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Added AnIML plotting hints #206

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merged 2 commits into from
Feb 10, 2022
Merged

Added AnIML plotting hints #206

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39f9f11
Set more required fields.
Mailaender Feb 9, 2022
295c509
Set plotting hints.
Mailaender Feb 9, 2022
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3 changes: 3 additions & 0 deletions ....supplier.animl/src/net/openchrom/csd/converter/supplier/animl/io/ChromatogramWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleType;
Expand Down Expand Up @@ -134,6 +135,7 @@ private ResultType createResult(IChromatogramCSD chromatogram) {
retentionTimeSeries.setUnit(retentionTimeUnit);
retentionTimeSeries.setDependency(DependencyType.INDEPENDENT);
retentionTimeSeries.setSeriesType(ParameterTypeType.FLOAT_32);
retentionTimeSeries.setPlotScale(PlotScaleType.LINEAR);
//
SeriesType totalSignalSeries = new SeriesType();
totalSignalSeries.setSeriesID("TOTAL_SIGNAL");
Expand All @@ -144,6 +146,7 @@ private ResultType createResult(IChromatogramCSD chromatogram) {
totalSignalSeries.setUnit(totalSignalUnit);
totalSignalSeries.setDependency(DependencyType.DEPENDENT);
totalSignalSeries.setSeriesType(ParameterTypeType.FLOAT_32);
totalSignalSeries.setPlotScale(PlotScaleType.LINEAR);
//
if(PreferenceSupplier.getChromatogramSaveEncoded()) {
int scans = chromatogram.getNumberOfScans();
Expand Down
9 changes: 7 additions & 2 deletions ....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/ChromatogramWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleType;
Expand Down Expand Up @@ -151,6 +152,7 @@ private List<ResultType> createMS(IChromatogramMSD chromatogram) {
massChargeSeries.setUnit(massChargeUnit);
massChargeSeries.setDependency(DependencyType.DEPENDENT);
massChargeSeries.setSeriesType(ParameterTypeType.FLOAT_64);
massChargeSeries.setPlotScale(PlotScaleType.LINEAR);
//
SeriesType intensitySeries = new SeriesType();
intensitySeries.setSeriesID("INTENSITY");
Expand All @@ -159,8 +161,9 @@ private List<ResultType> createMS(IChromatogramMSD chromatogram) {
intensityUnit.setLabel("Abundance");
intensityUnit.setQuantity("arbitrary");
intensitySeries.setUnit(intensityUnit);
massChargeSeries.setDependency(DependencyType.DEPENDENT);
massChargeSeries.setSeriesType(ParameterTypeType.FLOAT_32);
intensitySeries.setDependency(DependencyType.DEPENDENT);
intensitySeries.setSeriesType(ParameterTypeType.FLOAT_32);
intensitySeries.setPlotScale(PlotScaleType.LINEAR);
//
if(PreferenceSupplier.getChromatogramSaveEncoded()) {
int scans = scanMSD.getNumberOfIons();
Expand Down Expand Up @@ -214,6 +217,7 @@ private ResultType createTIC(IChromatogramMSD chromatogram) {
retentionTimeSeries.setUnit(retentionTimeUnit);
retentionTimeSeries.setDependency(DependencyType.INDEPENDENT);
retentionTimeSeries.setSeriesType(ParameterTypeType.INT_32);
retentionTimeSeries.setPlotScale(PlotScaleType.LINEAR);
//
SeriesType totalSignalSeries = new SeriesType();
totalSignalSeries.setSeriesID("TOTAL_SIGNAL");
Expand All @@ -224,6 +228,7 @@ private ResultType createTIC(IChromatogramMSD chromatogram) {
totalSignalSeries.setUnit(totalSignalUnit);
totalSignalSeries.setDependency(DependencyType.DEPENDENT);
totalSignalSeries.setSeriesType(ParameterTypeType.FLOAT_32);
totalSignalSeries.setPlotScale(PlotScaleType.LINEAR);
//
if(PreferenceSupplier.getChromatogramSaveEncoded()) {
int scans = chromatogram.getNumberOfScans();
Expand Down
23 changes: 20 additions & 3 deletions ....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumWriter.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2021 Lablicate GmbH.
* Copyright (c) 2021, 2022 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -19,6 +19,7 @@
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;

import org.apache.commons.io.FilenameUtils;
import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.msd.converter.io.IMassSpectraWriter;
Expand All @@ -34,12 +35,15 @@
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AuditTrailEntrySetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.AuditTrailEntryType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.CategoryType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.DependencyType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.EncodedValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ExperimentStepSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ExperimentStepType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.MethodType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SampleType;
Expand Down Expand Up @@ -95,6 +99,7 @@ private void writeAnIML(FileWriter fileWriter, IVendorMassSpectrum massSpectrum)
Marshaller marshaller = jaxbContext.createMarshaller();
//
AnIMLType anIML = new AnIMLType();
anIML.setVersion("0.90");
anIML.setSampleSet(createSampleSet(massSpectrum));
anIML.setExperimentStepSet(createExperimentStep(massSpectrum));
anIML.setAuditTrailEntrySet(createAuditTrail());
Expand All @@ -105,8 +110,10 @@ private SampleSetType createSampleSet(IVendorMassSpectrum massSpectrum) {

SampleSetType sampleSet = new SampleSetType();
SampleType sample = new SampleType();
sample.setId("OPENCHROM_MASS_SPECTRUM_EXPORT");
sample.setName(massSpectrum.getName());
sample.setSampleID(massSpectrum.getIdentifier());
sample.setComment(massSpectrum.getIdentifier());
sample.setSampleID(FilenameUtils.removeExtension(massSpectrum.getFile().getName()));
sample.setSourceDataLocation(massSpectrum.getFile().getAbsolutePath());
sampleSet.getSample().add(sample);
return sampleSet;
Expand All @@ -116,6 +123,8 @@ private ExperimentStepSetType createExperimentStep(IVendorMassSpectrum massSpect

ExperimentStepSetType experimentStepSet = new ExperimentStepSetType();
ExperimentStepType massSpecStep = new ExperimentStepType();
massSpecStep.setName("Mass Spectrometry");
massSpecStep.setId("MASS_SPECTROMETRY");
massSpecStep.setTechnique(createMassSpecTechnique());
massSpecStep.getResult().add(createResult(massSpectrum));
massSpecStep.setMethod(createMethod());
Expand All @@ -139,17 +148,24 @@ private ResultType createResult(IVendorMassSpectrum massSpectrum) {
//
SeriesType massChargeSeries = new SeriesType();
massChargeSeries.setName("Mass/Charge");
massChargeSeries.setSeriesID("MASS_CHARGE");
UnitType massChargeUnit = new UnitType();
massChargeUnit.setLabel("Mass/Charge Ratio");
massChargeUnit.setQuantity("mz");
massChargeSeries.setUnit(massChargeUnit);
massChargeSeries.setDependency(DependencyType.INDEPENDENT);
massChargeSeries.setSeriesType(ParameterTypeType.FLOAT_64);
massChargeSeries.setPlotScale(PlotScaleType.LINEAR);
//
SeriesType intensitySeries = new SeriesType();
intensitySeries.setName("Intensity");
UnitType intensityUnit = new UnitType();
intensityUnit.setLabel("Abundance");
intensityUnit.setQuantity("arbitrary");
intensitySeries.setUnit(intensityUnit);
intensitySeries.setDependency(DependencyType.DEPENDENT);
intensitySeries.setSeriesType(ParameterTypeType.FLOAT_32);
intensitySeries.setPlotScale(PlotScaleType.LINEAR);
//
if(PreferenceSupplier.getMassSpectrumSaveEncoded()) {
int scans = massSpectrum.getNumberOfIons();
Expand Down Expand Up @@ -186,8 +202,9 @@ private ResultType createResult(IVendorMassSpectrum massSpectrum) {
parameter.setName("Type");
if(massSpectrum.getMassSpectrumType() == 0) {
parameter.getS().add("Centroided");
} else
} else {
parameter.getS().add("Continuous");
}
category.getParameter().add(parameter);
result.getCategory().add(category);
result.setSeriesSet(seriesSet);
Expand Down
15 changes: 15 additions & 0 deletions ...plier.animl/src/net/openchrom/xxd/converter/supplier/animl/internal/converter/Common.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.DependencyType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.IndividualValueSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ParameterTypeType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.PlotScaleType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.ResultType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SeriesSetType;
import net.openchrom.xxd.converter.supplier.animl.internal.model.astm.core.SeriesType;
Expand All @@ -38,6 +39,11 @@

public class Common {

private Common() {

// only static access
}

public static SoftwareType createSoftware() {

SoftwareType software = new SoftwareType();
Expand All @@ -62,21 +68,25 @@ public static ResultType createPeaks(IChromatogram chromatogram) {
numberSeries.setSeriesID("NUMBER");
numberSeries.setName("Number");
numberSeries.setSeriesType(ParameterTypeType.INT_32);
numberSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType idSeries = new SeriesType();
idSeries.setSeriesID("ID");
idSeries.setName("ID");
idSeries.setSeriesType(ParameterTypeType.STRING);
idSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType groupIdSeries = new SeriesType();
groupIdSeries.setSeriesID("GROUP_ID");
groupIdSeries.setName("Group ID");
groupIdSeries.setSeriesType(ParameterTypeType.STRING);
groupIdSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType nameSeries = new SeriesType();
nameSeries.setSeriesID("NAME");
nameSeries.setName("Name");
nameSeries.setSeriesType(ParameterTypeType.STRING);
nameSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType retentionTimeSeries = new SeriesType();
retentionTimeSeries.setSeriesID("RETENTION_TIME");
Expand All @@ -87,6 +97,7 @@ public static ResultType createPeaks(IChromatogram chromatogram) {
retentionTimeSeries.setUnit(retentionTimeUnit);
retentionTimeSeries.setSeriesType(ParameterTypeType.FLOAT_32);
retentionTimeSeries.setDependency(DependencyType.INDEPENDENT);
retentionTimeSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType adjustedRetentionTimeSeries = new SeriesType();
adjustedRetentionTimeSeries.setSeriesID("ADJUSTED_RETENTION_TIME");
Expand All @@ -97,6 +108,7 @@ public static ResultType createPeaks(IChromatogram chromatogram) {
adjustedRetentionTimeSeries.setUnit(adjustedRetentionTimeUnit);
adjustedRetentionTimeSeries.setSeriesType(ParameterTypeType.FLOAT_32);
adjustedRetentionTimeSeries.setDependency(DependencyType.DEPENDENT);
adjustedRetentionTimeSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType startTimeSeries = new SeriesType();
startTimeSeries.setSeriesID("START_TIME");
Expand All @@ -107,6 +119,7 @@ public static ResultType createPeaks(IChromatogram chromatogram) {
startTimeSeries.setUnit(startTimeUnit);
startTimeSeries.setSeriesType(ParameterTypeType.FLOAT_32);
startTimeSeries.setDependency(DependencyType.DEPENDENT);
startTimeSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType endTimeSeries = new SeriesType();
endTimeSeries.setName("End Time");
Expand All @@ -116,6 +129,7 @@ public static ResultType createPeaks(IChromatogram chromatogram) {
endTimeSeries.setUnit(endTimeUnit);
endTimeSeries.setSeriesType(ParameterTypeType.FLOAT_32);
endTimeSeries.setDependency(DependencyType.DEPENDENT);
endTimeSeries.setPlotScale(PlotScaleType.NONE);
//
SeriesType peakHeightSeries = new SeriesType();
peakHeightSeries.setName("Value");
Expand All @@ -125,6 +139,7 @@ public static ResultType createPeaks(IChromatogram chromatogram) {
peakHeightSeries.setUnit(peakHeightUnit);
peakHeightSeries.setSeriesType(ParameterTypeType.FLOAT_32);
peakHeightSeries.setDependency(DependencyType.DEPENDENT);
peakHeightSeries.setPlotScale(PlotScaleType.NONE);
//
IndividualValueSetType numbers = new IndividualValueSetType();
IndividualValueSetType ids = new IndividualValueSetType();
Expand Down