Fixed #154 - Standards Assigner - Traces for Identification

OpenChrom · Oct 10, 2021 · 72be80b · 72be80b
1 parent 255e9cf
commit 72be80b
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Showing 23 changed files with 287 additions and 117 deletions.
diff --git a/...tests/src/net/openchrom/xxd/process/supplier/templates/model/AssignerStandard_1_Test.java b/...tests/src/net/openchrom/xxd/process/supplier/templates/model/AssignerStandard_1_Test.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2019 Lablicate GmbH.
+ * Copyright (c) 2019, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -59,4 +59,9 @@ public void test6() {
 
 		assertEquals(1.0d, setting.getResponseFactor());
 	}
-}
+
+	public void test7() {
+
+		assertEquals("", setting.getTracesIdentification());
+	}
+}
diff --git a/...tests/src/net/openchrom/xxd/process/supplier/templates/model/AssignerStandard_2_Test.java b/...tests/src/net/openchrom/xxd/process/supplier/templates/model/AssignerStandard_2_Test.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2019 Lablicate GmbH.
+ * Copyright (c) 2019, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -64,4 +64,10 @@ public void test6() {
 		setting.setResponseFactor(0.98d);
 		assertEquals(0.98d, setting.getResponseFactor());
 	}
-}
+
+	public void test7() {
+
+		setting.setTracesIdentification("104 103");
+		assertEquals("104 103", setting.getTracesIdentification());
+	}
+}
diff --git a/...ragment.tests/src/net/openchrom/xxd/process/supplier/templates/util/TraceUtil_1_Test.java b/...ragment.tests/src/net/openchrom/xxd/process/supplier/templates/util/TraceUtil_1_Test.java
@@ -0,0 +1,55 @@
+/*******************************************************************************
+ * Copyright (c) 2021 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:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.process.supplier.templates.util;
+
+import org.eclipse.chemclipse.model.core.IPeak;
+import org.eclipse.chemclipse.model.implementation.Peak;
+
+import junit.framework.TestCase;
+
+public class TraceUtil_1_Test extends TestCase {
+
+	private TracesUtil tracesUtil = new TracesUtil();
+	private IPeak peak = new Peak();
+
+	@Override
+	protected void setUp() throws Exception {
+
+		super.setUp();
+	}
+
+	@Override
+	protected void tearDown() throws Exception {
+
+		super.tearDown();
+	}
+
+	public void test1() {
+
+		assertFalse(tracesUtil.isTraceMatch(null, null));
+	}
+
+	public void test2() {
+
+		assertFalse(tracesUtil.isTraceMatch(null, ""));
+	}
+
+	public void test3() {
+
+		assertTrue(tracesUtil.isTraceMatch(peak, null));
+	}
+
+	public void test4() {
+
+		assertTrue(tracesUtil.isTraceMatch(peak, ""));
+	}
+}
diff --git a/...hrom/xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerComparator.java b/...hrom/xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerComparator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2018, 2019 Lablicate GmbH.
+ * Copyright (c) 2018, 2021 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -47,6 +47,9 @@ public int compare(Viewer viewer, Object e1, Object e2) {
 				case 5:
 					sortOrder = Double.compare(setting2.getResponseFactor(), setting1.getResponseFactor());
 					break;
+				case 6:
+					sortOrder = setting2.getTracesIdentification().compareTo(setting1.getTracesIdentification());
+					break;
 				default:
 					sortOrder = 0;
 			}

diff --git a/.../xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerEditingSupport.java b/.../xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerEditingSupport.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2018, 2019 Lablicate GmbH.
+ * Copyright (c) 2018, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -25,6 +25,7 @@ public class StandardsAssignerEditingSupport extends EditingSupport {
 	private String column;
 
 	public StandardsAssignerEditingSupport(ExtendedTableViewer tableViewer, String column) {
+
 		super(tableViewer);
 		this.column = column;
 		this.cellEditor = new TextCellEditor(tableViewer.getTable());
@@ -62,6 +63,8 @@ protected Object getValue(Object element) {
 					return setting.getConcentrationUnit();
 				case StandardsAssignerLabelProvider.RESPONSE_FACTOR:
 					return Double.toString(setting.getResponseFactor());
+				case StandardsAssignerLabelProvider.TRACES_IDENTIFICATION:
+					return setting.getTracesIdentification();
 			}
 		}
 		return false;
@@ -115,6 +118,9 @@ protected void setValue(Object element, Object value) {
 						}
 					}
 					break;
+				case StandardsAssignerLabelProvider.TRACES_IDENTIFICATION:
+					setting.setTracesIdentification(((String)value).trim());
+					break;
 			}
 			tableViewer.refresh();
 		}
@@ -130,4 +136,4 @@ private double convertValue(Object value) {
 		}
 		return result;
 	}
-}
+}
diff --git a/...penchrom/xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerFilter.java b/...penchrom/xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerFilter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2018 Lablicate GmbH.
+ * Copyright (c) 2018, 2021 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -38,11 +38,13 @@ public boolean select(Viewer viewer, Object parentElement, Object element) {
 			AssignerStandard setting = (AssignerStandard)element;
 			String name = setting.getName();
 			String concentrationUnit = setting.getConcentrationUnit();
+			String tracesIdentification = setting.getTracesIdentification();
 			//
 			if(!caseSensitive) {
 				searchText = searchText.toLowerCase();
 				name = name.toLowerCase();
 				concentrationUnit = concentrationUnit.toLowerCase();
+				tracesIdentification = tracesIdentification.toLowerCase();
 			}
 			//
 			if(name.contains(searchText)) {
@@ -52,8 +54,12 @@ public boolean select(Viewer viewer, Object parentElement, Object element) {
 			if(concentrationUnit.contains(searchText)) {
 				return true;
 			}
+			//
+			if(tracesIdentification.contains(searchText)) {
+				return true;
+			}
 		}
 		//
 		return false;
 	}
-}
+}
diff --git a/.../xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerInputValidator.java b/.../xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerInputValidator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2018 Lablicate GmbH.
+ * Copyright (c) 2018, 2021 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -26,6 +26,7 @@ public class StandardsAssignerInputValidator implements IInputValidator {
 	private Set<String> names = new HashSet<>();
 
 	public StandardsAssignerInputValidator(Set<String> names) {
+
 		if(names != null) {
 			this.names = names;
 		}
@@ -46,4 +47,4 @@ public String isValid(String target) {
 		}
 		return null;
 	}
-}
+}
diff --git a/...m/xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerLabelProvider.java b/...m/xxd/process/supplier/templates/ui/internal/provider/StandardsAssignerLabelProvider.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2018, 2020 Lablicate GmbH.
+ * Copyright (c) 2018, 2021 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -29,6 +29,7 @@ public class StandardsAssignerLabelProvider extends AbstractChemClipseLabelProvi
 	public static final String CONCENTRATION = "Concentration";
 	public static final String CONCENTRATION_UNIT = "Concentration Unit";
 	public static final String RESPONSE_FACTOR = "Response Factor";
+	public static final String TRACES_IDENTIFICATION = "Traces Identification";
 	//
 	private DecimalFormat decimalFormat = ValueFormat.getDecimalFormatEnglish("0.0##");
 	//
@@ -38,15 +39,17 @@ public class StandardsAssignerLabelProvider extends AbstractChemClipseLabelProvi
 			STOP_RETENTION_TIME, //
 			CONCENTRATION, //
 			CONCENTRATION_UNIT, //
-			RESPONSE_FACTOR//
+			RESPONSE_FACTOR, //
+			TRACES_IDENTIFICATION //
 	};
 	public static final int[] BOUNDS = { //
 			200, //
 			100, //
 			100, //
 			50, //
 			50, //
-			50 //
+			50, //
+			100 //
 	};
 
 	@Override
@@ -83,6 +86,9 @@ public String getColumnText(Object element, int columnIndex) {
 				case 5:
 					text = decimalFormat.format(setting.getResponseFactor());
 					break;
+				case 6:
+					text = setting.getTracesIdentification();
+					break;
 				default:
 					text = "n.v.";
 			}

diff --git a/...i/src/net/openchrom/xxd/process/supplier/templates/ui/preferences/PageExportAssigner.java b/...i/src/net/openchrom/xxd/process/supplier/templates/ui/preferences/PageExportAssigner.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2020 Lablicate GmbH.
+ * Copyright (c) 2020, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -36,6 +36,7 @@ public PageExportAssigner() {
 	 */
 	public void createFieldEditors() {
 
+		addField(new IntegerFieldEditor(PreferenceSupplier.P_EXPORT_NUMBER_TRACES_ASSIGNER, "Number Traces for Identification (0 = TIC)", PreferenceSupplier.MIN_NUMBER_TRACES, PreferenceSupplier.MAX_NUMBER_TRACES, getFieldEditorParent()));
 		addField(new IntegerFieldEditor(PreferenceSupplier.P_EXPORT_DELTA_LEFT_MILLISECONDS_STANDARDS, "Delta Left [ms]", PreferenceSupplier.MIN_DELTA_MILLISECONDS, PreferenceSupplier.MAX_DELTA_MILLISECONDS, getFieldEditorParent()));
 		addField(new IntegerFieldEditor(PreferenceSupplier.P_EXPORT_DELTA_RIGHT_MILLISECONDS_STANDARDS, "Delta Right [ms]", PreferenceSupplier.MIN_DELTA_MILLISECONDS, PreferenceSupplier.MAX_DELTA_MILLISECONDS, getFieldEditorParent()));
 	}

diff --git a/...s.ui/src/net/openchrom/xxd/process/supplier/templates/ui/swt/StandardsAssignerListUI.java b/...s.ui/src/net/openchrom/xxd/process/supplier/templates/ui/swt/StandardsAssignerListUI.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2018 Lablicate GmbH.
+ * Copyright (c) 2018, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -34,6 +34,7 @@ public class StandardsAssignerListUI extends ExtendedTableViewer {
 	private StandardsAssignerFilter listFilter = new StandardsAssignerFilter();
 
 	public StandardsAssignerListUI(Composite parent, int style) {
+
 		super(parent, style);
 		createColumns();
 	}
@@ -70,4 +71,4 @@ private void setEditingSupport() {
 			}
 		}
 	}
-}
+}
diff --git a/...lates/src/net/openchrom/xxd/process/supplier/templates/comparator/StandardComparator.java b/...lates/src/net/openchrom/xxd/process/supplier/templates/comparator/StandardComparator.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2019 Lablicate GmbH.
+ * Copyright (c) 2019, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -26,4 +26,4 @@ public int compare(AssignerStandard setting1, AssignerStandard setting2) {
 		}
 		return result;
 	}
-}
+}
diff --git a/...upplier.templates/src/net/openchrom/xxd/process/supplier/templates/io/DetectorExport.java b/...upplier.templates/src/net/openchrom/xxd/process/supplier/templates/io/DetectorExport.java
@@ -60,12 +60,7 @@ public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> c
 			float retentionIndex = peak.getPeakModel().getPeakMaximum().getRetentionIndex();
 			IdentificationTargetComparator identificationTargetComparator = new IdentificationTargetComparator(retentionIndex);
 			IIdentificationTarget identificationTarget = IIdentificationTarget.getBestIdentificationTarget(peak.getTargets(), identificationTargetComparator);
-			//
-			if(identificationTarget != null) {
-				detectorSetting.setName(identificationTarget.getLibraryInformation().getName());
-			} else {
-				detectorSetting.setName("");
-			}
+			detectorSetting.setName(identificationTarget != null ? identificationTarget.getLibraryInformation().getName() : "");
 			detectorSettings.add(detectorSetting);
 		}
 		//

diff --git a/...pplier.templates/src/net/openchrom/xxd/process/supplier/templates/io/StandardsExport.java b/...pplier.templates/src/net/openchrom/xxd/process/supplier/templates/io/StandardsExport.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2019, 2020 Lablicate GmbH.
+ * Copyright (c) 2019, 2021 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -39,6 +39,7 @@ public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> c
 		List<? extends IPeak> peaks = chromatogram.getPeaks();
 		AssignerStandards assignerStandards = new AssignerStandards();
 		//
+		int numberTraces = PreferenceSupplier.getExportNumberTracesAssigner();
 		int deltaLeft = PreferenceSupplier.getExportDeltaLeftMillisecondsStandards();
 		int deltaRight = PreferenceSupplier.getExportDeltaRightMillisecondsStandards();
 		//
@@ -54,6 +55,7 @@ public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> c
 					assignerStandard.setConcentration(internalStandard.getConcentration());
 					assignerStandard.setConcentrationUnit(internalStandard.getConcentrationUnit());
 					assignerStandard.setResponseFactor(internalStandard.getResponseFactor());
+					assignerStandard.setTracesIdentification(extractTraces(peak, numberTraces));
 					assignerStandards.add(assignerStandard);
 				}
 			}
@@ -65,4 +67,4 @@ public IProcessingInfo<File> convert(File file, IChromatogram<? extends IPeak> c
 		processingInfo.addInfoMessage(DESCRIPTION, "The standards template has been exported successfully.");
 		return processingInfo;
 	}
-}
+}