support for older RDML versions. --- .../META-INF/MANIFEST.MF | 3 +- .../v10/model/CdnaSynthesisMethodType.java | 71 +++++++ .../v10/model/CommercialAssayType.java | 51 +++++ .../v10/model/CqDetectionMethodType.java | 52 +++++ .../v10/model/DataCollectionSoftwareType.java | 50 +++++ .../rdml/internal/v10/model/DataType.java | 125 ++++++++++++ .../internal/v10/model/DocumentationType.java | 50 +++++ .../internal/v10/model/DpAmpCurveType.java | 58 ++++++ .../v10/model/DpMeltingCurveType.java | 47 +++++ .../internal/v10/model/ExperimentType.java | 70 +++++++ .../internal/v10/model/ExperimenterType.java | 96 ++++++++++ .../rdml/internal/v10/model/GradientType.java | 109 +++++++++++ .../internal/v10/model/IdReferencesType.java | 70 +++++++ .../rdml/internal/v10/model/LidOpenType.java | 27 +++ .../rdml/internal/v10/model/LoopType.java | 57 ++++++ .../rdml/internal/v10/model/MeasureType.java | 47 +++++ .../internal/v10/model/ObjectFactory.java | 167 ++++++++++++++++ .../rdml/internal/v10/model/OligoType.java | 57 ++++++ .../rdml/internal/v10/model/PauseType.java | 37 ++++ .../internal/v10/model/PrimingMethodType.java | 52 +++++ .../rdml/internal/v10/model/QuantityType.java | 51 +++++ .../internal/v10/model/QuantityUnitType.java | 56 ++++++ .../rdml/internal/v10/model/Rdml.java | 145 ++++++++++++++ .../rdml/internal/v10/model/RdmlIdType.java | 62 ++++++ .../rdml/internal/v10/model/ReactType.java | 66 +++++++ .../rdml/internal/v10/model/RunType.java | 164 ++++++++++++++++ .../rdml/internal/v10/model/SampleType.java | 180 +++++++++++++++++ .../internal/v10/model/SampleTypeType.java | 54 ++++++ .../internal/v10/model/SequencesType.java | 77 ++++++++ .../rdml/internal/v10/model/StepType.java | 105 ++++++++++ .../rdml/internal/v10/model/TargetType.java | 141 ++++++++++++++ .../internal/v10/model/TargetTypeType.java | 48 +++++ .../internal/v10/model/TemperatureType.java | 98 ++++++++++ .../v10/model/TemplateQualityType.java | 46 +++++ .../model/ThermalCyclingConditionsType.java | 92 +++++++++ .../v10/model/ThirdPartyExtensionsType.java | 41 ++++ .../rdml/internal/v10/model/XRefType.java | 44 +++++ .../v11/model/CdnaSynthesisMethodType.java | 71 +++++++ .../v11/model/CommercialAssayType.java | 51 +++++ .../v11/model/CqDetectionMethodType.java | 52 +++++ .../v11/model/DataCollectionSoftwareType.java | 50 +++++ .../rdml/internal/v11/model/DataType.java | 114 +++++++++++ .../internal/v11/model/DocumentationType.java | 50 +++++ .../internal/v11/model/DpAmpCurveType.java | 58 ++++++ .../v11/model/DpMeltingCurveType.java | 47 +++++ .../rdml/internal/v11/model/DyeType.java | 49 +++++ .../internal/v11/model/ExperimentType.java | 70 +++++++ .../internal/v11/model/ExperimenterType.java | 96 ++++++++++ .../rdml/internal/v11/model/GradientType.java | 109 +++++++++++ .../internal/v11/model/IdReferencesType.java | 35 ++++ .../rdml/internal/v11/model/LidOpenType.java | 27 +++ .../rdml/internal/v11/model/LoopType.java | 57 ++++++ .../rdml/internal/v11/model/MeasureType.java | 48 +++++ .../internal/v11/model/ObjectFactory.java | 172 +++++++++++++++++ .../rdml/internal/v11/model/OligoType.java | 57 ++++++ .../rdml/internal/v11/model/PauseType.java | 37 ++++ .../internal/v11/model/PcrFormatType.java | 98 ++++++++++ .../internal/v11/model/PrimingMethodType.java | 54 ++++++ .../rdml/internal/v11/model/QuantityType.java | 51 +++++ .../internal/v11/model/QuantityUnitType.java | 56 ++++++ .../rdml/internal/v11/model/Rdml.java | 143 ++++++++++++++ .../rdml/internal/v11/model/RdmlIdType.java | 62 ++++++ .../rdml/internal/v11/model/ReactType.java | 69 +++++++ .../rdml/internal/v11/model/RunType.java | 164 ++++++++++++++++ .../rdml/internal/v11/model/SampleType.java | 181 ++++++++++++++++++ .../internal/v11/model/SampleTypeType.java | 60 ++++++ .../internal/v11/model/SequencesType.java | 77 ++++++++ .../rdml/internal/v11/model/StepType.java | 105 ++++++++++ .../rdml/internal/v11/model/TargetType.java | 153 +++++++++++++++ .../internal/v11/model/TargetTypeType.java | 48 +++++ .../internal/v11/model/TemperatureType.java | 98 ++++++++++ .../v11/model/TemplateQualityType.java | 46 +++++ .../model/ThermalCyclingConditionsType.java | 92 +++++++++ .../rdml/internal/v11/model/XRefType.java | 44 +++++ .../internal/v12/model/AnnotationType.java | 51 +++++ .../v12/model/CdnaSynthesisMethodType.java | 71 +++++++ .../v12/model/CommercialAssayType.java | 51 +++++ .../v12/model/CqDetectionMethodType.java | 52 +++++ .../v12/model/DataCollectionSoftwareType.java | 50 +++++ .../rdml/internal/v12/model/DataType.java | 125 ++++++++++++ .../internal/v12/model/DocumentationType.java | 50 +++++ .../internal/v12/model/DpAmpCurveType.java | 58 ++++++ .../v12/model/DpMeltingCurveType.java | 47 +++++ .../rdml/internal/v12/model/DyeType.java | 49 +++++ .../internal/v12/model/ExperimentType.java | 70 +++++++ .../internal/v12/model/ExperimenterType.java | 96 ++++++++++ .../rdml/internal/v12/model/GradientType.java | 109 +++++++++++ .../internal/v12/model/IdReferencesType.java | 35 ++++ .../rdml/internal/v12/model/LidOpenType.java | 27 +++ .../rdml/internal/v12/model/LoopType.java | 57 ++++++ .../rdml/internal/v12/model/MeasureType.java | 47 +++++ .../internal/v12/model/NucleotideType.java | 50 +++++ .../internal/v12/model/ObjectFactory.java | 173 +++++++++++++++++ .../rdml/internal/v12/model/OligoType.java | 57 ++++++ .../rdml/internal/v12/model/PauseType.java | 37 ++++ .../internal/v12/model/PcrFormatType.java | 98 ++++++++++ .../internal/v12/model/PrimingMethodType.java | 54 ++++++ .../rdml/internal/v12/model/QuantityType.java | 51 +++++ .../internal/v12/model/QuantityUnitType.java | 56 ++++++ .../rdml/internal/v12/model/Rdml.java | 143 ++++++++++++++ .../rdml/internal/v12/model/RdmlIdType.java | 62 ++++++ .../rdml/internal/v12/model/ReactType.java | 69 +++++++ .../rdml/internal/v12/model/RunType.java | 164 ++++++++++++++++ .../rdml/internal/v12/model/SampleType.java | 157 +++++++++++++++ .../internal/v12/model/SampleTypeType.java | 60 ++++++ .../internal/v12/model/SequencesType.java | 77 ++++++++ .../rdml/internal/v12/model/StepType.java | 105 ++++++++++ .../rdml/internal/v12/model/TargetType.java | 164 ++++++++++++++++ .../internal/v12/model/TargetTypeType.java | 48 +++++ .../internal/v12/model/TemperatureType.java | 98 ++++++++++ .../v12/model/TemplateQuantityType.java | 48 +++++ .../model/ThermalCyclingConditionsType.java | 92 +++++++++ .../rdml/internal/v12/model/XRefType.java | 44 +++++ .../internal/v13/model/PcrFormatType.java | 55 +++--- .../converter/supplier/rdml/io/PCRReader.java | 136 ++----------- .../supplier/rdml/io/PCRReaderVersion11.java | 146 ++++++++++++++ .../supplier/rdml/io/PCRReaderVersion12.java | 146 ++++++++++++++ .../supplier/rdml/io/PCRReaderVersion13.java | 146 ++++++++++++++ .../supplier/rdml/model/IPCRReader.java | 28 +++ .../test/io/Test_Example_11_ITest.java | 69 +++++++ .../test/io/Test_Example_12_ITest.java | 69 +++++++ .../test/io/Test_Example_13_ITest.java | 69 +++++++ .../rdml/fragment/test/TestPathHelper.java | 4 + .../testdata/example_1_1.rdml | Bin 0 -> 75794 bytes .../testdata/example_1_2.rdml | Bin 0 -> 75810 bytes .../testdata/example_1_3.rdml | Bin 0 -> 75841 bytes 126 files changed, 9292 insertions(+), 145 deletions(-) create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CdnaSynthesisMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CommercialAssayType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CqDetectionMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataCollectionSoftwareType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DocumentationType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpAmpCurveType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpMeltingCurveType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimentType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimenterType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/GradientType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/IdReferencesType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LidOpenType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LoopType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/MeasureType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ObjectFactory.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/OligoType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PauseType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PrimingMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityUnitType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/Rdml.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RdmlIdType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ReactType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RunType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleTypeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SequencesType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/StepType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetTypeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemperatureType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemplateQualityType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThermalCyclingConditionsType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThirdPartyExtensionsType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/XRefType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CdnaSynthesisMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CommercialAssayType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CqDetectionMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataCollectionSoftwareType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DocumentationType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpAmpCurveType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpMeltingCurveType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DyeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimentType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimenterType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/GradientType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/IdReferencesType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LidOpenType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LoopType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/MeasureType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ObjectFactory.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/OligoType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PauseType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PcrFormatType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PrimingMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityUnitType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/Rdml.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RdmlIdType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ReactType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RunType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleTypeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SequencesType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/StepType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetTypeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemperatureType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemplateQualityType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ThermalCyclingConditionsType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/XRefType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/AnnotationType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CdnaSynthesisMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CommercialAssayType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CqDetectionMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataCollectionSoftwareType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DocumentationType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpAmpCurveType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpMeltingCurveType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DyeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimentType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimenterType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/GradientType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/IdReferencesType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LidOpenType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LoopType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/MeasureType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/NucleotideType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ObjectFactory.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/OligoType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PauseType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PcrFormatType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PrimingMethodType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityUnitType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/Rdml.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RdmlIdType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ReactType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RunType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleTypeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SequencesType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/StepType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetTypeType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemperatureType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemplateQuantityType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ThermalCyclingConditionsType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/XRefType.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion11.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion12.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion13.java create mode 100644 chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/model/IPCRReader.java create mode 100644 chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_11_ITest.java create mode 100644 chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_12_ITest.java create mode 100644 chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_13_ITest.java create mode 100644 chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/testdata/example_1_1.rdml create mode 100644 chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/testdata/example_1_2.rdml create mode 100644 chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/testdata/example_1_3.rdml diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/META-INF/MANIFEST.MF b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/META-INF/MANIFEST.MF index 8f09c9adeb..c0a93e51b8 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/META-INF/MANIFEST.MF +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/META-INF/MANIFEST.MF @@ -14,7 +14,8 @@ Require-Bundle: org.eclipse.core.runtime, org.eclipse.chemclipse.logging;bundle-version="0.8.0", org.eclipse.chemclipse.processing;bundle-version="0.8.0", org.eclipse.chemclipse.support;bundle-version="0.8.0", - jakarta.xml.bind-api;bundle-version="4.0.0" + jakarta.xml.bind-api;bundle-version="4.0.0", + org.eclipse.chemclipse.xxd.converter.supplier.chemclipse;bundle-version="0.9.0" Bundle-RequiredExecutionEnvironment: JavaSE-17 Bundle-ActivationPolicy: lazy Import-Package: jakarta.xml.bind, diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CdnaSynthesisMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CdnaSynthesisMethodType.java new file mode 100644 index 0000000000..cd2b65f06d --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CdnaSynthesisMethodType.java @@ -0,0 +1,71 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Description of the cDNA synthesis method. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "cdnaSynthesisMethodType", propOrder = {"enzyme", "primingMethod", "dnaseTreatment", "thermalCyclingConditions"}) +public class CdnaSynthesisMethodType { + + protected String enzyme; + @XmlSchemaType(name = "string") + protected PrimingMethodType primingMethod; + protected Boolean dnaseTreatment; + protected IdReferencesType thermalCyclingConditions; + + public String getEnzyme() { + + return enzyme; + } + + public void setEnzyme(String value) { + + this.enzyme = value; + } + + public PrimingMethodType getPrimingMethod() { + + return primingMethod; + } + + public void setPrimingMethod(PrimingMethodType value) { + + this.primingMethod = value; + } + + public Boolean isDnaseTreatment() { + + return dnaseTreatment; + } + + public void setDnaseTreatment(Boolean value) { + + this.dnaseTreatment = value; + } + + public IdReferencesType getThermalCyclingConditions() { + + return thermalCyclingConditions; + } + + public void setThermalCyclingConditions(IdReferencesType value) { + + this.thermalCyclingConditions = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CommercialAssayType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CommercialAssayType.java new file mode 100644 index 0000000000..616fedfd33 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CommercialAssayType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * For some commercial assays the primer sequences may be unknown. This element + * allows to describe commercial assays. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "commercialAssayType", propOrder = {"company", "orderNumber"}) +public class CommercialAssayType { + + @XmlElement(required = true) + protected String company; + @XmlElement(required = true) + protected String orderNumber; + + public String getCompany() { + + return company; + } + + public void setCompany(String value) { + + this.company = value; + } + + public String getOrderNumber() { + + return orderNumber; + } + + public void setOrderNumber(String value) { + + this.orderNumber = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CqDetectionMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CqDetectionMethodType.java new file mode 100644 index 0000000000..1265ebeb73 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/CqDetectionMethodType.java @@ -0,0 +1,52 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "cqDetectionMethodType") +@XmlEnum +public enum CqDetectionMethodType { + + @XmlEnumValue("automated threshold and baseline settings") + AUTOMATED_THRESHOLD_AND_BASELINE_SETTINGS("automated threshold and baseline settings"), // + @XmlEnumValue("manual threshold and baseline settings") + MANUAL_THRESHOLD_AND_BASELINE_SETTINGS("manual threshold and baseline settings"), // + @XmlEnumValue("second derivative maximum") + SECOND_DERIVATIVE_MAXIMUM("second derivative maximum"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + CqDetectionMethodType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static CqDetectionMethodType fromValue(String v) { + + for(CqDetectionMethodType c : CqDetectionMethodType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataCollectionSoftwareType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataCollectionSoftwareType.java new file mode 100644 index 0000000000..8635e81ee9 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataCollectionSoftwareType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Software name and version used to collect the data. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dataCollectionSoftwareType", propOrder = {"name", "version"}) +public class DataCollectionSoftwareType { + + @XmlElement(required = true) + protected String name; + @XmlElement(required = true) + protected String version; + + public String getName() { + + return name; + } + + public void setName(String value) { + + this.name = value; + } + + public String getVersion() { + + return version; + } + + public void setVersion(String value) { + + this.version = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataType.java new file mode 100644 index 0000000000..bb545dc686 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DataType.java @@ -0,0 +1,125 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the high numbers of this elements names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dataType", propOrder = {"tar", "cq", "quantity", "excl", "adp", "mdp", "endPt", "bgFluor", "quantFluor"}) +public class DataType { + + @XmlElement(required = true) + protected IdReferencesType tar; + protected Float cq; + protected QuantityType quantity; + protected String excl; + protected List adp; + protected List mdp; + protected Float endPt; + protected Float bgFluor; + protected Float quantFluor; + + public IdReferencesType getTar() { + + return tar; + } + + public void setTar(IdReferencesType value) { + + this.tar = value; + } + + public Float getCq() { + + return cq; + } + + public void setCq(Float value) { + + this.cq = value; + } + + public QuantityType getQuantity() { + + return quantity; + } + + public void setQuantity(QuantityType value) { + + this.quantity = value; + } + + public String getExcl() { + + return excl; + } + + public void setExcl(String value) { + + this.excl = value; + } + + public List getAdp() { + + if(adp == null) { + adp = new ArrayList<>(); + } + return this.adp; + } + + public List getMdp() { + + if(mdp == null) { + mdp = new ArrayList<>(); + } + return this.mdp; + } + + public Float getEndPt() { + + return endPt; + } + + public void setEndPt(Float value) { + + this.endPt = value; + } + + public Float getBgFluor() { + + return bgFluor; + } + + public void setBgFluor(Float value) { + + this.bgFluor = value; + } + + public Float getQuantFluor() { + + return quantFluor; + } + + public void setQuantFluor(Float value) { + + this.quantFluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DocumentationType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DocumentationType.java new file mode 100644 index 0000000000..84c3948cb3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DocumentationType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * These elements should be used if the same description applies to many samples, + * targets or experiments. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "documentationType", propOrder = {}) +public class DocumentationType { + + protected String text; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getText() { + + return text; + } + + public void setText(String value) { + + this.text = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpAmpCurveType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpAmpCurveType.java new file mode 100644 index 0000000000..b4ccaedf63 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpAmpCurveType.java @@ -0,0 +1,58 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the high numbers of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dpAmpCurveType", propOrder = {"cyc", "tmp", "fluor"}) +public class DpAmpCurveType { + + protected float cyc; + protected Float tmp; + protected float fluor; + + public float getCyc() { + + return cyc; + } + + public void setCyc(float value) { + + this.cyc = value; + } + + public Float getTmp() { + + return tmp; + } + + public void setTmp(Float value) { + + this.tmp = value; + } + + public float getFluor() { + + return fluor; + } + + public void setFluor(float value) { + + this.fluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpMeltingCurveType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpMeltingCurveType.java new file mode 100644 index 0000000000..0cdd3d2059 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/DpMeltingCurveType.java @@ -0,0 +1,47 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the high numbers of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dpMeltingCurveType", propOrder = {"tmp", "fluor"}) +public class DpMeltingCurveType { + + protected float tmp; + protected float fluor; + + public float getTmp() { + + return tmp; + } + + public void setTmp(float value) { + + this.tmp = value; + } + + public float getFluor() { + + return fluor; + } + + public void setFluor(float value) { + + this.fluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimentType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimentType.java new file mode 100644 index 0000000000..b46945e188 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimentType.java @@ -0,0 +1,70 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * An experiment can contain several independent runs. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "experimentType", propOrder = {"description", "documentation", "run"}) +public class ExperimentType { + + protected String description; + protected List documentation; + protected List run; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getRun() { + + if(run == null) { + run = new ArrayList<>(); + } + return this.run; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimenterType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimenterType.java new file mode 100644 index 0000000000..92a532e2ed --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ExperimenterType.java @@ -0,0 +1,96 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Contact details of an experimenter. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "experimenterType", propOrder = {"firstName", "lastName", "email", "labName", "labAddress"}) +public class ExperimenterType { + + @XmlElement(required = true) + protected String firstName; + @XmlElement(required = true) + protected String lastName; + protected String email; + protected String labName; + protected String labAddress; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getFirstName() { + + return firstName; + } + + public void setFirstName(String value) { + + this.firstName = value; + } + + public String getLastName() { + + return lastName; + } + + public void setLastName(String value) { + + this.lastName = value; + } + + public String getEmail() { + + return email; + } + + public void setEmail(String value) { + + this.email = value; + } + + public String getLabName() { + + return labName; + } + + public void setLabName(String value) { + + this.labName = value; + } + + public String getLabAddress() { + + return labAddress; + } + + public void setLabAddress(String value) { + + this.labAddress = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/GradientType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/GradientType.java new file mode 100644 index 0000000000..7ae9e594c5 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/GradientType.java @@ -0,0 +1,109 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step forms a temperature gradient on the heat block. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "gradientType", propOrder = {"highTemperature", "lowTemperature", "duration", "temperatureChange", "durationChange", "measure", "ramp"}) +public class GradientType { + + protected float highTemperature; + protected float lowTemperature; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger duration; + protected Float temperatureChange; + protected Integer durationChange; + @XmlSchemaType(name = "string") + protected MeasureType measure; + protected Float ramp; + + public float getHighTemperature() { + + return highTemperature; + } + + public void setHighTemperature(float value) { + + this.highTemperature = value; + } + + public float getLowTemperature() { + + return lowTemperature; + } + + public void setLowTemperature(float value) { + + this.lowTemperature = value; + } + + public BigInteger getDuration() { + + return duration; + } + + public void setDuration(BigInteger value) { + + this.duration = value; + } + + public Float getTemperatureChange() { + + return temperatureChange; + } + + public void setTemperatureChange(Float value) { + + this.temperatureChange = value; + } + + public Integer getDurationChange() { + + return durationChange; + } + + public void setDurationChange(Integer value) { + + this.durationChange = value; + } + + public MeasureType getMeasure() { + + return measure; + } + + public void setMeasure(MeasureType value) { + + this.measure = value; + } + + public Float getRamp() { + + return ramp; + } + + public void setRamp(Float value) { + + this.ramp = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/IdReferencesType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/IdReferencesType.java new file mode 100644 index 0000000000..b80ed3e93e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/IdReferencesType.java @@ -0,0 +1,70 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + *

+ * Java-Klasse für idReferencesType complex type. + * + *

+ * Das folgende Schemafragment gibt den erwarteten Content an, der in dieser Klasse enthalten ist. + * + * 

+ * <complexType name="idReferencesType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <attribute name="id" use="required" type="{http://www.rdml.org}idType" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "idReferencesType") +public class IdReferencesType { + + @XmlAttribute(name = "id", required = true) + protected String id; + + /** + * Ruft den Wert der id-Eigenschaft ab. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + + return id; + } + + /** + * Legt den Wert der id-Eigenschaft fest. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LidOpenType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LidOpenType.java new file mode 100644 index 0000000000..fecbf8f272 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LidOpenType.java @@ -0,0 +1,27 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step waits for the user to open the lid and continues after. It + * allows to stop the program and to wait for the user to add for example + * enzymes and continue the program after. The temperature of the previous + * step is maintained. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "lidOpenType") +public class LidOpenType { +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LoopType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LoopType.java new file mode 100644 index 0000000000..eee4346c6c --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/LoopType.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step allows to form a loop or to exclude some steps. It allows to + * jump to a certain "goto" step for "repeat" times. If the "goto" step is + * higher than the step of the loop, "repeat" must be "0". + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "loopType", propOrder = {"gotoStep", "repeat"}) +public class LoopType { + + @XmlElement(name = "goto", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger gotoStep; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger repeat; + + public BigInteger getGoto() { + + return gotoStep; + } + + public void setGoto(BigInteger value) { + + this.gotoStep = value; + } + + public BigInteger getRepeat() { + + return repeat; + } + + public void setRepeat(BigInteger value) { + + this.repeat = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/MeasureType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/MeasureType.java new file mode 100644 index 0000000000..339ab3806a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/MeasureType.java @@ -0,0 +1,47 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "measureType") +@XmlEnum +public enum MeasureType { + + @XmlEnumValue("real time") + REAL_TIME("real time"), @XmlEnumValue("meltcurve") + MELTCURVE("meltcurve"); + + private final String value; + + MeasureType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static MeasureType fromValue(String v) { + + for(MeasureType c : MeasureType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ObjectFactory.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ObjectFactory.java new file mode 100644 index 0000000000..10945969fb --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ObjectFactory.java @@ -0,0 +1,167 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlRegistry; + +@XmlRegistry +public class ObjectFactory { + + public ObjectFactory() { + + } + + public Rdml createRdml() { + + return new Rdml(); + } + + public RdmlIdType createRdmlIdType() { + + return new RdmlIdType(); + } + + public ExperimenterType createExperimenterType() { + + return new ExperimenterType(); + } + + public DocumentationType createDocumentationType() { + + return new DocumentationType(); + } + + public SampleType createSampleType() { + + return new SampleType(); + } + + public TargetType createTargetType() { + + return new TargetType(); + } + + public ThermalCyclingConditionsType createThermalCyclingConditionsType() { + + return new ThermalCyclingConditionsType(); + } + + public ExperimentType createExperimentType() { + + return new ExperimentType(); + } + + public ThirdPartyExtensionsType createThirdPartyExtensionsType() { + + return new ThirdPartyExtensionsType(); + } + + public QuantityType createQuantityType() { + + return new QuantityType(); + } + + public IdReferencesType createIdReferencesType() { + + return new IdReferencesType(); + } + + public TemperatureType createTemperatureType() { + + return new TemperatureType(); + } + + public StepType createStepType() { + + return new StepType(); + } + + public RunType createRunType() { + + return new RunType(); + } + + public OligoType createOligoType() { + + return new OligoType(); + } + + public LidOpenType createLidOpenType() { + + return new LidOpenType(); + } + + public GradientType createGradientType() { + + return new GradientType(); + } + + public DpMeltingCurveType createDpMeltingCurveType() { + + return new DpMeltingCurveType(); + } + + public ReactType createReactType() { + + return new ReactType(); + } + + public PauseType createPauseType() { + + return new PauseType(); + } + + public DataCollectionSoftwareType createDataCollectionSoftwareType() { + + return new DataCollectionSoftwareType(); + } + + public DataType createDataType() { + + return new DataType(); + } + + public CdnaSynthesisMethodType createCdnaSynthesisMethodType() { + + return new CdnaSynthesisMethodType(); + } + + public DpAmpCurveType createDpAmpCurveType() { + + return new DpAmpCurveType(); + } + + public LoopType createLoopType() { + + return new LoopType(); + } + + public CommercialAssayType createCommercialAssayType() { + + return new CommercialAssayType(); + } + + public SequencesType createSequencesType() { + + return new SequencesType(); + } + + public TemplateQualityType createTemplateQualityType() { + + return new TemplateQualityType(); + } + + public XRefType createXRefType() { + + return new XRefType(); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/OligoType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/OligoType.java new file mode 100644 index 0000000000..2d181aef41 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/OligoType.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "oligoType", propOrder = {"threePrimeTag", "fivePrimeTag", "sequence"}) +public class OligoType { + + protected String threePrimeTag; + protected String fivePrimeTag; + @XmlElement(required = true) + protected String sequence; + + public String getThreePrimeTag() { + + return threePrimeTag; + } + + public void setThreePrimeTag(String value) { + + this.threePrimeTag = value; + } + + public String getFivePrimeTag() { + + return fivePrimeTag; + } + + public void setFivePrimeTag(String value) { + + this.fivePrimeTag = value; + } + + public String getSequence() { + + return sequence; + } + + public void setSequence(String value) { + + this.sequence = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PauseType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PauseType.java new file mode 100644 index 0000000000..1cb2a4c8bc --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PauseType.java @@ -0,0 +1,37 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step allows to pause at a certain temperature. It is typically the + * last step in an amplification protocol. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "pauseType", propOrder = {"temperature"}) +public class PauseType { + + protected float temperature; + + public float getTemperature() { + + return temperature; + } + + public void setTemperature(float value) { + + this.temperature = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PrimingMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PrimingMethodType.java new file mode 100644 index 0000000000..7290a99c65 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/PrimingMethodType.java @@ -0,0 +1,52 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "primingMethodType") +@XmlEnum +public enum PrimingMethodType { + + @XmlEnumValue("oligo-dt") + OLIGO_DT("oligo-dt"), // + @XmlEnumValue("random") + RANDOM("random"), // + @XmlEnumValue("target-specific") + TARGET_SPECIFIC("target-specific"), // + @XmlEnumValue("oligo-dt and random") + OLIGO_DT_AND_RANDOM("oligo-dt and random"); + + private final String value; + + PrimingMethodType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static PrimingMethodType fromValue(String v) { + + for(PrimingMethodType c : PrimingMethodType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityType.java new file mode 100644 index 0000000000..43bd662019 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A quantity is always defined by its value and its unit. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "quantityType", propOrder = {"value", "unit"}) +public class QuantityType { + + protected float value; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected QuantityUnitType unit; + + public float getValue() { + + return value; + } + + public void setValue(float value) { + + this.value = value; + } + + public QuantityUnitType getUnit() { + + return unit; + } + + public void setUnit(QuantityUnitType value) { + + this.unit = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityUnitType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityUnitType.java new file mode 100644 index 0000000000..4e3cbf78cb --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/QuantityUnitType.java @@ -0,0 +1,56 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "quantityUnitType") +@XmlEnum +public enum QuantityUnitType { + + @XmlEnumValue("cop") + COP("cop"), // + @XmlEnumValue("fold") + FOLD("fold"), // + @XmlEnumValue("dil") + DIL("dil"), // + @XmlEnumValue("ng") + NG("ng"), // + @XmlEnumValue("nMol") + N_MOL("nMol"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + QuantityUnitType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static QuantityUnitType fromValue(String v) { + + for(QuantityUnitType c : QuantityUnitType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/Rdml.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/Rdml.java new file mode 100644 index 0000000000..d3e015fa6d --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/Rdml.java @@ -0,0 +1,145 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.datatype.XMLGregorianCalendar; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlRootElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = {"dateMade", "dateUpdated", "id", "experimenter", "documentation", "sample", "target", "thermalCyclingConditions", "experiment", "thirdPartyExtensions"}) +@XmlRootElement(name = "rdml") +public class Rdml { + + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar dateMade; + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar dateUpdated; + protected List id; + protected List experimenter; + protected List documentation; + protected List sample; + protected List target; + protected List thermalCyclingConditions; + protected List experiment; + protected ThirdPartyExtensionsType thirdPartyExtensions; + @XmlAttribute(name = "version", required = true) + protected String version; + + public XMLGregorianCalendar getDateMade() { + + return dateMade; + } + + public void setDateMade(XMLGregorianCalendar value) { + + this.dateMade = value; + } + + public XMLGregorianCalendar getDateUpdated() { + + return dateUpdated; + } + + public void setDateUpdated(XMLGregorianCalendar value) { + + this.dateUpdated = value; + } + + public List getId() { + + if(id == null) { + id = new ArrayList<>(); + } + return this.id; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getSample() { + + if(sample == null) { + sample = new ArrayList<>(); + } + return this.sample; + } + + public List getTarget() { + + if(target == null) { + target = new ArrayList<>(); + } + return this.target; + } + + public List getThermalCyclingConditions() { + + if(thermalCyclingConditions == null) { + thermalCyclingConditions = new ArrayList<>(); + } + return this.thermalCyclingConditions; + } + + public List getExperiment() { + + if(experiment == null) { + experiment = new ArrayList<>(); + } + return this.experiment; + } + + public ThirdPartyExtensionsType getThirdPartyExtensions() { + + return thirdPartyExtensions; + } + + public void setThirdPartyExtensions(ThirdPartyExtensionsType value) { + + this.thirdPartyExtensions = value; + } + + public String getVersion() { + + if(version == null) { + return "1.0"; + } else { + return version; + } + } + + public void setVersion(String value) { + + this.version = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RdmlIdType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RdmlIdType.java new file mode 100644 index 0000000000..c9ae90f0f7 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RdmlIdType.java @@ -0,0 +1,62 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This element can be used to assign an publisher and id to the RDML file. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "rdmlIdType", propOrder = {"publisher", "serialNumber", "md5Hash"}) +public class RdmlIdType { + + @XmlElement(required = true) + protected String publisher; + @XmlElement(required = true) + protected String serialNumber; + @XmlElement(name = "MD5Hash") + protected String md5Hash; + + public String getPublisher() { + + return publisher; + } + + public void setPublisher(String value) { + + this.publisher = value; + } + + public String getSerialNumber() { + + return serialNumber; + } + + public void setSerialNumber(String value) { + + this.serialNumber = value; + } + + public String getMD5Hash() { + + return md5Hash; + } + + public void setMD5Hash(String value) { + + this.md5Hash = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ReactType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ReactType.java new file mode 100644 index 0000000000..0ced9e6e6f --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ReactType.java @@ -0,0 +1,66 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A reaction is an independent chemical reaction corresponding for example + * to a well in a 96 well plate, a capillary in a rotor or a droplet on the + * biotrophe slides. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "reactType", propOrder = {"sample", "data"}) +public class ReactType { + + @XmlElement(required = true) + protected IdReferencesType sample; + @XmlElement(required = true) + protected List data; + @XmlAttribute(name = "id", required = true) + protected String id; + + public IdReferencesType getSample() { + + return sample; + } + + public void setSample(IdReferencesType value) { + + this.sample = value; + } + + public List getData() { + + if(data == null) { + data = new ArrayList<>(); + } + return this.data; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RunType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RunType.java new file mode 100644 index 0000000000..815420d75b --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/RunType.java @@ -0,0 +1,164 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.datatype.XMLGregorianCalendar; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A run is a set of reactions performed in one "run", for example + * one plate, a slide in a biotrophe or one rotor. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "runType", propOrder = {"description", "documentation", "experimenter", "instrument", "dataCollectionSoftware", "backgroundDeterminationMethod", "cqDetectionMethod", "thermalCyclingConditions", "pcrFormat", "runDate", "react"}) +public class RunType { + + protected String description; + protected List documentation; + protected List experimenter; + protected String instrument; + protected DataCollectionSoftwareType dataCollectionSoftware; + protected String backgroundDeterminationMethod; + @XmlSchemaType(name = "string") + protected CqDetectionMethodType cqDetectionMethod; + protected IdReferencesType thermalCyclingConditions; + @XmlElement(required = true) + protected String pcrFormat; + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar runDate; + protected List react; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public String getInstrument() { + + return instrument; + } + + public void setInstrument(String value) { + + this.instrument = value; + } + + public DataCollectionSoftwareType getDataCollectionSoftware() { + + return dataCollectionSoftware; + } + + public void setDataCollectionSoftware(DataCollectionSoftwareType value) { + + this.dataCollectionSoftware = value; + } + + public String getBackgroundDeterminationMethod() { + + return backgroundDeterminationMethod; + } + + public void setBackgroundDeterminationMethod(String value) { + + this.backgroundDeterminationMethod = value; + } + + public CqDetectionMethodType getCqDetectionMethod() { + + return cqDetectionMethod; + } + + public void setCqDetectionMethod(CqDetectionMethodType value) { + + this.cqDetectionMethod = value; + } + + public IdReferencesType getThermalCyclingConditions() { + + return thermalCyclingConditions; + } + + public void setThermalCyclingConditions(IdReferencesType value) { + + this.thermalCyclingConditions = value; + } + + public String getPcrFormat() { + + return pcrFormat; + } + + public void setPcrFormat(String value) { + + this.pcrFormat = value; + } + + public XMLGregorianCalendar getRunDate() { + + return runDate; + } + + public void setRunDate(XMLGregorianCalendar value) { + + this.runDate = value; + } + + public List getReact() { + + if(react == null) { + react = new ArrayList<>(); + } + return this.react; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleType.java new file mode 100644 index 0000000000..1ce1122f59 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleType.java @@ -0,0 +1,180 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A sample is a defined template solution. Dilutions of the same stock + * material differ in concentration and are considered different samples. + * A technical replicate samples should contain the same name (reactions + * are performed on the same material), and biological replicates should + * contain different names (the nucleic acids derived from the different + * biological replicates are not the same). + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "sampleType", propOrder = {"description", "documentation", "xRef", "type", "interRunCalibrator", "quantity", "calibratorSample", "cdnaSynthesisMethod", "templateRNAQuantity", "templateRNAQuality", "templateDNAQuantity", "templateDNAQuality"}) +public class SampleType { + + protected String description; + protected List documentation; + protected List xRef; + @XmlElement(required = true, defaultValue = "unkn") + @XmlSchemaType(name = "string") + protected SampleTypeType type; + @XmlElement(defaultValue = "false") + protected Boolean interRunCalibrator; + protected QuantityType quantity; + @XmlElement(defaultValue = "false") + protected Boolean calibratorSample; + protected CdnaSynthesisMethodType cdnaSynthesisMethod; + protected Double templateRNAQuantity; + protected TemplateQualityType templateRNAQuality; + protected Double templateDNAQuantity; + protected TemplateQualityType templateDNAQuality; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList(); + } + return this.documentation; + } + + public List getXRef() { + + if(xRef == null) { + xRef = new ArrayList<>(); + } + return this.xRef; + } + + public SampleTypeType getType() { + + return type; + } + + public void setType(SampleTypeType value) { + + this.type = value; + } + + public Boolean isInterRunCalibrator() { + + return interRunCalibrator; + } + + public void setInterRunCalibrator(Boolean value) { + + this.interRunCalibrator = value; + } + + public QuantityType getQuantity() { + + return quantity; + } + + public void setQuantity(QuantityType value) { + + this.quantity = value; + } + + public Boolean isCalibratorSample() { + + return calibratorSample; + } + + public void setCalibratorSample(Boolean value) { + + this.calibratorSample = value; + } + + public CdnaSynthesisMethodType getCdnaSynthesisMethod() { + + return cdnaSynthesisMethod; + } + + public void setCdnaSynthesisMethod(CdnaSynthesisMethodType value) { + + this.cdnaSynthesisMethod = value; + } + + public Double getTemplateRNAQuantity() { + + return templateRNAQuantity; + } + + public void setTemplateRNAQuantity(Double value) { + + this.templateRNAQuantity = value; + } + + public TemplateQualityType getTemplateRNAQuality() { + + return templateRNAQuality; + } + + public void setTemplateRNAQuality(TemplateQualityType value) { + + this.templateRNAQuality = value; + } + + public Double getTemplateDNAQuantity() { + + return templateDNAQuantity; + } + + public void setTemplateDNAQuantity(Double value) { + + this.templateDNAQuantity = value; + } + + public TemplateQualityType getTemplateDNAQuality() { + + return templateDNAQuality; + } + + public void setTemplateDNAQuality(TemplateQualityType value) { + + this.templateDNAQuality = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleTypeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleTypeType.java new file mode 100644 index 0000000000..296884c2b2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SampleTypeType.java @@ -0,0 +1,54 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "sampleTypeType") +@XmlEnum +public enum SampleTypeType { + + @XmlEnumValue("unkn") + UNKN("unkn"), // + @XmlEnumValue("ntc") + NTC("ntc"), // + @XmlEnumValue("nac") + NAC("nac"), // + @XmlEnumValue("std") + STD("std"), // + @XmlEnumValue("opt") + OPT("opt"); + + private final String value; + + SampleTypeType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static SampleTypeType fromValue(String v) { + + for(SampleTypeType c : SampleTypeType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SequencesType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SequencesType.java new file mode 100644 index 0000000000..057efccdd9 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/SequencesType.java @@ -0,0 +1,77 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "sequencesType", propOrder = {"forwardPrimer", "reversePrimer", "probe1", "probe2", "amplicon"}) +public class SequencesType { + + protected OligoType forwardPrimer; + protected OligoType reversePrimer; + protected OligoType probe1; + protected OligoType probe2; + protected OligoType amplicon; + + public OligoType getForwardPrimer() { + + return forwardPrimer; + } + + public void setForwardPrimer(OligoType value) { + + this.forwardPrimer = value; + } + + public OligoType getReversePrimer() { + + return reversePrimer; + } + + public void setReversePrimer(OligoType value) { + + this.reversePrimer = value; + } + + public OligoType getProbe1() { + + return probe1; + } + + public void setProbe1(OligoType value) { + + this.probe1 = value; + } + + public OligoType getProbe2() { + + return probe2; + } + + public void setProbe2(OligoType value) { + + this.probe2 = value; + } + + public OligoType getAmplicon() { + + return amplicon; + } + + public void setAmplicon(OligoType value) { + + this.amplicon = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/StepType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/StepType.java new file mode 100644 index 0000000000..1b3ed98050 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/StepType.java @@ -0,0 +1,105 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "stepType", propOrder = {"nr", "description", "temperature", "gradient", "loop", "pause", "lidOpen"}) +public class StepType { + + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger nr; + protected String description; + protected TemperatureType temperature; + protected GradientType gradient; + protected LoopType loop; + protected PauseType pause; + protected LidOpenType lidOpen; + + public BigInteger getNr() { + + return nr; + } + + public void setNr(BigInteger value) { + + this.nr = value; + } + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public TemperatureType getTemperature() { + + return temperature; + } + + public void setTemperature(TemperatureType value) { + + this.temperature = value; + } + + public GradientType getGradient() { + + return gradient; + } + + public void setGradient(GradientType value) { + + this.gradient = value; + } + + public LoopType getLoop() { + + return loop; + } + + public void setLoop(LoopType value) { + + this.loop = value; + } + + public PauseType getPause() { + + return pause; + } + + public void setPause(PauseType value) { + + this.pause = value; + } + + public LidOpenType getLidOpen() { + + return lidOpen; + } + + public void setLidOpen(LidOpenType value) { + + this.lidOpen = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetType.java new file mode 100644 index 0000000000..594b4ab063 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetType.java @@ -0,0 +1,141 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A target is a defined PCR reaction. PCR reactions at the same gene + * which differ in primer sequences are considered different samples. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "targetType", propOrder = {"description", "documentation", "xRef", "type", "amplificationEfficiency", "detectionLimit", "dyeId", "sequences", "commercialAssay"}) +public class TargetType { + + protected String description; + protected List documentation; + protected List xRef; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected TargetTypeType type; + protected Float amplificationEfficiency; + protected Float detectionLimit; + protected String dyeId; + protected SequencesType sequences; + protected CommercialAssayType commercialAssay; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getXRef() { + + if(xRef == null) { + xRef = new ArrayList<>(); + } + return this.xRef; + } + + public TargetTypeType getType() { + + return type; + } + + public void setType(TargetTypeType value) { + + this.type = value; + } + + public Float getAmplificationEfficiency() { + + return amplificationEfficiency; + } + + public void setAmplificationEfficiency(Float value) { + + this.amplificationEfficiency = value; + } + + public Float getDetectionLimit() { + + return detectionLimit; + } + + public void setDetectionLimit(Float value) { + + this.detectionLimit = value; + } + + public String getDyeId() { + + return dyeId; + } + + public void setDyeId(String value) { + + this.dyeId = value; + } + + public SequencesType getSequences() { + + return sequences; + } + + public void setSequences(SequencesType value) { + + this.sequences = value; + } + + public CommercialAssayType getCommercialAssay() { + + return commercialAssay; + } + + public void setCommercialAssay(CommercialAssayType value) { + + this.commercialAssay = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetTypeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetTypeType.java new file mode 100644 index 0000000000..3b8d8c4555 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TargetTypeType.java @@ -0,0 +1,48 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "targetTypeType") +@XmlEnum +public enum TargetTypeType { + + @XmlEnumValue("ref") + REF("ref"), // + @XmlEnumValue("toi") + TOI("toi"); + + private final String value; + + TargetTypeType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static TargetTypeType fromValue(String v) { + + for(TargetTypeType c : TargetTypeType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemperatureType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemperatureType.java new file mode 100644 index 0000000000..f909069b08 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemperatureType.java @@ -0,0 +1,98 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step keeps a constant temperature on the heat block. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "temperatureType", propOrder = {"temperature", "duration", "temperatureChange", "durationChange", "measure", "ramp"}) +public class TemperatureType { + + protected float temperature; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger duration; + protected Float temperatureChange; + protected Integer durationChange; + @XmlSchemaType(name = "string") + protected MeasureType measure; + protected Float ramp; + + public float getTemperature() { + + return temperature; + } + + public void setTemperature(float value) { + + this.temperature = value; + } + + public BigInteger getDuration() { + + return duration; + } + + public void setDuration(BigInteger value) { + + this.duration = value; + } + + public Float getTemperatureChange() { + + return temperatureChange; + } + + public void setTemperatureChange(Float value) { + + this.temperatureChange = value; + } + + public Integer getDurationChange() { + + return durationChange; + } + + public void setDurationChange(Integer value) { + + this.durationChange = value; + } + + public MeasureType getMeasure() { + + return measure; + } + + public void setMeasure(MeasureType value) { + + this.measure = value; + } + + public Float getRamp() { + + return ramp; + } + + public void setRamp(Float value) { + + this.ramp = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemplateQualityType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemplateQualityType.java new file mode 100644 index 0000000000..b175c21799 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/TemplateQualityType.java @@ -0,0 +1,46 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "templateQualityType", propOrder = {"method", "result"}) +public class TemplateQualityType { + + @XmlElement(required = true) + protected String method; + protected float result; + + public String getMethod() { + + return method; + } + + public void setMethod(String value) { + + this.method = value; + } + + public float getResult() { + + return result; + } + + public void setResult(float value) { + + this.result = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThermalCyclingConditionsType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThermalCyclingConditionsType.java new file mode 100644 index 0000000000..84357188e1 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThermalCyclingConditionsType.java @@ -0,0 +1,92 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A cycling program for PCR or to amplify cDNA. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "thermalCyclingConditionsType", propOrder = {"description", "documentation", "lidTemperature", "experimenter", "step"}) +public class ThermalCyclingConditionsType { + + protected String description; + protected List documentation; + protected Float lidTemperature; + protected List experimenter; + @XmlElement(required = true) + protected List step; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public Float getLidTemperature() { + + return lidTemperature; + } + + public void setLidTemperature(Float value) { + + this.lidTemperature = value; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public List getStep() { + + if(step == null) { + step = new ArrayList<>(); + } + return this.step; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThirdPartyExtensionsType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThirdPartyExtensionsType.java new file mode 100644 index 0000000000..ea476f01a8 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/ThirdPartyExtensionsType.java @@ -0,0 +1,41 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAnyElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This is the place to insert extensions not supported by RDML. Please use + * a descriptive and unique root element to avoid interference with other + * third party extensions. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "thirdPartyExtensionsType", propOrder = {"any"}) +public class ThirdPartyExtensionsType { + + @XmlAnyElement(lax = true) + protected List any; + + public List getAny() { + + if(any == null) { + any = new ArrayList<>(); + } + return this.any; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/XRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/XRefType.java new file mode 100644 index 0000000000..96a7a5361e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v10/model/XRefType.java @@ -0,0 +1,44 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v10.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "xRefType", propOrder = {"name", "id"}) +public class XRefType { + + protected String name; + protected String id; + + public String getName() { + + return name; + } + + public void setName(String value) { + + this.name = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CdnaSynthesisMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CdnaSynthesisMethodType.java new file mode 100644 index 0000000000..e634e0cb2a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CdnaSynthesisMethodType.java @@ -0,0 +1,71 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Description of the cDNA synthesis method. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "cdnaSynthesisMethodType", propOrder = {"enzyme", "primingMethod", "dnaseTreatment", "thermalCyclingConditions"}) +public class CdnaSynthesisMethodType { + + protected String enzyme; + @XmlSchemaType(name = "string") + protected PrimingMethodType primingMethod; + protected Boolean dnaseTreatment; + protected IdReferencesType thermalCyclingConditions; + + public String getEnzyme() { + + return enzyme; + } + + public void setEnzyme(String value) { + + this.enzyme = value; + } + + public PrimingMethodType getPrimingMethod() { + + return primingMethod; + } + + public void setPrimingMethod(PrimingMethodType value) { + + this.primingMethod = value; + } + + public Boolean isDnaseTreatment() { + + return dnaseTreatment; + } + + public void setDnaseTreatment(Boolean value) { + + this.dnaseTreatment = value; + } + + public IdReferencesType getThermalCyclingConditions() { + + return thermalCyclingConditions; + } + + public void setThermalCyclingConditions(IdReferencesType value) { + + this.thermalCyclingConditions = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CommercialAssayType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CommercialAssayType.java new file mode 100644 index 0000000000..3ab105b582 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CommercialAssayType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * For some commercial assays, the primer sequences may be unknown. This element + * allows to describe commercial assays. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "commercialAssayType", propOrder = {"company", "orderNumber"}) +public class CommercialAssayType { + + @XmlElement(required = true) + protected String company; + @XmlElement(required = true) + protected String orderNumber; + + public String getCompany() { + + return company; + } + + public void setCompany(String value) { + + this.company = value; + } + + public String getOrderNumber() { + + return orderNumber; + } + + public void setOrderNumber(String value) { + + this.orderNumber = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CqDetectionMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CqDetectionMethodType.java new file mode 100644 index 0000000000..b75b8803d5 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/CqDetectionMethodType.java @@ -0,0 +1,52 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "cqDetectionMethodType") +@XmlEnum +public enum CqDetectionMethodType { + + @XmlEnumValue("automated threshold and baseline settings") + AUTOMATED_THRESHOLD_AND_BASELINE_SETTINGS("automated threshold and baseline settings"), // + @XmlEnumValue("manual threshold and baseline settings") + MANUAL_THRESHOLD_AND_BASELINE_SETTINGS("manual threshold and baseline settings"), // + @XmlEnumValue("second derivative maximum") + SECOND_DERIVATIVE_MAXIMUM("second derivative maximum"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + CqDetectionMethodType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static CqDetectionMethodType fromValue(String v) { + + for(CqDetectionMethodType c : CqDetectionMethodType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataCollectionSoftwareType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataCollectionSoftwareType.java new file mode 100644 index 0000000000..a153f21cff --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataCollectionSoftwareType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Software name and version used to collect and analyze the data. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dataCollectionSoftwareType", propOrder = {"name", "version"}) +public class DataCollectionSoftwareType { + + @XmlElement(required = true) + protected String name; + @XmlElement(required = true) + protected String version; + + public String getName() { + + return name; + } + + public void setName(String value) { + + this.name = value; + } + + public String getVersion() { + + return version; + } + + public void setVersion(String value) { + + this.version = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataType.java new file mode 100644 index 0000000000..61fefa011e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DataType.java @@ -0,0 +1,114 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the frequent occurrence of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dataType", propOrder = {"tar", "cq", "excl", "adp", "mdp", "endPt", "bgFluor", "quantFluor"}) +public class DataType { + + @XmlElement(required = true) + protected IdReferencesType tar; + protected Float cq; + protected String excl; + protected List adp; + protected List mdp; + protected Float endPt; + protected Float bgFluor; + protected Float quantFluor; + + public IdReferencesType getTar() { + + return tar; + } + + public void setTar(IdReferencesType value) { + + this.tar = value; + } + + public Float getCq() { + + return cq; + } + + public void setCq(Float value) { + + this.cq = value; + } + + public String getExcl() { + + return excl; + } + + public void setExcl(String value) { + + this.excl = value; + } + + public List getAdp() { + + if(adp == null) { + adp = new ArrayList<>(); + } + return this.adp; + } + + public List getMdp() { + + if(mdp == null) { + mdp = new ArrayList<>(); + } + return this.mdp; + } + + public Float getEndPt() { + + return endPt; + } + + public void setEndPt(Float value) { + + this.endPt = value; + } + + public Float getBgFluor() { + + return bgFluor; + } + + public void setBgFluor(Float value) { + + this.bgFluor = value; + } + + public Float getQuantFluor() { + + return quantFluor; + } + + public void setQuantFluor(Float value) { + + this.quantFluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DocumentationType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DocumentationType.java new file mode 100644 index 0000000000..d1fc443c53 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DocumentationType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * These elements should be used if the same description applies to many samples, + * targets or experiments. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "documentationType", propOrder = {}) +public class DocumentationType { + + protected String text; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getText() { + + return text; + } + + public void setText(String value) { + + this.text = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpAmpCurveType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpAmpCurveType.java new file mode 100644 index 0000000000..6b90f77219 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpAmpCurveType.java @@ -0,0 +1,58 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the frequent occurrence of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dpAmpCurveType", propOrder = {"cyc", "tmp", "fluor"}) +public class DpAmpCurveType { + + protected float cyc; + protected Float tmp; + protected float fluor; + + public float getCyc() { + + return cyc; + } + + public void setCyc(float value) { + + this.cyc = value; + } + + public Float getTmp() { + + return tmp; + } + + public void setTmp(Float value) { + + this.tmp = value; + } + + public float getFluor() { + + return fluor; + } + + public void setFluor(float value) { + + this.fluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpMeltingCurveType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpMeltingCurveType.java new file mode 100644 index 0000000000..dda969a15f --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DpMeltingCurveType.java @@ -0,0 +1,47 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the frequent occurrence of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dpMeltingCurveType", propOrder = {"tmp", "fluor"}) +public class DpMeltingCurveType { + + protected float tmp; + protected float fluor; + + public float getTmp() { + + return tmp; + } + + public void setTmp(float value) { + + this.tmp = value; + } + + public float getFluor() { + + return fluor; + } + + public void setFluor(float value) { + + this.fluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DyeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DyeType.java new file mode 100644 index 0000000000..7c34e60b1b --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/DyeType.java @@ -0,0 +1,49 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Information on a dye. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dyeType", propOrder = {"description"}) +public class DyeType { + + protected String description; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimentType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimentType.java new file mode 100644 index 0000000000..2494f61b57 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimentType.java @@ -0,0 +1,70 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * An experiment can contain several runs. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "experimentType", propOrder = {"description", "documentation", "run"}) +public class ExperimentType { + + protected String description; + protected List documentation; + protected List run; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getRun() { + + if(run == null) { + run = new ArrayList<>(); + } + return this.run; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimenterType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimenterType.java new file mode 100644 index 0000000000..2c13e87dbb --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ExperimenterType.java @@ -0,0 +1,96 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Contact details of the experimenter. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "experimenterType", propOrder = {"firstName", "lastName", "email", "labName", "labAddress"}) +public class ExperimenterType { + + @XmlElement(required = true) + protected String firstName; + @XmlElement(required = true) + protected String lastName; + protected String email; + protected String labName; + protected String labAddress; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getFirstName() { + + return firstName; + } + + public void setFirstName(String value) { + + this.firstName = value; + } + + public String getLastName() { + + return lastName; + } + + public void setLastName(String value) { + + this.lastName = value; + } + + public String getEmail() { + + return email; + } + + public void setEmail(String value) { + + this.email = value; + } + + public String getLabName() { + + return labName; + } + + public void setLabName(String value) { + + this.labName = value; + } + + public String getLabAddress() { + + return labAddress; + } + + public void setLabAddress(String value) { + + this.labAddress = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/GradientType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/GradientType.java new file mode 100644 index 0000000000..1e8b924077 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/GradientType.java @@ -0,0 +1,109 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step forms a temperature gradient across the PCR block. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "gradientType", propOrder = {"highTemperature", "lowTemperature", "duration", "temperatureChange", "durationChange", "measure", "ramp"}) +public class GradientType { + + protected float highTemperature; + protected float lowTemperature; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger duration; + protected Float temperatureChange; + protected Integer durationChange; + @XmlSchemaType(name = "string") + protected MeasureType measure; + protected Float ramp; + + public float getHighTemperature() { + + return highTemperature; + } + + public void setHighTemperature(float value) { + + this.highTemperature = value; + } + + public float getLowTemperature() { + + return lowTemperature; + } + + public void setLowTemperature(float value) { + + this.lowTemperature = value; + } + + public BigInteger getDuration() { + + return duration; + } + + public void setDuration(BigInteger value) { + + this.duration = value; + } + + public Float getTemperatureChange() { + + return temperatureChange; + } + + public void setTemperatureChange(Float value) { + + this.temperatureChange = value; + } + + public Integer getDurationChange() { + + return durationChange; + } + + public void setDurationChange(Integer value) { + + this.durationChange = value; + } + + public MeasureType getMeasure() { + + return measure; + } + + public void setMeasure(MeasureType value) { + + this.measure = value; + } + + public Float getRamp() { + + return ramp; + } + + public void setRamp(Float value) { + + this.ramp = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/IdReferencesType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/IdReferencesType.java new file mode 100644 index 0000000000..91bf5e5680 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/IdReferencesType.java @@ -0,0 +1,35 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "idReferencesType") +public class IdReferencesType { + + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LidOpenType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LidOpenType.java new file mode 100644 index 0000000000..df3bbe0398 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LidOpenType.java @@ -0,0 +1,27 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step waits for the user to open the lid and continues afterwards. It + * allows to stop the program and to wait for the user to add for example + * enzymes and continue the program afterwards. The temperature of the previous + * step is maintained. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "lidOpenType") +public class LidOpenType { +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LoopType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LoopType.java new file mode 100644 index 0000000000..f984f68a0b --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/LoopType.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step allows to form a loop or to exclude some steps. It allows to + * jump to a certain "goto" step for "repeat" times. If the "goto" step is + * higher than the step of the loop, "repeat" must be "0". + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "loopType", propOrder = {"gotoStep", "repeat"}) +public class LoopType { + + @XmlElement(name = "goto", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger gotoStep; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger repeat; + + public BigInteger getGoto() { + + return gotoStep; + } + + public void setGoto(BigInteger value) { + + this.gotoStep = value; + } + + public BigInteger getRepeat() { + + return repeat; + } + + public void setRepeat(BigInteger value) { + + this.repeat = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/MeasureType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/MeasureType.java new file mode 100644 index 0000000000..5ab0d60bf1 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/MeasureType.java @@ -0,0 +1,48 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "measureType") +@XmlEnum +public enum MeasureType { + + @XmlEnumValue("real time") + REAL_TIME("real time"), // + @XmlEnumValue("meltcurve") + MELTCURVE("meltcurve"); + + private final String value; + + MeasureType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static MeasureType fromValue(String v) { + + for(MeasureType c : MeasureType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ObjectFactory.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ObjectFactory.java new file mode 100644 index 0000000000..a1355317e2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ObjectFactory.java @@ -0,0 +1,172 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlRegistry; + +@XmlRegistry +public class ObjectFactory { + + public ObjectFactory() { + + } + + public Rdml createRdml() { + + return new Rdml(); + } + + public RdmlIdType createRdmlIdType() { + + return new RdmlIdType(); + } + + public ExperimenterType createExperimenterType() { + + return new ExperimenterType(); + } + + public DocumentationType createDocumentationType() { + + return new DocumentationType(); + } + + public DyeType createDyeType() { + + return new DyeType(); + } + + public SampleType createSampleType() { + + return new SampleType(); + } + + public TargetType createTargetType() { + + return new TargetType(); + } + + public ThermalCyclingConditionsType createThermalCyclingConditionsType() { + + return new ThermalCyclingConditionsType(); + } + + public ExperimentType createExperimentType() { + + return new ExperimentType(); + } + + public QuantityType createQuantityType() { + + return new QuantityType(); + } + + public IdReferencesType createIdReferencesType() { + + return new IdReferencesType(); + } + + public TemperatureType createTemperatureType() { + + return new TemperatureType(); + } + + public StepType createStepType() { + + return new StepType(); + } + + public RunType createRunType() { + + return new RunType(); + } + + public OligoType createOligoType() { + + return new OligoType(); + } + + public LidOpenType createLidOpenType() { + + return new LidOpenType(); + } + + public GradientType createGradientType() { + + return new GradientType(); + } + + public DpMeltingCurveType createDpMeltingCurveType() { + + return new DpMeltingCurveType(); + } + + public ReactType createReactType() { + + return new ReactType(); + } + + public PauseType createPauseType() { + + return new PauseType(); + } + + public DataCollectionSoftwareType createDataCollectionSoftwareType() { + + return new DataCollectionSoftwareType(); + } + + public DataType createDataType() { + + return new DataType(); + } + + public CdnaSynthesisMethodType createCdnaSynthesisMethodType() { + + return new CdnaSynthesisMethodType(); + } + + public PcrFormatType createPcrFormatType() { + + return new PcrFormatType(); + } + + public DpAmpCurveType createDpAmpCurveType() { + + return new DpAmpCurveType(); + } + + public LoopType createLoopType() { + + return new LoopType(); + } + + public CommercialAssayType createCommercialAssayType() { + + return new CommercialAssayType(); + } + + public SequencesType createSequencesType() { + + return new SequencesType(); + } + + public TemplateQualityType createTemplateQualityType() { + + return new TemplateQualityType(); + } + + public XRefType createXRefType() { + + return new XRefType(); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/OligoType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/OligoType.java new file mode 100644 index 0000000000..910ccb2128 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/OligoType.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "oligoType", propOrder = {"threePrimeTag", "fivePrimeTag", "sequence"}) +public class OligoType { + + protected String threePrimeTag; + protected String fivePrimeTag; + @XmlElement(required = true) + protected String sequence; + + public String getThreePrimeTag() { + + return threePrimeTag; + } + + public void setThreePrimeTag(String value) { + + this.threePrimeTag = value; + } + + public String getFivePrimeTag() { + + return fivePrimeTag; + } + + public void setFivePrimeTag(String value) { + + this.fivePrimeTag = value; + } + + public String getSequence() { + + return sequence; + } + + public void setSequence(String value) { + + this.sequence = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PauseType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PauseType.java new file mode 100644 index 0000000000..830d4b3aa3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PauseType.java @@ -0,0 +1,37 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step allows to pause at a certain temperature. It is typically the + * last step in an amplification protocol. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "pauseType", propOrder = {"temperature"}) +public class PauseType { + + protected float temperature; + + public float getTemperature() { + + return temperature; + } + + public void setTemperature(float value) { + + this.temperature = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PcrFormatType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PcrFormatType.java new file mode 100644 index 0000000000..cdf57e8bf0 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PcrFormatType.java @@ -0,0 +1,98 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * 
+ *        The format of the run - This allows the software to display the data
+ *        according to the qPCR instrument run format.
+ *        Rotor formats always have 1 column; rows correspond to the number
+ *        of places in the rotor.
+ *        
+ *        Values for common formats are:
+ *        
+ *        Format            |    rows    |   columns   |  rowLabel  | columnLabel
+ *        --------------------------------------------------------------------------
+ *        single-well       |     1      |      1      |    123     |     123
+ *        48-well plate     |     6      |      8      |    ABC     |     123
+ *        96-well plate     |     8      |     12      |    ABC     |     123
+ *        384-well plate    |    16      |     24      |    ABC     |     123
+ *        1536-well plate   |    32      |     48      |    ABC     |     123
+ *        3072-well array   |    32      |     96      |   A1a1     |    A1a1
+ *        5184-well chip    |    72      |     72      |    ABC     |     123
+ *        32-well rotor     |    32      |      1      |    123     |     123
+ *        72-well rotor     |    72      |      1      |    123     |     123
+ *        100-well rotor    |   100      |      1      |    123     |     123
+ *        free format       |    -1      |      1      |    123     |     123
+ *        
+ *        If rows are -1 then the software should not try to reconstruct a plate and 
+ *        just display all react data in list (1 column) form.
+ *        
+ *        If columns is 1 then the software should not display a column label.
+ *
+ */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "pcrFormatType", propOrder = {"rows", "columns", "rowLabel", "columnLabel"}) +public class PcrFormatType { + + protected int rows; + protected int columns; + @XmlElement(required = true) + protected String rowLabel; + @XmlElement(required = true) + protected String columnLabel; + + public int getRows() { + + return rows; + } + + public void setRows(int value) { + + this.rows = value; + } + + public int getColumns() { + + return columns; + } + + public void setColumns(int value) { + + this.columns = value; + } + + public String getRowLabel() { + + return rowLabel; + } + + public void setRowLabel(String value) { + + this.rowLabel = value; + } + + public String getColumnLabel() { + + return columnLabel; + } + + public void setColumnLabel(String value) { + + this.columnLabel = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PrimingMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PrimingMethodType.java new file mode 100644 index 0000000000..9f83c7db8b --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/PrimingMethodType.java @@ -0,0 +1,54 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "primingMethodType") +@XmlEnum +public enum PrimingMethodType { + + @XmlEnumValue("oligo-dt") + OLIGO_DT("oligo-dt"), // + @XmlEnumValue("random") + RANDOM("random"), // + @XmlEnumValue("target-specific") + TARGET_SPECIFIC("target-specific"), // + @XmlEnumValue("oligo-dt and random") + OLIGO_DT_AND_RANDOM("oligo-dt and random"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + PrimingMethodType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static PrimingMethodType fromValue(String v) { + + for(PrimingMethodType c : PrimingMethodType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityType.java new file mode 100644 index 0000000000..71c4f8867f --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A quantity is always defined by its value and its unit. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "quantityType", propOrder = {"value", "unit"}) +public class QuantityType { + + protected float value; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected QuantityUnitType unit; + + public float getValue() { + + return value; + } + + public void setValue(float value) { + + this.value = value; + } + + public QuantityUnitType getUnit() { + + return unit; + } + + public void setUnit(QuantityUnitType value) { + + this.unit = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityUnitType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityUnitType.java new file mode 100644 index 0000000000..a082c7127d --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/QuantityUnitType.java @@ -0,0 +1,56 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "quantityUnitType") +@XmlEnum +public enum QuantityUnitType { + + @XmlEnumValue("cop") + COP("cop"), // + @XmlEnumValue("fold") + FOLD("fold"), // + @XmlEnumValue("dil") + DIL("dil"), // + @XmlEnumValue("ng") + NG("ng"), // + @XmlEnumValue("nMol") + N_MOL("nMol"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + QuantityUnitType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static QuantityUnitType fromValue(String v) { + + for(QuantityUnitType c : QuantityUnitType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/Rdml.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/Rdml.java new file mode 100644 index 0000000000..98c861d5c2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/Rdml.java @@ -0,0 +1,143 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.datatype.XMLGregorianCalendar; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlRootElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = {"dateMade", "dateUpdated", "id", "experimenter", "documentation", "dye", "sample", "target", "thermalCyclingConditions", "experiment"}) +@XmlRootElement(name = "rdml") +public class Rdml { + + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar dateMade; + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar dateUpdated; + protected List id; + protected List experimenter; + protected List documentation; + protected List dye; + protected List sample; + protected List target; + protected List thermalCyclingConditions; + protected List experiment; + @XmlAttribute(name = "version", required = true) + protected String version; + + public XMLGregorianCalendar getDateMade() { + + return dateMade; + } + + public void setDateMade(XMLGregorianCalendar value) { + + this.dateMade = value; + } + + public XMLGregorianCalendar getDateUpdated() { + + return dateUpdated; + } + + public void setDateUpdated(XMLGregorianCalendar value) { + + this.dateUpdated = value; + } + + public List getId() { + + if(id == null) { + id = new ArrayList<>(); + } + return this.id; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getDye() { + + if(dye == null) { + dye = new ArrayList<>(); + } + return this.dye; + } + + public List getSample() { + + if(sample == null) { + sample = new ArrayList<>(); + } + return this.sample; + } + + public List getTarget() { + + if(target == null) { + target = new ArrayList<>(); + } + return this.target; + } + + public List getThermalCyclingConditions() { + + if(thermalCyclingConditions == null) { + thermalCyclingConditions = new ArrayList<>(); + } + return this.thermalCyclingConditions; + } + + public List getExperiment() { + + if(experiment == null) { + experiment = new ArrayList<>(); + } + return this.experiment; + } + + public String getVersion() { + + if(version == null) { + return "1.1"; + } else { + return version; + } + } + + public void setVersion(String value) { + + this.version = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RdmlIdType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RdmlIdType.java new file mode 100644 index 0000000000..ba4e0fc836 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RdmlIdType.java @@ -0,0 +1,62 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This element can be used to assign a publisher and id to the RDML file. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "rdmlIdType", propOrder = {"publisher", "serialNumber", "md5Hash"}) +public class RdmlIdType { + + @XmlElement(required = true) + protected String publisher; + @XmlElement(required = true) + protected String serialNumber; + @XmlElement(name = "MD5Hash") + protected String md5Hash; + + public String getPublisher() { + + return publisher; + } + + public void setPublisher(String value) { + + this.publisher = value; + } + + public String getSerialNumber() { + + return serialNumber; + } + + public void setSerialNumber(String value) { + + this.serialNumber = value; + } + + public String getMD5Hash() { + + return md5Hash; + } + + public void setMD5Hash(String value) { + + this.md5Hash = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ReactType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ReactType.java new file mode 100644 index 0000000000..29b9e29ee1 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ReactType.java @@ -0,0 +1,69 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.math.BigInteger; +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A reaction is an independent chemical reaction corresponding for example + * to a well in a 96 well plate, a capillary in a rotor, a through-hole on + * an array, etc. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "reactType", propOrder = {"sample", "data"}) +public class ReactType { + + @XmlElement(required = true) + protected IdReferencesType sample; + @XmlElement(required = true) + protected List data; + @XmlAttribute(name = "id", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger id; + + public IdReferencesType getSample() { + + return sample; + } + + public void setSample(IdReferencesType value) { + + this.sample = value; + } + + public List getData() { + + if(data == null) { + data = new ArrayList<>(); + } + return this.data; + } + + public BigInteger getId() { + + return id; + } + + public void setId(BigInteger value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RunType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RunType.java new file mode 100644 index 0000000000..c7b2e68ad3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/RunType.java @@ -0,0 +1,164 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.datatype.XMLGregorianCalendar; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A run is a set of reactions performed in one "run", for example + * one plate, one rotor, one array, one chip. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "runType", propOrder = {"description", "documentation", "experimenter", "instrument", "dataCollectionSoftware", "backgroundDeterminationMethod", "cqDetectionMethod", "thermalCyclingConditions", "pcrFormat", "runDate", "react"}) +public class RunType { + + protected String description; + protected List documentation; + protected List experimenter; + protected String instrument; + protected DataCollectionSoftwareType dataCollectionSoftware; + protected String backgroundDeterminationMethod; + @XmlSchemaType(name = "string") + protected CqDetectionMethodType cqDetectionMethod; + protected IdReferencesType thermalCyclingConditions; + @XmlElement(required = true) + protected PcrFormatType pcrFormat; + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar runDate; + protected List react; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public String getInstrument() { + + return instrument; + } + + public void setInstrument(String value) { + + this.instrument = value; + } + + public DataCollectionSoftwareType getDataCollectionSoftware() { + + return dataCollectionSoftware; + } + + public void setDataCollectionSoftware(DataCollectionSoftwareType value) { + + this.dataCollectionSoftware = value; + } + + public String getBackgroundDeterminationMethod() { + + return backgroundDeterminationMethod; + } + + public void setBackgroundDeterminationMethod(String value) { + + this.backgroundDeterminationMethod = value; + } + + public CqDetectionMethodType getCqDetectionMethod() { + + return cqDetectionMethod; + } + + public void setCqDetectionMethod(CqDetectionMethodType value) { + + this.cqDetectionMethod = value; + } + + public IdReferencesType getThermalCyclingConditions() { + + return thermalCyclingConditions; + } + + public void setThermalCyclingConditions(IdReferencesType value) { + + this.thermalCyclingConditions = value; + } + + public PcrFormatType getPcrFormat() { + + return pcrFormat; + } + + public void setPcrFormat(PcrFormatType value) { + + this.pcrFormat = value; + } + + public XMLGregorianCalendar getRunDate() { + + return runDate; + } + + public void setRunDate(XMLGregorianCalendar value) { + + this.runDate = value; + } + + public List getReact() { + + if(react == null) { + react = new ArrayList<>(); + } + return this.react; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleType.java new file mode 100644 index 0000000000..831633b558 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleType.java @@ -0,0 +1,181 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A sample is a defined template solution. Dilutions of the same + * material differ in concentration and are considered different samples. + * A technical replicate samples should contain the same name (reactions + * are performed on the same material), and biological replicates should + * contain different names (the nucleic acids derived from the different + * biological replicates are not the same). Serial dilutions in a standard + * curve must have a different name. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "sampleType", propOrder = {"description", "documentation", "xRef", "type", "interRunCalibrator", "quantity", "calibratorSample", "cdnaSynthesisMethod", "templateRNAQuantity", "templateRNAQuality", "templateDNAQuantity", "templateDNAQuality"}) +public class SampleType { + + protected String description; + protected List documentation; + protected List xRef; + @XmlElement(required = true, defaultValue = "unkn") + @XmlSchemaType(name = "string") + protected SampleTypeType type; + @XmlElement(defaultValue = "false") + protected Boolean interRunCalibrator; + protected QuantityType quantity; + @XmlElement(defaultValue = "false") + protected Boolean calibratorSample; + protected CdnaSynthesisMethodType cdnaSynthesisMethod; + protected QuantityType templateRNAQuantity; + protected TemplateQualityType templateRNAQuality; + protected QuantityType templateDNAQuantity; + protected TemplateQualityType templateDNAQuality; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getXRef() { + + if(xRef == null) { + xRef = new ArrayList<>(); + } + return this.xRef; + } + + public SampleTypeType getType() { + + return type; + } + + public void setType(SampleTypeType value) { + + this.type = value; + } + + public Boolean isInterRunCalibrator() { + + return interRunCalibrator; + } + + public void setInterRunCalibrator(Boolean value) { + + this.interRunCalibrator = value; + } + + public QuantityType getQuantity() { + + return quantity; + } + + public void setQuantity(QuantityType value) { + + this.quantity = value; + } + + public Boolean isCalibratorSample() { + + return calibratorSample; + } + + public void setCalibratorSample(Boolean value) { + + this.calibratorSample = value; + } + + public CdnaSynthesisMethodType getCdnaSynthesisMethod() { + + return cdnaSynthesisMethod; + } + + public void setCdnaSynthesisMethod(CdnaSynthesisMethodType value) { + + this.cdnaSynthesisMethod = value; + } + + public QuantityType getTemplateRNAQuantity() { + + return templateRNAQuantity; + } + + public void setTemplateRNAQuantity(QuantityType value) { + + this.templateRNAQuantity = value; + } + + public TemplateQualityType getTemplateRNAQuality() { + + return templateRNAQuality; + } + + public void setTemplateRNAQuality(TemplateQualityType value) { + + this.templateRNAQuality = value; + } + + public QuantityType getTemplateDNAQuantity() { + + return templateDNAQuantity; + } + + public void setTemplateDNAQuantity(QuantityType value) { + + this.templateDNAQuantity = value; + } + + public TemplateQualityType getTemplateDNAQuality() { + + return templateDNAQuality; + } + + public void setTemplateDNAQuality(TemplateQualityType value) { + + this.templateDNAQuality = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleTypeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleTypeType.java new file mode 100644 index 0000000000..d701b37f14 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SampleTypeType.java @@ -0,0 +1,60 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "sampleTypeType") +@XmlEnum +public enum SampleTypeType { + + @XmlEnumValue("unkn") + UNKN("unkn"), // + @XmlEnumValue("ntc") + NTC("ntc"), // + @XmlEnumValue("nac") + NAC("nac"), // + @XmlEnumValue("std") + STD("std"), // + @XmlEnumValue("ntp") + NTP("ntp"), // + @XmlEnumValue("nrt") + NRT("nrt"), // + @XmlEnumValue("pos") + POS("pos"), // + @XmlEnumValue("opt") + OPT("opt"); + + private final String value; + + SampleTypeType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static SampleTypeType fromValue(String v) { + + for(SampleTypeType c : SampleTypeType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SequencesType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SequencesType.java new file mode 100644 index 0000000000..3762e1004f --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/SequencesType.java @@ -0,0 +1,77 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "sequencesType", propOrder = {"forwardPrimer", "reversePrimer", "probe1", "probe2", "amplicon"}) +public class SequencesType { + + protected OligoType forwardPrimer; + protected OligoType reversePrimer; + protected OligoType probe1; + protected OligoType probe2; + protected OligoType amplicon; + + public OligoType getForwardPrimer() { + + return forwardPrimer; + } + + public void setForwardPrimer(OligoType value) { + + this.forwardPrimer = value; + } + + public OligoType getReversePrimer() { + + return reversePrimer; + } + + public void setReversePrimer(OligoType value) { + + this.reversePrimer = value; + } + + public OligoType getProbe1() { + + return probe1; + } + + public void setProbe1(OligoType value) { + + this.probe1 = value; + } + + public OligoType getProbe2() { + + return probe2; + } + + public void setProbe2(OligoType value) { + + this.probe2 = value; + } + + public OligoType getAmplicon() { + + return amplicon; + } + + public void setAmplicon(OligoType value) { + + this.amplicon = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/StepType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/StepType.java new file mode 100644 index 0000000000..4c7e1a5bc3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/StepType.java @@ -0,0 +1,105 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "stepType", propOrder = {"nr", "description", "temperature", "gradient", "loop", "pause", "lidOpen"}) +public class StepType { + + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger nr; + protected String description; + protected TemperatureType temperature; + protected GradientType gradient; + protected LoopType loop; + protected PauseType pause; + protected LidOpenType lidOpen; + + public BigInteger getNr() { + + return nr; + } + + public void setNr(BigInteger value) { + + this.nr = value; + } + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public TemperatureType getTemperature() { + + return temperature; + } + + public void setTemperature(TemperatureType value) { + + this.temperature = value; + } + + public GradientType getGradient() { + + return gradient; + } + + public void setGradient(GradientType value) { + + this.gradient = value; + } + + public LoopType getLoop() { + + return loop; + } + + public void setLoop(LoopType value) { + + this.loop = value; + } + + public PauseType getPause() { + + return pause; + } + + public void setPause(PauseType value) { + + this.pause = value; + } + + public LidOpenType getLidOpen() { + + return lidOpen; + } + + public void setLidOpen(LidOpenType value) { + + this.lidOpen = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetType.java new file mode 100644 index 0000000000..d00b670d94 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetType.java @@ -0,0 +1,153 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A target is a defined PCR reaction. PCR reactions for the same gene + * which differ in primer sequences are considered different samples. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "targetType", propOrder = {"description", "documentation", "xRef", "type", "amplificationEfficiencyMethod", "amplificationEfficiency", "detectionLimit", "dyeId", "sequences", "commercialAssay"}) +public class TargetType { + + protected String description; + protected List documentation; + protected List xRef; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected TargetTypeType type; + protected String amplificationEfficiencyMethod; + protected Float amplificationEfficiency; + protected Float detectionLimit; + @XmlElement(required = true) + protected IdReferencesType dyeId; + protected SequencesType sequences; + protected CommercialAssayType commercialAssay; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getXRef() { + + if(xRef == null) { + xRef = new ArrayList<>(); + } + return this.xRef; + } + + public TargetTypeType getType() { + + return type; + } + + public void setType(TargetTypeType value) { + + this.type = value; + } + + public String getAmplificationEfficiencyMethod() { + + return amplificationEfficiencyMethod; + } + + public void setAmplificationEfficiencyMethod(String value) { + + this.amplificationEfficiencyMethod = value; + } + + public Float getAmplificationEfficiency() { + + return amplificationEfficiency; + } + + public void setAmplificationEfficiency(Float value) { + + this.amplificationEfficiency = value; + } + + public Float getDetectionLimit() { + + return detectionLimit; + } + + public void setDetectionLimit(Float value) { + + this.detectionLimit = value; + } + + public IdReferencesType getDyeId() { + + return dyeId; + } + + public void setDyeId(IdReferencesType value) { + + this.dyeId = value; + } + + public SequencesType getSequences() { + + return sequences; + } + + public void setSequences(SequencesType value) { + + this.sequences = value; + } + + public CommercialAssayType getCommercialAssay() { + + return commercialAssay; + } + + public void setCommercialAssay(CommercialAssayType value) { + + this.commercialAssay = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetTypeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetTypeType.java new file mode 100644 index 0000000000..19ae6a79e9 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TargetTypeType.java @@ -0,0 +1,48 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "targetTypeType") +@XmlEnum +public enum TargetTypeType { + + @XmlEnumValue("ref") + REF("ref"), // + @XmlEnumValue("toi") + TOI("toi"); + + private final String value; + + TargetTypeType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static TargetTypeType fromValue(String v) { + + for(TargetTypeType c : TargetTypeType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemperatureType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemperatureType.java new file mode 100644 index 0000000000..6446a867aa --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemperatureType.java @@ -0,0 +1,98 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step keeps a constant temperature on the heat block. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "temperatureType", propOrder = {"temperature", "duration", "temperatureChange", "durationChange", "measure", "ramp"}) +public class TemperatureType { + + protected float temperature; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger duration; + protected float temperatureChange; + protected int durationChange; + @XmlSchemaType(name = "string") + protected MeasureType measure; + protected float ramp; + + public float getTemperature() { + + return temperature; + } + + public void setTemperature(float value) { + + this.temperature = value; + } + + public BigInteger getDuration() { + + return duration; + } + + public void setDuration(BigInteger value) { + + this.duration = value; + } + + public float getTemperatureChange() { + + return temperatureChange; + } + + public void setTemperatureChange(float value) { + + this.temperatureChange = value; + } + + public Integer getDurationChange() { + + return durationChange; + } + + public void setDurationChange(int value) { + + this.durationChange = value; + } + + public MeasureType getMeasure() { + + return measure; + } + + public void setMeasure(MeasureType value) { + + this.measure = value; + } + + public float getRamp() { + + return ramp; + } + + public void setRamp(float value) { + + this.ramp = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemplateQualityType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemplateQualityType.java new file mode 100644 index 0000000000..1add1f832a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/TemplateQualityType.java @@ -0,0 +1,46 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "templateQualityType", propOrder = {"method", "result"}) +public class TemplateQualityType { + + @XmlElement(required = true) + protected String method; + protected float result; + + public String getMethod() { + + return method; + } + + public void setMethod(String value) { + + this.method = value; + } + + public float getResult() { + + return result; + } + + public void setResult(float value) { + + this.result = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ThermalCyclingConditionsType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ThermalCyclingConditionsType.java new file mode 100644 index 0000000000..cbfd9f32c8 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/ThermalCyclingConditionsType.java @@ -0,0 +1,92 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A cycling program for PCR or to amplify cDNA. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "thermalCyclingConditionsType", propOrder = {"description", "documentation", "lidTemperature", "experimenter", "step"}) +public class ThermalCyclingConditionsType { + + protected String description; + protected List documentation; + protected Float lidTemperature; + protected List experimenter; + @XmlElement(required = true) + protected List step; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public Float getLidTemperature() { + + return lidTemperature; + } + + public void setLidTemperature(Float value) { + + this.lidTemperature = value; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public List getStep() { + + if(step == null) { + step = new ArrayList<>(); + } + return this.step; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/XRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/XRefType.java new file mode 100644 index 0000000000..650c3c1956 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v11/model/XRefType.java @@ -0,0 +1,44 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "xRefType", propOrder = {"name", "id"}) +public class XRefType { + + protected String name; + protected String id; + + public String getName() { + + return name; + } + + public void setName(String value) { + + this.name = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/AnnotationType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/AnnotationType.java new file mode 100644 index 0000000000..5cceebab8f --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/AnnotationType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * These elements should be used to annotate samples by setting a + * property and a value. A property could be sex, the value M or F. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "annotationType", propOrder = {}) +public class AnnotationType { + + @XmlElement(required = true) + protected String property; + @XmlElement(required = true) + protected String value; + + public String getProperty() { + + return property; + } + + public void setProperty(String value) { + + this.property = value; + } + + public String getValue() { + + return value; + } + + public void setValue(String value) { + + this.value = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CdnaSynthesisMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CdnaSynthesisMethodType.java new file mode 100644 index 0000000000..f410ff3f01 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CdnaSynthesisMethodType.java @@ -0,0 +1,71 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Description of the cDNA synthesis method. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "cdnaSynthesisMethodType", propOrder = {"enzyme", "primingMethod", "dnaseTreatment", "thermalCyclingConditions"}) +public class CdnaSynthesisMethodType { + + protected String enzyme; + @XmlSchemaType(name = "string") + protected PrimingMethodType primingMethod; + protected Boolean dnaseTreatment; + protected IdReferencesType thermalCyclingConditions; + + public String getEnzyme() { + + return enzyme; + } + + public void setEnzyme(String value) { + + this.enzyme = value; + } + + public PrimingMethodType getPrimingMethod() { + + return primingMethod; + } + + public void setPrimingMethod(PrimingMethodType value) { + + this.primingMethod = value; + } + + public Boolean isDnaseTreatment() { + + return dnaseTreatment; + } + + public void setDnaseTreatment(Boolean value) { + + this.dnaseTreatment = value; + } + + public IdReferencesType getThermalCyclingConditions() { + + return thermalCyclingConditions; + } + + public void setThermalCyclingConditions(IdReferencesType value) { + + this.thermalCyclingConditions = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CommercialAssayType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CommercialAssayType.java new file mode 100644 index 0000000000..8b6784a7a0 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CommercialAssayType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * For some commercial assays, the primer sequences may be unknown. This element + * allows to describe commercial assays. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "commercialAssayType", propOrder = {"company", "orderNumber"}) +public class CommercialAssayType { + + @XmlElement(required = true) + protected String company; + @XmlElement(required = true) + protected String orderNumber; + + public String getCompany() { + + return company; + } + + public void setCompany(String value) { + + this.company = value; + } + + public String getOrderNumber() { + + return orderNumber; + } + + public void setOrderNumber(String value) { + + this.orderNumber = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CqDetectionMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CqDetectionMethodType.java new file mode 100644 index 0000000000..0b2ead46d2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/CqDetectionMethodType.java @@ -0,0 +1,52 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "cqDetectionMethodType") +@XmlEnum +public enum CqDetectionMethodType { + + @XmlEnumValue("automated threshold and baseline settings") + AUTOMATED_THRESHOLD_AND_BASELINE_SETTINGS("automated threshold and baseline settings"), // + @XmlEnumValue("manual threshold and baseline settings") + MANUAL_THRESHOLD_AND_BASELINE_SETTINGS("manual threshold and baseline settings"), // + @XmlEnumValue("second derivative maximum") + SECOND_DERIVATIVE_MAXIMUM("second derivative maximum"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + CqDetectionMethodType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static CqDetectionMethodType fromValue(String v) { + + for(CqDetectionMethodType c : CqDetectionMethodType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataCollectionSoftwareType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataCollectionSoftwareType.java new file mode 100644 index 0000000000..60b0e725ee --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataCollectionSoftwareType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Software name and version used to collect and analyze the data. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dataCollectionSoftwareType", propOrder = {"name", "version"}) +public class DataCollectionSoftwareType { + + @XmlElement(required = true) + protected String name; + @XmlElement(required = true) + protected String version; + + public String getName() { + + return name; + } + + public void setName(String value) { + + this.name = value; + } + + public String getVersion() { + + return version; + } + + public void setVersion(String value) { + + this.version = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataType.java new file mode 100644 index 0000000000..4440c21d03 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DataType.java @@ -0,0 +1,125 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the frequent occurrence of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dataType", propOrder = {"tar", "cq", "excl", "adp", "mdp", "endPt", "bgFluor", "bgFluorSlp", "quantFluor"}) +public class DataType { + + @XmlElement(required = true) + protected IdReferencesType tar; + protected float cq; + protected String excl; + protected List adp; + protected List mdp; + protected float endPt; + protected float bgFluor; + protected float bgFluorSlp; + protected float quantFluor; + + public IdReferencesType getTar() { + + return tar; + } + + public void setTar(IdReferencesType value) { + + this.tar = value; + } + + public Float getCq() { + + return cq; + } + + public void setCq(Float value) { + + this.cq = value; + } + + public String getExcl() { + + return excl; + } + + public void setExcl(String value) { + + this.excl = value; + } + + public List getAdp() { + + if(adp == null) { + adp = new ArrayList<>(); + } + return this.adp; + } + + public List getMdp() { + + if(mdp == null) { + mdp = new ArrayList<>(); + } + return this.mdp; + } + + public float getEndPt() { + + return endPt; + } + + public void setEndPt(float value) { + + this.endPt = value; + } + + public float getBgFluor() { + + return bgFluor; + } + + public void setBgFluor(float value) { + + this.bgFluor = value; + } + + public float getBgFluorSlp() { + + return bgFluorSlp; + } + + public void setBgFluorSlp(float value) { + + this.bgFluorSlp = value; + } + + public float getQuantFluor() { + + return quantFluor; + } + + public void setQuantFluor(float value) { + + this.quantFluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DocumentationType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DocumentationType.java new file mode 100644 index 0000000000..291c61fe45 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DocumentationType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * These elements should be used if the same description applies to many samples, + * targets or experiments. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "documentationType", propOrder = {}) +public class DocumentationType { + + protected String text; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getText() { + + return text; + } + + public void setText(String value) { + + this.text = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpAmpCurveType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpAmpCurveType.java new file mode 100644 index 0000000000..7a037d8239 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpAmpCurveType.java @@ -0,0 +1,58 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the frequent occurrence of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dpAmpCurveType", propOrder = {"cyc", "tmp", "fluor"}) +public class DpAmpCurveType { + + protected float cyc; + protected float tmp; + protected float fluor; + + public float getCyc() { + + return cyc; + } + + public void setCyc(float value) { + + this.cyc = value; + } + + public float getTmp() { + + return tmp; + } + + public void setTmp(float value) { + + this.tmp = value; + } + + public float getFluor() { + + return fluor; + } + + public void setFluor(float value) { + + this.fluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpMeltingCurveType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpMeltingCurveType.java new file mode 100644 index 0000000000..efbddd11ad --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DpMeltingCurveType.java @@ -0,0 +1,47 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Due to the frequent occurrence of this element, names are kept short. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dpMeltingCurveType", propOrder = {"tmp", "fluor"}) +public class DpMeltingCurveType { + + protected float tmp; + protected float fluor; + + public float getTmp() { + + return tmp; + } + + public void setTmp(float value) { + + this.tmp = value; + } + + public float getFluor() { + + return fluor; + } + + public void setFluor(float value) { + + this.fluor = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DyeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DyeType.java new file mode 100644 index 0000000000..d070e93a0c --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/DyeType.java @@ -0,0 +1,49 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Information on a dye. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "dyeType", propOrder = {"description"}) +public class DyeType { + + protected String description; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimentType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimentType.java new file mode 100644 index 0000000000..84429b89cd --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimentType.java @@ -0,0 +1,70 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +/** + * An experiment can contain several runs. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "experimentType", propOrder = {"description", "documentation", "run"}) +public class ExperimentType { + + protected String description; + protected List documentation; + protected List run; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getRun() { + + if(run == null) { + run = new ArrayList<>(); + } + return this.run; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimenterType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimenterType.java new file mode 100644 index 0000000000..1dd23259db --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ExperimenterType.java @@ -0,0 +1,96 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * Contact details of the experimenter. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "experimenterType", propOrder = {"firstName", "lastName", "email", "labName", "labAddress"}) +public class ExperimenterType { + + @XmlElement(required = true) + protected String firstName; + @XmlElement(required = true) + protected String lastName; + protected String email; + protected String labName; + protected String labAddress; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getFirstName() { + + return firstName; + } + + public void setFirstName(String value) { + + this.firstName = value; + } + + public String getLastName() { + + return lastName; + } + + public void setLastName(String value) { + + this.lastName = value; + } + + public String getEmail() { + + return email; + } + + public void setEmail(String value) { + + this.email = value; + } + + public String getLabName() { + + return labName; + } + + public void setLabName(String value) { + + this.labName = value; + } + + public String getLabAddress() { + + return labAddress; + } + + public void setLabAddress(String value) { + + this.labAddress = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/GradientType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/GradientType.java new file mode 100644 index 0000000000..ca9dbb7ca4 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/GradientType.java @@ -0,0 +1,109 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step forms a temperature gradient across the PCR block. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "gradientType", propOrder = {"highTemperature", "lowTemperature", "duration", "temperatureChange", "durationChange", "measure", "ramp"}) +public class GradientType { + + protected float highTemperature; + protected float lowTemperature; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger duration; + protected Float temperatureChange; + protected Integer durationChange; + @XmlSchemaType(name = "string") + protected MeasureType measure; + protected Float ramp; + + public float getHighTemperature() { + + return highTemperature; + } + + public void setHighTemperature(float value) { + + this.highTemperature = value; + } + + public float getLowTemperature() { + + return lowTemperature; + } + + public void setLowTemperature(float value) { + + this.lowTemperature = value; + } + + public BigInteger getDuration() { + + return duration; + } + + public void setDuration(BigInteger value) { + + this.duration = value; + } + + public Float getTemperatureChange() { + + return temperatureChange; + } + + public void setTemperatureChange(Float value) { + + this.temperatureChange = value; + } + + public Integer getDurationChange() { + + return durationChange; + } + + public void setDurationChange(Integer value) { + + this.durationChange = value; + } + + public MeasureType getMeasure() { + + return measure; + } + + public void setMeasure(MeasureType value) { + + this.measure = value; + } + + public Float getRamp() { + + return ramp; + } + + public void setRamp(Float value) { + + this.ramp = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/IdReferencesType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/IdReferencesType.java new file mode 100644 index 0000000000..58b6e3696c --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/IdReferencesType.java @@ -0,0 +1,35 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "idReferencesType") +public class IdReferencesType { + + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LidOpenType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LidOpenType.java new file mode 100644 index 0000000000..3be0722d78 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LidOpenType.java @@ -0,0 +1,27 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step waits for the user to open the lid and continues afterwards. It + * allows to stop the program and to wait for the user to add for example + * enzymes and continue the program afterwards. The temperature of the previous + * step is maintained. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "lidOpenType") +public class LidOpenType { +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LoopType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LoopType.java new file mode 100644 index 0000000000..d95cbcf2b3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/LoopType.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step allows to form a loop or to exclude some steps. It allows to + * jump to a certain "goto" step for "repeat" times. If the "goto" step is + * higher than the step of the loop, "repeat" must be "0". + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "loopType", propOrder = {"gotoStep", "repeat"}) +public class LoopType { + + @XmlElement(name = "goto", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger gotoStep; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger repeat; + + public BigInteger getGoto() { + + return gotoStep; + } + + public void setGoto(BigInteger value) { + + this.gotoStep = value; + } + + public BigInteger getRepeat() { + + return repeat; + } + + public void setRepeat(BigInteger value) { + + this.repeat = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/MeasureType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/MeasureType.java new file mode 100644 index 0000000000..af21ae5708 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/MeasureType.java @@ -0,0 +1,47 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "measureType") +@XmlEnum +public enum MeasureType { + + @XmlEnumValue("real time") + REAL_TIME("real time"), @XmlEnumValue("meltcurve") + MELTCURVE("meltcurve"); + + private final String value; + + MeasureType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static MeasureType fromValue(String v) { + + for(MeasureType c : MeasureType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/NucleotideType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/NucleotideType.java new file mode 100644 index 0000000000..1024f9c0e2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/NucleotideType.java @@ -0,0 +1,50 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "nucleotideType") +@XmlEnum +public enum NucleotideType { + + DNA("DNA"), // + @XmlEnumValue("genomic DNA") + GENOMIC_DNA("genomic DNA"), // + @XmlEnumValue("cDNA") + C_DNA("cDNA"), // + RNA("RNA"); + + private final String value; + + NucleotideType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static NucleotideType fromValue(String v) { + + for(NucleotideType c : NucleotideType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ObjectFactory.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ObjectFactory.java new file mode 100644 index 0000000000..47f2af0f73 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ObjectFactory.java @@ -0,0 +1,173 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlRegistry; + +@XmlRegistry +public class ObjectFactory { + + public Rdml createRdml() { + + return new Rdml(); + } + + public RdmlIdType createRdmlIdType() { + + return new RdmlIdType(); + } + + public ExperimenterType createExperimenterType() { + + return new ExperimenterType(); + } + + public DocumentationType createDocumentationType() { + + return new DocumentationType(); + } + + public DyeType createDyeType() { + + return new DyeType(); + } + + public SampleType createSampleType() { + + return new SampleType(); + } + + public TargetType createTargetType() { + + return new TargetType(); + } + + public ThermalCyclingConditionsType createThermalCyclingConditionsType() { + + return new ThermalCyclingConditionsType(); + } + + public ExperimentType createExperimentType() { + + return new ExperimentType(); + } + + public QuantityType createQuantityType() { + + return new QuantityType(); + } + + public IdReferencesType createIdReferencesType() { + + return new IdReferencesType(); + } + + public TemperatureType createTemperatureType() { + + return new TemperatureType(); + } + + public StepType createStepType() { + + return new StepType(); + } + + public RunType createRunType() { + + return new RunType(); + } + + public OligoType createOligoType() { + + return new OligoType(); + } + + public LidOpenType createLidOpenType() { + + return new LidOpenType(); + } + + public GradientType createGradientType() { + + return new GradientType(); + } + + public DpMeltingCurveType createDpMeltingCurveType() { + + return new DpMeltingCurveType(); + } + + public ReactType createReactType() { + + return new ReactType(); + } + + public PauseType createPauseType() { + + return new PauseType(); + } + + public DataCollectionSoftwareType createDataCollectionSoftwareType() { + + return new DataCollectionSoftwareType(); + } + + public DataType createDataType() { + + return new DataType(); + } + + public AnnotationType createAnnotationType() { + + return new AnnotationType(); + } + + public CdnaSynthesisMethodType createCdnaSynthesisMethodType() { + + return new CdnaSynthesisMethodType(); + } + + public PcrFormatType createPcrFormatType() { + + return new PcrFormatType(); + } + + public DpAmpCurveType createDpAmpCurveType() { + + return new DpAmpCurveType(); + } + + public LoopType createLoopType() { + + return new LoopType(); + } + + public TemplateQuantityType createTemplateQuantityType() { + + return new TemplateQuantityType(); + } + + public CommercialAssayType createCommercialAssayType() { + + return new CommercialAssayType(); + } + + public SequencesType createSequencesType() { + + return new SequencesType(); + } + + public XRefType createXRefType() { + + return new XRefType(); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/OligoType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/OligoType.java new file mode 100644 index 0000000000..32eaa02320 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/OligoType.java @@ -0,0 +1,57 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "oligoType", propOrder = {"threePrimeTag", "fivePrimeTag", "sequence"}) +public class OligoType { + + protected String threePrimeTag; + protected String fivePrimeTag; + @XmlElement(required = true) + protected String sequence; + + public String getThreePrimeTag() { + + return threePrimeTag; + } + + public void setThreePrimeTag(String value) { + + this.threePrimeTag = value; + } + + public String getFivePrimeTag() { + + return fivePrimeTag; + } + + public void setFivePrimeTag(String value) { + + this.fivePrimeTag = value; + } + + public String getSequence() { + + return sequence; + } + + public void setSequence(String value) { + + this.sequence = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PauseType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PauseType.java new file mode 100644 index 0000000000..fa75d6fb0a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PauseType.java @@ -0,0 +1,37 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step allows to pause at a certain temperature. It is typically the + * last step in an amplification protocol. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "pauseType", propOrder = {"temperature"}) +public class PauseType { + + protected float temperature; + + public float getTemperature() { + + return temperature; + } + + public void setTemperature(float value) { + + this.temperature = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PcrFormatType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PcrFormatType.java new file mode 100644 index 0000000000..1dbc149b69 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PcrFormatType.java @@ -0,0 +1,98 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * 
+ *        The format of the run - This allows the software to display the data
+ *        according to the qPCR instrument run format.
+ *        Rotor formats always have 1 column; rows correspond to the number
+ *        of places in the rotor.
+ *        
+ *        Values for common formats are:
+ *        
+ *        Format            |    rows    |   columns   |  rowLabel  | columnLabel
+ *        --------------------------------------------------------------------------
+ *        single-well       |     1      |      1      |    123     |     123
+ *        48-well plate     |     6      |      8      |    ABC     |     123
+ *        96-well plate     |     8      |     12      |    ABC     |     123
+ *        384-well plate    |    16      |     24      |    ABC     |     123
+ *        1536-well plate   |    32      |     48      |    ABC     |     123
+ *        3072-well array   |    32      |     96      |   A1a1     |    A1a1
+ *        5184-well chip    |    72      |     72      |    ABC     |     123
+ *        32-well rotor     |    32      |      1      |    123     |     123
+ *        72-well rotor     |    72      |      1      |    123     |     123
+ *        100-well rotor    |   100      |      1      |    123     |     123
+ *        free format       |    -1      |      1      |    123     |     123
+ *        
+ *        If rows are -1 then the software should not try to reconstruct a plate and 
+ *        just display all react data in list (1 column) form.
+ *        
+ *        If columns is 1 then the software should not display a column label.
+ *
+ */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "pcrFormatType", propOrder = {"rows", "columns", "rowLabel", "columnLabel"}) +public class PcrFormatType { + + protected int rows; + protected int columns; + @XmlElement(required = true) + protected String rowLabel; + @XmlElement(required = true) + protected String columnLabel; + + public int getRows() { + + return rows; + } + + public void setRows(int value) { + + this.rows = value; + } + + public int getColumns() { + + return columns; + } + + public void setColumns(int value) { + + this.columns = value; + } + + public String getRowLabel() { + + return rowLabel; + } + + public void setRowLabel(String value) { + + this.rowLabel = value; + } + + public String getColumnLabel() { + + return columnLabel; + } + + public void setColumnLabel(String value) { + + this.columnLabel = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PrimingMethodType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PrimingMethodType.java new file mode 100644 index 0000000000..d0321fe7cf --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/PrimingMethodType.java @@ -0,0 +1,54 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "primingMethodType") +@XmlEnum +public enum PrimingMethodType { + + @XmlEnumValue("oligo-dt") + OLIGO_DT("oligo-dt"), // + @XmlEnumValue("random") + RANDOM("random"), // + @XmlEnumValue("target-specific") + TARGET_SPECIFIC("target-specific"), // + @XmlEnumValue("oligo-dt and random") + OLIGO_DT_AND_RANDOM("oligo-dt and random"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + PrimingMethodType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static PrimingMethodType fromValue(String v) { + + for(PrimingMethodType c : PrimingMethodType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityType.java new file mode 100644 index 0000000000..79afd2f94a --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityType.java @@ -0,0 +1,51 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A quantity is always defined by its value and its unit. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "quantityType", propOrder = {"value", "unit"}) +public class QuantityType { + + protected float value; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected QuantityUnitType unit; + + public float getValue() { + + return value; + } + + public void setValue(float value) { + + this.value = value; + } + + public QuantityUnitType getUnit() { + + return unit; + } + + public void setUnit(QuantityUnitType value) { + + this.unit = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityUnitType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityUnitType.java new file mode 100644 index 0000000000..f390b193b9 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/QuantityUnitType.java @@ -0,0 +1,56 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "quantityUnitType") +@XmlEnum +public enum QuantityUnitType { + + @XmlEnumValue("cop") + COP("cop"), // + @XmlEnumValue("fold") + FOLD("fold"), // + @XmlEnumValue("dil") + DIL("dil"), // + @XmlEnumValue("ng") + NG("ng"), // + @XmlEnumValue("nMol") + N_MOL("nMol"), // + @XmlEnumValue("other") + OTHER("other"); + + private final String value; + + QuantityUnitType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static QuantityUnitType fromValue(String v) { + + for(QuantityUnitType c : QuantityUnitType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/Rdml.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/Rdml.java new file mode 100644 index 0000000000..5826cbf77b --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/Rdml.java @@ -0,0 +1,143 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.datatype.XMLGregorianCalendar; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlRootElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = {"dateMade", "dateUpdated", "id", "experimenter", "documentation", "dye", "sample", "target", "thermalCyclingConditions", "experiment"}) +@XmlRootElement(name = "rdml") +public class Rdml { + + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar dateMade; + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar dateUpdated; + protected List id; + protected List experimenter; + protected List documentation; + protected List dye; + protected List sample; + protected List target; + protected List thermalCyclingConditions; + protected List experiment; + @XmlAttribute(name = "version", required = true) + protected String version; + + public XMLGregorianCalendar getDateMade() { + + return dateMade; + } + + public void setDateMade(XMLGregorianCalendar value) { + + this.dateMade = value; + } + + public XMLGregorianCalendar getDateUpdated() { + + return dateUpdated; + } + + public void setDateUpdated(XMLGregorianCalendar value) { + + this.dateUpdated = value; + } + + public List getId() { + + if(id == null) { + id = new ArrayList<>(); + } + return this.id; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList(); + } + return this.documentation; + } + + public List getDye() { + + if(dye == null) { + dye = new ArrayList<>(); + } + return this.dye; + } + + public List getSample() { + + if(sample == null) { + sample = new ArrayList<>(); + } + return this.sample; + } + + public List getTarget() { + + if(target == null) { + target = new ArrayList<>(); + } + return this.target; + } + + public List getThermalCyclingConditions() { + + if(thermalCyclingConditions == null) { + thermalCyclingConditions = new ArrayList<>(); + } + return this.thermalCyclingConditions; + } + + public List getExperiment() { + + if(experiment == null) { + experiment = new ArrayList<>(); + } + return this.experiment; + } + + public String getVersion() { + + if(version == null) { + return "1.2"; + } else { + return version; + } + } + + public void setVersion(String value) { + + this.version = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RdmlIdType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RdmlIdType.java new file mode 100644 index 0000000000..a79aee9468 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RdmlIdType.java @@ -0,0 +1,62 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This element can be used to assign a publisher and id to the RDML file. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "rdmlIdType", propOrder = {"publisher", "serialNumber", "md5Hash"}) +public class RdmlIdType { + + @XmlElement(required = true) + protected String publisher; + @XmlElement(required = true) + protected String serialNumber; + @XmlElement(name = "MD5Hash") + protected String md5Hash; + + public String getPublisher() { + + return publisher; + } + + public void setPublisher(String value) { + + this.publisher = value; + } + + public String getSerialNumber() { + + return serialNumber; + } + + public void setSerialNumber(String value) { + + this.serialNumber = value; + } + + public String getMD5Hash() { + + return md5Hash; + } + + public void setMD5Hash(String value) { + + this.md5Hash = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ReactType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ReactType.java new file mode 100644 index 0000000000..b7937acd12 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ReactType.java @@ -0,0 +1,69 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.math.BigInteger; +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A reaction is an independent chemical reaction corresponding for example + * to a well in a 96 well plate, a capillary in a rotor, a through-hole on + * an array, etc. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "reactType", propOrder = {"sample", "data"}) +public class ReactType { + + @XmlElement(required = true) + protected IdReferencesType sample; + @XmlElement(required = true) + protected List data; + @XmlAttribute(name = "id", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger id; + + public IdReferencesType getSample() { + + return sample; + } + + public void setSample(IdReferencesType value) { + + this.sample = value; + } + + public List getData() { + + if(data == null) { + data = new ArrayList<>(); + } + return this.data; + } + + public BigInteger getId() { + + return id; + } + + public void setId(BigInteger value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RunType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RunType.java new file mode 100644 index 0000000000..c2595cdec3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/RunType.java @@ -0,0 +1,164 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import javax.xml.datatype.XMLGregorianCalendar; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A run is a set of reactions performed in one "run", for example + * one plate, one rotor, one array, one chip. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "runType", propOrder = {"description", "documentation", "experimenter", "instrument", "dataCollectionSoftware", "backgroundDeterminationMethod", "cqDetectionMethod", "thermalCyclingConditions", "pcrFormat", "runDate", "react"}) +public class RunType { + + protected String description; + protected List documentation; + protected List experimenter; + protected String instrument; + protected DataCollectionSoftwareType dataCollectionSoftware; + protected String backgroundDeterminationMethod; + @XmlSchemaType(name = "string") + protected CqDetectionMethodType cqDetectionMethod; + protected IdReferencesType thermalCyclingConditions; + @XmlElement(required = true) + protected PcrFormatType pcrFormat; + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar runDate; + protected List react; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public String getInstrument() { + + return instrument; + } + + public void setInstrument(String value) { + + this.instrument = value; + } + + public DataCollectionSoftwareType getDataCollectionSoftware() { + + return dataCollectionSoftware; + } + + public void setDataCollectionSoftware(DataCollectionSoftwareType value) { + + this.dataCollectionSoftware = value; + } + + public String getBackgroundDeterminationMethod() { + + return backgroundDeterminationMethod; + } + + public void setBackgroundDeterminationMethod(String value) { + + this.backgroundDeterminationMethod = value; + } + + public CqDetectionMethodType getCqDetectionMethod() { + + return cqDetectionMethod; + } + + public void setCqDetectionMethod(CqDetectionMethodType value) { + + this.cqDetectionMethod = value; + } + + public IdReferencesType getThermalCyclingConditions() { + + return thermalCyclingConditions; + } + + public void setThermalCyclingConditions(IdReferencesType value) { + + this.thermalCyclingConditions = value; + } + + public PcrFormatType getPcrFormat() { + + return pcrFormat; + } + + public void setPcrFormat(PcrFormatType value) { + + this.pcrFormat = value; + } + + public XMLGregorianCalendar getRunDate() { + + return runDate; + } + + public void setRunDate(XMLGregorianCalendar value) { + + this.runDate = value; + } + + public List getReact() { + + if(react == null) { + react = new ArrayList<>(); + } + return this.react; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleType.java new file mode 100644 index 0000000000..af38d65172 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleType.java @@ -0,0 +1,157 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A sample is a defined template solution. Dilutions of the same + * material differ in concentration and are considered different samples. + * A technical replicate samples should contain the same name (reactions + * are performed on the same material), and biological replicates should + * contain different names (the nucleic acids derived from the different + * biological replicates are not the same). Serial dilutions in a standard + * curve must have a different name. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "sampleType", propOrder = {"description", "documentation", "xRef", "annotation", "type", "interRunCalibrator", "quantity", "calibratorSample", "cdnaSynthesisMethod", "templateQuantity"}) +public class SampleType { + + protected String description; + protected List documentation; + protected List xRef; + protected List annotation; + @XmlElement(required = true, defaultValue = "unkn") + @XmlSchemaType(name = "string") + protected SampleTypeType type; + @XmlElement(defaultValue = "false") + protected Boolean interRunCalibrator; + protected QuantityType quantity; + @XmlElement(defaultValue = "false") + protected Boolean calibratorSample; + protected CdnaSynthesisMethodType cdnaSynthesisMethod; + protected TemplateQuantityType templateQuantity; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getXRef() { + + if(xRef == null) { + xRef = new ArrayList<>(); + } + return this.xRef; + } + + public List getAnnotation() { + + if(annotation == null) { + annotation = new ArrayList<>(); + } + return this.annotation; + } + + public SampleTypeType getType() { + + return type; + } + + public void setType(SampleTypeType value) { + + this.type = value; + } + + public Boolean isInterRunCalibrator() { + + return interRunCalibrator; + } + + public void setInterRunCalibrator(Boolean value) { + + this.interRunCalibrator = value; + } + + public QuantityType getQuantity() { + + return quantity; + } + + public void setQuantity(QuantityType value) { + + this.quantity = value; + } + + public Boolean isCalibratorSample() { + + return calibratorSample; + } + + public void setCalibratorSample(Boolean value) { + + this.calibratorSample = value; + } + + public CdnaSynthesisMethodType getCdnaSynthesisMethod() { + + return cdnaSynthesisMethod; + } + + public void setCdnaSynthesisMethod(CdnaSynthesisMethodType value) { + + this.cdnaSynthesisMethod = value; + } + + public TemplateQuantityType getTemplateQuantity() { + + return templateQuantity; + } + + public void setTemplateQuantity(TemplateQuantityType value) { + + this.templateQuantity = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleTypeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleTypeType.java new file mode 100644 index 0000000000..7c4ef3d02d --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SampleTypeType.java @@ -0,0 +1,60 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "sampleTypeType") +@XmlEnum +public enum SampleTypeType { + + @XmlEnumValue("unkn") + UNKN("unkn"), // + @XmlEnumValue("ntc") + NTC("ntc"), // + @XmlEnumValue("nac") + NAC("nac"), // + @XmlEnumValue("std") + STD("std"), // + @XmlEnumValue("ntp") + NTP("ntp"), // + @XmlEnumValue("nrt") + NRT("nrt"), // + @XmlEnumValue("pos") + POS("pos"), // + @XmlEnumValue("opt") + OPT("opt"); // + + private final String value; + + SampleTypeType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static SampleTypeType fromValue(String v) { + + for(SampleTypeType c : SampleTypeType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SequencesType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SequencesType.java new file mode 100644 index 0000000000..396acbccd3 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/SequencesType.java @@ -0,0 +1,77 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "sequencesType", propOrder = {"forwardPrimer", "reversePrimer", "probe1", "probe2", "amplicon"}) +public class SequencesType { + + protected OligoType forwardPrimer; + protected OligoType reversePrimer; + protected OligoType probe1; + protected OligoType probe2; + protected OligoType amplicon; + + public OligoType getForwardPrimer() { + + return forwardPrimer; + } + + public void setForwardPrimer(OligoType value) { + + this.forwardPrimer = value; + } + + public OligoType getReversePrimer() { + + return reversePrimer; + } + + public void setReversePrimer(OligoType value) { + + this.reversePrimer = value; + } + + public OligoType getProbe1() { + + return probe1; + } + + public void setProbe1(OligoType value) { + + this.probe1 = value; + } + + public OligoType getProbe2() { + + return probe2; + } + + public void setProbe2(OligoType value) { + + this.probe2 = value; + } + + public OligoType getAmplicon() { + + return amplicon; + } + + public void setAmplicon(OligoType value) { + + this.amplicon = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/StepType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/StepType.java new file mode 100644 index 0000000000..ecf9674f54 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/StepType.java @@ -0,0 +1,105 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "stepType", propOrder = {"nr", "description", "temperature", "gradient", "loop", "pause", "lidOpen"}) +public class StepType { + + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger nr; + protected String description; + protected TemperatureType temperature; + protected GradientType gradient; + protected LoopType loop; + protected PauseType pause; + protected LidOpenType lidOpen; + + public BigInteger getNr() { + + return nr; + } + + public void setNr(BigInteger value) { + + this.nr = value; + } + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public TemperatureType getTemperature() { + + return temperature; + } + + public void setTemperature(TemperatureType value) { + + this.temperature = value; + } + + public GradientType getGradient() { + + return gradient; + } + + public void setGradient(GradientType value) { + + this.gradient = value; + } + + public LoopType getLoop() { + + return loop; + } + + public void setLoop(LoopType value) { + + this.loop = value; + } + + public PauseType getPause() { + + return pause; + } + + public void setPause(PauseType value) { + + this.pause = value; + } + + public LidOpenType getLidOpen() { + + return lidOpen; + } + + public void setLidOpen(LidOpenType value) { + + this.lidOpen = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetType.java new file mode 100644 index 0000000000..1abbb8762e --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetType.java @@ -0,0 +1,164 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A target is a defined PCR reaction. PCR reactions for the same gene + * which differ in primer sequences are considered different targets. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "targetType", propOrder = {"description", "documentation", "xRef", "type", "amplificationEfficiencyMethod", "amplificationEfficiency", "amplificationEfficiencySE", "detectionLimit", "dyeId", "sequences", "commercialAssay"}) +public class TargetType { + + protected String description; + protected List documentation; + protected List xRef; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected TargetTypeType type; + protected String amplificationEfficiencyMethod; + protected Float amplificationEfficiency; + protected Float amplificationEfficiencySE; + protected Float detectionLimit; + @XmlElement(required = true) + protected IdReferencesType dyeId; + protected SequencesType sequences; + protected CommercialAssayType commercialAssay; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public List getXRef() { + + if(xRef == null) { + xRef = new ArrayList<>(); + } + return this.xRef; + } + + public TargetTypeType getType() { + + return type; + } + + public void setType(TargetTypeType value) { + + this.type = value; + } + + public String getAmplificationEfficiencyMethod() { + + return amplificationEfficiencyMethod; + } + + public void setAmplificationEfficiencyMethod(String value) { + + this.amplificationEfficiencyMethod = value; + } + + public Float getAmplificationEfficiency() { + + return amplificationEfficiency; + } + + public void setAmplificationEfficiency(Float value) { + + this.amplificationEfficiency = value; + } + + public Float getAmplificationEfficiencySE() { + + return amplificationEfficiencySE; + } + + public void setAmplificationEfficiencySE(Float value) { + + this.amplificationEfficiencySE = value; + } + + public Float getDetectionLimit() { + + return detectionLimit; + } + + public void setDetectionLimit(Float value) { + + this.detectionLimit = value; + } + + public IdReferencesType getDyeId() { + + return dyeId; + } + + public void setDyeId(IdReferencesType value) { + + this.dyeId = value; + } + + public SequencesType getSequences() { + + return sequences; + } + + public void setSequences(SequencesType value) { + + this.sequences = value; + } + + public CommercialAssayType getCommercialAssay() { + + return commercialAssay; + } + + public void setCommercialAssay(CommercialAssayType value) { + + this.commercialAssay = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetTypeType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetTypeType.java new file mode 100644 index 0000000000..ebb89b42a9 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TargetTypeType.java @@ -0,0 +1,48 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlEnum; +import jakarta.xml.bind.annotation.XmlEnumValue; +import jakarta.xml.bind.annotation.XmlType; + +@XmlType(name = "targetTypeType") +@XmlEnum +public enum TargetTypeType { + + @XmlEnumValue("ref") + REF("ref"), // + @XmlEnumValue("toi") + TOI("toi"); + + private final String value; + + TargetTypeType(String v) { + + value = v; + } + + public String value() { + + return value; + } + + public static TargetTypeType fromValue(String v) { + + for(TargetTypeType c : TargetTypeType.values()) { + if(c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemperatureType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemperatureType.java new file mode 100644 index 0000000000..5afdfed3e8 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemperatureType.java @@ -0,0 +1,98 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.math.BigInteger; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +/** + * This step keeps a constant temperature on the heat block. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "temperatureType", propOrder = {"temperature", "duration", "temperatureChange", "durationChange", "measure", "ramp"}) +public class TemperatureType { + + protected float temperature; + @XmlElement(required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger duration; + protected float temperatureChange; + protected int durationChange; + @XmlSchemaType(name = "string") + protected MeasureType measure; + protected float ramp; + + public float getTemperature() { + + return temperature; + } + + public void setTemperature(float value) { + + this.temperature = value; + } + + public BigInteger getDuration() { + + return duration; + } + + public void setDuration(BigInteger value) { + + this.duration = value; + } + + public float getTemperatureChange() { + + return temperatureChange; + } + + public void setTemperatureChange(float value) { + + this.temperatureChange = value; + } + + public int getDurationChange() { + + return durationChange; + } + + public void setDurationChange(int value) { + + this.durationChange = value; + } + + public MeasureType getMeasure() { + + return measure; + } + + public void setMeasure(MeasureType value) { + + this.measure = value; + } + + public float getRamp() { + + return ramp; + } + + public void setRamp(float value) { + + this.ramp = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemplateQuantityType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemplateQuantityType.java new file mode 100644 index 0000000000..2655c70691 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/TemplateQuantityType.java @@ -0,0 +1,48 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlSchemaType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "templateQuantityType", propOrder = {"conc", "nucleotide"}) +public class TemplateQuantityType { + + protected float conc; + @XmlElement(required = true) + @XmlSchemaType(name = "string") + protected NucleotideType nucleotide; + + public float getConc() { + + return conc; + } + + public void setConc(float value) { + + this.conc = value; + } + + public NucleotideType getNucleotide() { + + return nucleotide; + } + + public void setNucleotide(NucleotideType value) { + + this.nucleotide = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ThermalCyclingConditionsType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ThermalCyclingConditionsType.java new file mode 100644 index 0000000000..94d277b3b6 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/ThermalCyclingConditionsType.java @@ -0,0 +1,92 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import java.util.ArrayList; +import java.util.List; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlAttribute; +import jakarta.xml.bind.annotation.XmlElement; +import jakarta.xml.bind.annotation.XmlType; + +/** + * A cycling program for PCR or to amplify cDNA. + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "thermalCyclingConditionsType", propOrder = {"description", "documentation", "lidTemperature", "experimenter", "step"}) +public class ThermalCyclingConditionsType { + + protected String description; + protected List documentation; + protected Float lidTemperature; + protected List experimenter; + @XmlElement(required = true) + protected List step; + @XmlAttribute(name = "id", required = true) + protected String id; + + public String getDescription() { + + return description; + } + + public void setDescription(String value) { + + this.description = value; + } + + public List getDocumentation() { + + if(documentation == null) { + documentation = new ArrayList<>(); + } + return this.documentation; + } + + public Float getLidTemperature() { + + return lidTemperature; + } + + public void setLidTemperature(Float value) { + + this.lidTemperature = value; + } + + public List getExperimenter() { + + if(experimenter == null) { + experimenter = new ArrayList<>(); + } + return this.experimenter; + } + + public List getStep() { + + if(step == null) { + step = new ArrayList<>(); + } + return this.step; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/XRefType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/XRefType.java new file mode 100644 index 0000000000..9631021235 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v12/model/XRefType.java @@ -0,0 +1,44 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model; + +import jakarta.xml.bind.annotation.XmlAccessType; +import jakarta.xml.bind.annotation.XmlAccessorType; +import jakarta.xml.bind.annotation.XmlType; + +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "xRefType", propOrder = {"name", "id"}) +public class XRefType { + + protected String name; + protected String id; + + public String getName() { + + return name; + } + + public void setName(String value) { + + this.name = value; + } + + public String getId() { + + return id; + } + + public void setId(String value) { + + this.id = value; + } +} diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v13/model/PcrFormatType.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v13/model/PcrFormatType.java index 96f0517e62..3ba853c3a0 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v13/model/PcrFormatType.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/internal/v13/model/PcrFormatType.java @@ -17,34 +17,33 @@ import jakarta.xml.bind.annotation.XmlType; /** - * - * The format of the run - This allows the software to display the data - * according to the qPCR instrument run format. - * Rotor formats always have 1 column; rows correspond to the number - * of places in the rotor. - * - * Values for common formats are: - * - * Format | rows | columns | rowLabel | columnLabel - * ------------------------------------------------- - * single-well | 1 | 1 | 123 | 123 - * 48-well plate | 6 | 8 | ABC | 123 - * 96-well plate | 8 | 12 | ABC | 123 - * 384-well plate | 16 | 24 | ABC | 123 - * 1536-well plate | 32 | 48 | ABC | 123 - * 3072-well array | 32 | 96 | A1a1 | A1a1 - * 5184-well chip | 72 | 72 | ABC | 123 - * 32-well rotor | 32 | 1 | 123 | 123 - * 72-well rotor | 72 | 1 | 123 | 123 - * 100-well rotor | 100 | 1 | 123 | 123 - * free format | -1 | 1 | 123 | 123 - * - * If rows are -1 then the software should not try to reconstruct a plate and - * just display all react data in list (1 column) form. - * - * If columns is 1 then the software should not display a column label. - * - * + * 
+ *        The format of the run - This allows the software to display the data
+ *        according to the qPCR instrument run format.
+ *        Rotor formats always have 1 column; rows correspond to the number
+ *        of places in the rotor.
+ *        
+ *        Values for common formats are:
+ *        
+ *        Format            |    rows    |   columns   |  rowLabel  | columnLabel
+ *        --------------------------------------------------------------------------
+ *        single-well       |     1      |      1      |    123     |     123
+ *        48-well plate     |     6      |      8      |    ABC     |     123
+ *        96-well plate     |     8      |     12      |    ABC     |     123
+ *        384-well plate    |    16      |     24      |    ABC     |     123
+ *        1536-well plate   |    32      |     48      |    ABC     |     123
+ *        3072-well array   |    32      |     96      |   A1a1     |    A1a1
+ *        5184-well chip    |    72      |     72      |    ABC     |     123
+ *        32-well rotor     |    32      |      1      |    123     |     123
+ *        72-well rotor     |    72      |      1      |    123     |     123
+ *        100-well rotor    |   100      |      1      |    123     |     123
+ *        free format       |    -1      |      1      |    123     |     123
+ *        
+ *        If rows are -1 then the software should not try to reconstruct a plate and 
+ *        just display all react data in list (1 column) form.
+ *        
+ *        If columns is 1 then the software should not display a column label.
+ *
*/ @XmlAccessorType(XmlAccessType.FIELD) @XmlType(name = "pcrFormatType", propOrder = {"rows", "columns", "rowLabel", "columnLabel"}) diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReader.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReader.java index c32740425d..4fdd0e460e 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReader.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReader.java @@ -11,156 +11,60 @@ *******************************************************************************/ package org.eclipse.chemclipse.pcr.converter.supplier.rdml.io; +import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStream; +import java.io.InputStreamReader; import java.security.InvalidParameterException; import java.util.Enumeration; import java.util.zip.ZipEntry; import java.util.zip.ZipFile; -import javax.xml.datatype.XMLGregorianCalendar; -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.DataType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.DpAmpCurveType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.DyeType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.ExperimentType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.IdReferencesType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.ObjectFactory; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.PcrFormatType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.Rdml; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.ReactType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.RunType; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IVendorPlate; -import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.VendorPlate; -import org.eclipse.chemclipse.pcr.converter.support.AmplificationAnalysis; -import org.eclipse.chemclipse.pcr.model.core.Channel; -import org.eclipse.chemclipse.pcr.model.core.ChannelSpecification; -import org.eclipse.chemclipse.pcr.model.core.DetectionFormat; -import org.eclipse.chemclipse.pcr.model.core.IChannelSpecification; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IPCRReader; import org.eclipse.chemclipse.pcr.model.core.IPlate; -import org.eclipse.chemclipse.pcr.model.core.IWell; -import org.eclipse.chemclipse.pcr.model.core.Position; -import org.eclipse.chemclipse.pcr.model.core.Well; -import org.w3c.dom.Document; -import org.w3c.dom.NodeList; +import org.eclipse.chemclipse.xxd.converter.supplier.io.exception.UnknownVersionException; import org.xml.sax.SAXException; -import jakarta.xml.bind.JAXBContext; import jakarta.xml.bind.JAXBException; -import jakarta.xml.bind.Unmarshaller; public class PCRReader { public IPlate read(File file) throws IOException, SAXException, JAXBException, ParserConfigurationException, InvalidParameterException { - IPlate plate = null; try (ZipFile zipFile = new ZipFile(file)) { Enumeration zipEntries = zipFile.entries(); while(zipEntries.hasMoreElements()) { ZipEntry zipEntry = zipEntries.nextElement(); if(!zipEntry.isDirectory()) { if(zipEntry.getName().equals("rdml_data.xml")) { - plate = readData(zipFile.getInputStream(zipEntry)); - break; + IPCRReader reader = chooseReader(zipFile.getInputStream(zipEntry)); + return reader.readData(zipFile.getInputStream(zipEntry)); } } } } - return plate; + return null; } - private IPlate readData(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException, InvalidParameterException { + private IPCRReader chooseReader(InputStream inputStream) throws IOException { - IVendorPlate vendorPlate = new VendorPlate(); - Rdml rdml = getRDML(inputStream); - setDate(vendorPlate, rdml); - setDefaultDetectionFormat(vendorPlate); - readExperiment(vendorPlate, rdml); - AmplificationAnalysis.calculateCrossingPoints(vendorPlate); - return vendorPlate; - } - - private static Rdml getRDML(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException { - - DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); - DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); - Document document = documentBuilder.parse(inputStream); - NodeList topNode = document.getElementsByTagName("rdml"); + IPCRReader pcrReader = null; // - JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); - Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); - return (Rdml)unmarshaller.unmarshal(topNode.item(0)); - } - - private void setDate(IVendorPlate vendorPlate, Rdml rdml) { - - XMLGregorianCalendar dateMade = rdml.getDateMade(); - if(dateMade != null) { - vendorPlate.setDate(dateMade.toGregorianCalendar().getTime()); - } - } - - private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidParameterException { - - for(ExperimentType experiment : rdml.getExperiment()) { - vendorPlate.setName(experiment.getId()); - vendorPlate.setDetailedInfo(experiment.getDescription()); - for(RunType run : experiment.getRun()) { - PcrFormatType pcrFormatType = run.getPcrFormat(); - int w = 0; - for(ReactType react : run.getReact()) { - IdReferencesType sample = react.getSample(); - IWell well = new Well(); - well.setPosition(calculateCoordinate(w + 1, pcrFormatType)); - well.putHeaderData(IWell.SAMPLE_ID, sample.getId()); - Channel channel = createChannel(rdml); - for(DataType data : react.getData()) { - for(DpAmpCurveType adp : data.getAdp()) { - channel.getFluorescence().add((double)adp.getFluor()); - } - } - well.getChannels().put(0, channel); - well.putHeaderData(IWell.SAMPLE_SUBSET, "Default"); - vendorPlate.getWells().add(well); - w++; - } + try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream))) { + final String header = bufferedReader.readLine(); + if(header.contains("1.3")) { + pcrReader = new PCRReaderVersion13(); + } else if(header.contains("1.2")) { + pcrReader = new PCRReaderVersion12(); + } else if(header.contains("1.1")) { + pcrReader = new PCRReaderVersion11(); + } else { + throw new UnknownVersionException(); } } - } - - private Channel createChannel(Rdml rdml) { - - Channel channel = new Channel(); - channel.setId(0); - for(DyeType dye : rdml.getDye()) { - channel.setDetectionName(dye.getId()); - } - channel.setValid(true); - return channel; - } - - private void setDefaultDetectionFormat(IVendorPlate vendorPlate) { - - DetectionFormat detectionFormat = new DetectionFormat(); - IChannelSpecification channelSpecification = new ChannelSpecification(); - channelSpecification.putHeaderData(IChannelSpecification.NAME, "Default"); - detectionFormat.getChannelSpecifications().add(channelSpecification); - vendorPlate.setDetectionFormat(detectionFormat); - } - - private static Position calculateCoordinate(int id, PcrFormatType pcrFormatType) { - - id--; // adjust for 0-based indexing - int row = id % pcrFormatType.getRows(); - int column = id / pcrFormatType.getRows(); - char rowLetter = (char)('A' + row); - int columnNumber = column + 1; - Position position = new Position(String.valueOf(rowLetter), columnNumber); - position.setId(id); - return position; + return pcrReader; } } \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion11.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion11.java new file mode 100644 index 0000000000..7d2887acc2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion11.java @@ -0,0 +1,146 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. + * This program and the accompanying materials are made available under the + * terms of the Eclipse Public License v1.0 which accompanies this distribution, + * and is available at http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.io; + +import java.io.IOException; +import java.io.InputStream; +import java.security.InvalidParameterException; + +import javax.xml.datatype.XMLGregorianCalendar; +import javax.xml.parsers.DocumentBuilder; +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; + +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.DataType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.DpAmpCurveType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.DyeType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.ExperimentType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.IdReferencesType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.ObjectFactory; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.PcrFormatType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.Rdml; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.ReactType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v11.model.RunType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IPCRReader; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IVendorPlate; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.VendorPlate; +import org.eclipse.chemclipse.pcr.converter.support.AmplificationAnalysis; +import org.eclipse.chemclipse.pcr.model.core.Channel; +import org.eclipse.chemclipse.pcr.model.core.ChannelSpecification; +import org.eclipse.chemclipse.pcr.model.core.DetectionFormat; +import org.eclipse.chemclipse.pcr.model.core.IChannelSpecification; +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.eclipse.chemclipse.pcr.model.core.IWell; +import org.eclipse.chemclipse.pcr.model.core.Position; +import org.eclipse.chemclipse.pcr.model.core.Well; +import org.w3c.dom.Document; +import org.w3c.dom.NodeList; +import org.xml.sax.SAXException; + +import jakarta.xml.bind.JAXBContext; +import jakarta.xml.bind.JAXBException; +import jakarta.xml.bind.Unmarshaller; + +public class PCRReaderVersion11 implements IPCRReader { + + @Override + public IPlate readData(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException, InvalidParameterException { + + IVendorPlate vendorPlate = new VendorPlate(); + Rdml rdml = getRDML(inputStream); + setDate(vendorPlate, rdml); + setDefaultDetectionFormat(vendorPlate); + readExperiment(vendorPlate, rdml); + AmplificationAnalysis.calculateCrossingPoints(vendorPlate); + return vendorPlate; + } + + private static Rdml getRDML(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException { + + DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); + DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); + Document document = documentBuilder.parse(inputStream); + NodeList topNode = document.getElementsByTagName("rdml"); + // + JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); + Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); + return (Rdml)unmarshaller.unmarshal(topNode.item(0)); + } + + private void setDate(IVendorPlate vendorPlate, Rdml rdml) { + + XMLGregorianCalendar dateMade = rdml.getDateMade(); + if(dateMade != null) { + vendorPlate.setDate(dateMade.toGregorianCalendar().getTime()); + } + } + + private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidParameterException { + + for(ExperimentType experiment : rdml.getExperiment()) { + vendorPlate.setName(experiment.getId()); + vendorPlate.setDetailedInfo(experiment.getDescription()); + for(RunType run : experiment.getRun()) { + PcrFormatType pcrFormatType = run.getPcrFormat(); + int w = 0; + for(ReactType react : run.getReact()) { + IdReferencesType sample = react.getSample(); + IWell well = new Well(); + well.setPosition(calculateCoordinate(w + 1, pcrFormatType)); + well.putHeaderData(IWell.SAMPLE_ID, sample.getId()); + Channel channel = createChannel(rdml); + for(DataType data : react.getData()) { + for(DpAmpCurveType adp : data.getAdp()) { + channel.getFluorescence().add((double)adp.getFluor()); + } + } + well.getChannels().put(0, channel); + well.putHeaderData(IWell.SAMPLE_SUBSET, "Default"); + vendorPlate.getWells().add(well); + w++; + } + } + } + } + + private Channel createChannel(Rdml rdml) { + + Channel channel = new Channel(); + channel.setId(0); + for(DyeType dye : rdml.getDye()) { + channel.setDetectionName(dye.getId()); + } + channel.setValid(true); + return channel; + } + + private void setDefaultDetectionFormat(IVendorPlate vendorPlate) { + + DetectionFormat detectionFormat = new DetectionFormat(); + IChannelSpecification channelSpecification = new ChannelSpecification(); + channelSpecification.putHeaderData(IChannelSpecification.NAME, "Default"); + detectionFormat.getChannelSpecifications().add(channelSpecification); + vendorPlate.setDetectionFormat(detectionFormat); + } + + private static Position calculateCoordinate(int id, PcrFormatType pcrFormatType) { + + id--; // adjust for 0-based indexing + int row = id % pcrFormatType.getRows(); + int column = id / pcrFormatType.getRows(); + char rowLetter = (char)('A' + row); + int columnNumber = column + 1; + Position position = new Position(String.valueOf(rowLetter), columnNumber); + position.setId(id); + return position; + } +} \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion12.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion12.java new file mode 100644 index 0000000000..65c759f816 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion12.java @@ -0,0 +1,146 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. + * This program and the accompanying materials are made available under the + * terms of the Eclipse Public License v1.0 which accompanies this distribution, + * and is available at http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.io; + +import java.io.IOException; +import java.io.InputStream; +import java.security.InvalidParameterException; + +import javax.xml.datatype.XMLGregorianCalendar; +import javax.xml.parsers.DocumentBuilder; +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; + +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.DataType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.DpAmpCurveType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.DyeType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.ExperimentType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.IdReferencesType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.ObjectFactory; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.PcrFormatType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.Rdml; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.ReactType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v12.model.RunType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IPCRReader; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IVendorPlate; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.VendorPlate; +import org.eclipse.chemclipse.pcr.converter.support.AmplificationAnalysis; +import org.eclipse.chemclipse.pcr.model.core.Channel; +import org.eclipse.chemclipse.pcr.model.core.ChannelSpecification; +import org.eclipse.chemclipse.pcr.model.core.DetectionFormat; +import org.eclipse.chemclipse.pcr.model.core.IChannelSpecification; +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.eclipse.chemclipse.pcr.model.core.IWell; +import org.eclipse.chemclipse.pcr.model.core.Position; +import org.eclipse.chemclipse.pcr.model.core.Well; +import org.w3c.dom.Document; +import org.w3c.dom.NodeList; +import org.xml.sax.SAXException; + +import jakarta.xml.bind.JAXBContext; +import jakarta.xml.bind.JAXBException; +import jakarta.xml.bind.Unmarshaller; + +public class PCRReaderVersion12 implements IPCRReader { + + @Override + public IPlate readData(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException, InvalidParameterException { + + IVendorPlate vendorPlate = new VendorPlate(); + Rdml rdml = getRDML(inputStream); + setDate(vendorPlate, rdml); + setDefaultDetectionFormat(vendorPlate); + readExperiment(vendorPlate, rdml); + AmplificationAnalysis.calculateCrossingPoints(vendorPlate); + return vendorPlate; + } + + private static Rdml getRDML(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException { + + DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); + DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); + Document document = documentBuilder.parse(inputStream); + NodeList topNode = document.getElementsByTagName("rdml"); + // + JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); + Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); + return (Rdml)unmarshaller.unmarshal(topNode.item(0)); + } + + private void setDate(IVendorPlate vendorPlate, Rdml rdml) { + + XMLGregorianCalendar dateMade = rdml.getDateMade(); + if(dateMade != null) { + vendorPlate.setDate(dateMade.toGregorianCalendar().getTime()); + } + } + + private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidParameterException { + + for(ExperimentType experiment : rdml.getExperiment()) { + vendorPlate.setName(experiment.getId()); + vendorPlate.setDetailedInfo(experiment.getDescription()); + for(RunType run : experiment.getRun()) { + PcrFormatType pcrFormatType = run.getPcrFormat(); + int w = 0; + for(ReactType react : run.getReact()) { + IdReferencesType sample = react.getSample(); + IWell well = new Well(); + well.setPosition(calculateCoordinate(w + 1, pcrFormatType)); + well.putHeaderData(IWell.SAMPLE_ID, sample.getId()); + Channel channel = createChannel(rdml); + for(DataType data : react.getData()) { + for(DpAmpCurveType adp : data.getAdp()) { + channel.getFluorescence().add((double)adp.getFluor()); + } + } + well.getChannels().put(0, channel); + well.putHeaderData(IWell.SAMPLE_SUBSET, "Default"); + vendorPlate.getWells().add(well); + w++; + } + } + } + } + + private Channel createChannel(Rdml rdml) { + + Channel channel = new Channel(); + channel.setId(0); + for(DyeType dye : rdml.getDye()) { + channel.setDetectionName(dye.getId()); + } + channel.setValid(true); + return channel; + } + + private void setDefaultDetectionFormat(IVendorPlate vendorPlate) { + + DetectionFormat detectionFormat = new DetectionFormat(); + IChannelSpecification channelSpecification = new ChannelSpecification(); + channelSpecification.putHeaderData(IChannelSpecification.NAME, "Default"); + detectionFormat.getChannelSpecifications().add(channelSpecification); + vendorPlate.setDetectionFormat(detectionFormat); + } + + private static Position calculateCoordinate(int id, PcrFormatType pcrFormatType) { + + id--; // adjust for 0-based indexing + int row = id % pcrFormatType.getRows(); + int column = id / pcrFormatType.getRows(); + char rowLetter = (char)('A' + row); + int columnNumber = column + 1; + Position position = new Position(String.valueOf(rowLetter), columnNumber); + position.setId(id); + return position; + } +} \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion13.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion13.java new file mode 100644 index 0000000000..87c84dcdc2 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/io/PCRReaderVersion13.java @@ -0,0 +1,146 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. + * This program and the accompanying materials are made available under the + * terms of the Eclipse Public License v1.0 which accompanies this distribution, + * and is available at http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.io; + +import java.io.IOException; +import java.io.InputStream; +import java.security.InvalidParameterException; + +import javax.xml.datatype.XMLGregorianCalendar; +import javax.xml.parsers.DocumentBuilder; +import javax.xml.parsers.DocumentBuilderFactory; +import javax.xml.parsers.ParserConfigurationException; + +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.DataType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.DpAmpCurveType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.DyeType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.ExperimentType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.IdReferencesType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.ObjectFactory; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.PcrFormatType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.Rdml; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.ReactType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.internal.v13.model.RunType; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IPCRReader; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.IVendorPlate; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.model.VendorPlate; +import org.eclipse.chemclipse.pcr.converter.support.AmplificationAnalysis; +import org.eclipse.chemclipse.pcr.model.core.Channel; +import org.eclipse.chemclipse.pcr.model.core.ChannelSpecification; +import org.eclipse.chemclipse.pcr.model.core.DetectionFormat; +import org.eclipse.chemclipse.pcr.model.core.IChannelSpecification; +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.eclipse.chemclipse.pcr.model.core.IWell; +import org.eclipse.chemclipse.pcr.model.core.Position; +import org.eclipse.chemclipse.pcr.model.core.Well; +import org.w3c.dom.Document; +import org.w3c.dom.NodeList; +import org.xml.sax.SAXException; + +import jakarta.xml.bind.JAXBContext; +import jakarta.xml.bind.JAXBException; +import jakarta.xml.bind.Unmarshaller; + +public class PCRReaderVersion13 implements IPCRReader { + + @Override + public IPlate readData(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException, InvalidParameterException { + + IVendorPlate vendorPlate = new VendorPlate(); + Rdml rdml = getRDML(inputStream); + setDate(vendorPlate, rdml); + setDefaultDetectionFormat(vendorPlate); + readExperiment(vendorPlate, rdml); + AmplificationAnalysis.calculateCrossingPoints(vendorPlate); + return vendorPlate; + } + + private static Rdml getRDML(InputStream inputStream) throws SAXException, IOException, JAXBException, ParserConfigurationException { + + DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); + DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); + Document document = documentBuilder.parse(inputStream); + NodeList topNode = document.getElementsByTagName("rdml"); + // + JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class); + Unmarshaller unmarshaller = jaxbContext.createUnmarshaller(); + return (Rdml)unmarshaller.unmarshal(topNode.item(0)); + } + + private void setDate(IVendorPlate vendorPlate, Rdml rdml) { + + XMLGregorianCalendar dateMade = rdml.getDateMade(); + if(dateMade != null) { + vendorPlate.setDate(dateMade.toGregorianCalendar().getTime()); + } + } + + private void readExperiment(IVendorPlate vendorPlate, Rdml rdml) throws InvalidParameterException { + + for(ExperimentType experiment : rdml.getExperiment()) { + vendorPlate.setName(experiment.getId()); + vendorPlate.setDetailedInfo(experiment.getDescription()); + for(RunType run : experiment.getRun()) { + PcrFormatType pcrFormatType = run.getPcrFormat(); + int w = 0; + for(ReactType react : run.getReact()) { + IdReferencesType sample = react.getSample(); + IWell well = new Well(); + well.setPosition(calculateCoordinate(w + 1, pcrFormatType)); + well.putHeaderData(IWell.SAMPLE_ID, sample.getId()); + Channel channel = createChannel(rdml); + for(DataType data : react.getData()) { + for(DpAmpCurveType adp : data.getAdp()) { + channel.getFluorescence().add((double)adp.getFluor()); + } + } + well.getChannels().put(0, channel); + well.putHeaderData(IWell.SAMPLE_SUBSET, "Default"); + vendorPlate.getWells().add(well); + w++; + } + } + } + } + + private Channel createChannel(Rdml rdml) { + + Channel channel = new Channel(); + channel.setId(0); + for(DyeType dye : rdml.getDye()) { + channel.setDetectionName(dye.getId()); + } + channel.setValid(true); + return channel; + } + + private void setDefaultDetectionFormat(IVendorPlate vendorPlate) { + + DetectionFormat detectionFormat = new DetectionFormat(); + IChannelSpecification channelSpecification = new ChannelSpecification(); + channelSpecification.putHeaderData(IChannelSpecification.NAME, "Default"); + detectionFormat.getChannelSpecifications().add(channelSpecification); + vendorPlate.setDetectionFormat(detectionFormat); + } + + private static Position calculateCoordinate(int id, PcrFormatType pcrFormatType) { + + id--; // adjust for 0-based indexing + int row = id % pcrFormatType.getRows(); + int column = id / pcrFormatType.getRows(); + char rowLetter = (char)('A' + row); + int columnNumber = column + 1; + Position position = new Position(String.valueOf(rowLetter), columnNumber); + position.setId(id); + return position; + } +} \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/model/IPCRReader.java b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/model/IPCRReader.java new file mode 100644 index 0000000000..634154e8b0 --- /dev/null +++ b/chemclipse/plugins/org.eclipse.chemclipse.pcr.converter.supplier.rdml/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/model/IPCRReader.java @@ -0,0 +1,28 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. + * This program and the accompanying materials are made available under the + * terms of the Eclipse Public License v1.0 which accompanies this distribution, + * and is available at http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.model; + +import java.io.IOException; +import java.io.InputStream; +import java.security.InvalidParameterException; + +import javax.xml.parsers.ParserConfigurationException; + +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.xml.sax.SAXException; + +import jakarta.xml.bind.JAXBException; + +public interface IPCRReader { + + IPlate readData(InputStream inputStream) throws IOException, SAXException, JAXBException, ParserConfigurationException, InvalidParameterException; +} diff --git a/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_11_ITest.java b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_11_ITest.java new file mode 100644 index 0000000000..3eeb3f6ec6 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_11_ITest.java @@ -0,0 +1,69 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragement.test.io; + +import java.io.File; +import java.time.LocalDateTime; +import java.time.Month; +import java.time.ZoneId; +import java.time.ZonedDateTime; +import java.util.Date; + +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.PathResolver; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.core.PCRImportConverter; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test.TestPathHelper; +import org.eclipse.chemclipse.pcr.model.core.IChannel; +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.eclipse.chemclipse.pcr.model.core.IWell; +import org.eclipse.chemclipse.processing.core.IProcessingInfo; +import org.eclipse.core.runtime.NullProgressMonitor; + +import junit.framework.TestCase; + +public class Test_Example_11_ITest extends TestCase { + + private IPlate plate; + + @Override + protected void setUp() throws Exception { + + super.setUp(); + File importFile = new File(PathResolver.getAbsolutePath(TestPathHelper.EXAMPLE_1_1)); + IProcessingInfo importProcessingInfo = PCRImportConverter.getInstance().convert(importFile, new NullProgressMonitor()); + plate = importProcessingInfo.getProcessingResult(); + } + + @Override + protected void tearDown() throws Exception { + + super.tearDown(); + } + + public void testDate() { + + LocalDateTime localDateTime = LocalDateTime.of(2011, Month.JANUARY, 9, 17, 04, 55); + ZonedDateTime zonedDateTime = localDateTime.atZone(ZoneId.systemDefault()); + Date date = java.util.Date.from(zonedDateTime.toInstant()); + assertEquals(date, plate.getDate()); + } + + public void testWells() { + + assertEquals(90, plate.getWells().size()); + IWell well = plate.getWell(0); + assertEquals("A1: gDNA", well.getLabel()); + IChannel channel = well.getChannels().get(0); + assertEquals(0, channel.getId()); + assertEquals("SYBRGreen I", channel.getDetectionName()); + assertEquals(668.4299926757812, channel.getFluorescence().get(0)); + } +} diff --git a/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_12_ITest.java b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_12_ITest.java new file mode 100644 index 0000000000..4c3cc63d70 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_12_ITest.java @@ -0,0 +1,69 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragement.test.io; + +import java.io.File; +import java.time.LocalDateTime; +import java.time.Month; +import java.time.ZoneId; +import java.time.ZonedDateTime; +import java.util.Date; + +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.PathResolver; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.core.PCRImportConverter; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test.TestPathHelper; +import org.eclipse.chemclipse.pcr.model.core.IChannel; +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.eclipse.chemclipse.pcr.model.core.IWell; +import org.eclipse.chemclipse.processing.core.IProcessingInfo; +import org.eclipse.core.runtime.NullProgressMonitor; + +import junit.framework.TestCase; + +public class Test_Example_12_ITest extends TestCase { + + private IPlate plate; + + @Override + protected void setUp() throws Exception { + + super.setUp(); + File importFile = new File(PathResolver.getAbsolutePath(TestPathHelper.EXAMPLE_1_2)); + IProcessingInfo importProcessingInfo = PCRImportConverter.getInstance().convert(importFile, new NullProgressMonitor()); + plate = importProcessingInfo.getProcessingResult(); + } + + @Override + protected void tearDown() throws Exception { + + super.tearDown(); + } + + public void testDate() { + + LocalDateTime localDateTime = LocalDateTime.of(2011, Month.JANUARY, 9, 17, 04, 55); + ZonedDateTime zonedDateTime = localDateTime.atZone(ZoneId.systemDefault()); + Date date = java.util.Date.from(zonedDateTime.toInstant()); + assertEquals(date, plate.getDate()); + } + + public void testWells() { + + assertEquals(90, plate.getWells().size()); + IWell well = plate.getWell(0); + assertEquals("A1: gDNA", well.getLabel()); + IChannel channel = well.getChannels().get(0); + assertEquals(0, channel.getId()); + assertEquals("SYBRGreen I", channel.getDetectionName()); + assertEquals(668.4299926757812, channel.getFluorescence().get(0)); + } +} diff --git a/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_13_ITest.java b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_13_ITest.java new file mode 100644 index 0000000000..7ec09a1dc2 --- /dev/null +++ b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragement/test/io/Test_Example_13_ITest.java @@ -0,0 +1,69 @@ +/******************************************************************************* + * Copyright (c) 2023 Lablicate GmbH. + * + * All rights reserved. This program and the accompanying materials + * are made available under the terms of the Eclipse Public License v1.0 + * which accompanies this distribution, and is available at + * http://www.eclipse.org/legal/epl-v10.html + * + * Contributors: + * Matthias Mailänder - initial API and implementation + *******************************************************************************/ +package org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragement.test.io; + +import java.io.File; +import java.time.LocalDateTime; +import java.time.Month; +import java.time.ZoneId; +import java.time.ZonedDateTime; +import java.util.Date; + +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.PathResolver; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.core.PCRImportConverter; +import org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test.TestPathHelper; +import org.eclipse.chemclipse.pcr.model.core.IChannel; +import org.eclipse.chemclipse.pcr.model.core.IPlate; +import org.eclipse.chemclipse.pcr.model.core.IWell; +import org.eclipse.chemclipse.processing.core.IProcessingInfo; +import org.eclipse.core.runtime.NullProgressMonitor; + +import junit.framework.TestCase; + +public class Test_Example_13_ITest extends TestCase { + + private IPlate plate; + + @Override + protected void setUp() throws Exception { + + super.setUp(); + File importFile = new File(PathResolver.getAbsolutePath(TestPathHelper.EXAMPLE_1_3)); + IProcessingInfo importProcessingInfo = PCRImportConverter.getInstance().convert(importFile, new NullProgressMonitor()); + plate = importProcessingInfo.getProcessingResult(); + } + + @Override + protected void tearDown() throws Exception { + + super.tearDown(); + } + + public void testDate() { + + LocalDateTime localDateTime = LocalDateTime.of(2011, Month.JANUARY, 9, 17, 04, 55); + ZonedDateTime zonedDateTime = localDateTime.atZone(ZoneId.systemDefault()); + Date date = java.util.Date.from(zonedDateTime.toInstant()); + assertEquals(date, plate.getDate()); + } + + public void testWells() { + + assertEquals(90, plate.getWells().size()); + IWell well = plate.getWell(0); + assertEquals("A1: gDNA", well.getLabel()); + IChannel channel = well.getChannels().get(0); + assertEquals(0, channel.getId()); + assertEquals("SYBRGreen I", channel.getDetectionName()); + assertEquals(668.4299926757812, channel.getFluorescence().get(0)); + } +} diff --git a/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragment/test/TestPathHelper.java b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragment/test/TestPathHelper.java index 93bc476d3e..96dbd86023 100644 --- a/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragment/test/TestPathHelper.java +++ b/chemclipse/tests/org.eclipse.chemclipse.pcr.converter.supplier.rdml.fragment.test/src/org/eclipse/chemclipse/pcr/converter/supplier/rdml/fragment/test/TestPathHelper.java @@ -16,4 +16,8 @@ public class TestPathHelper extends PathResolver { public static final String TESTFILE_RAW_5 = "testdata/test_5_raw_data.rdml"; 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