Fixed #819 - Skip peak validation in edge cases

eclipse-chemclipse · Nov 23, 2021 · 29597d2 · 29597d2
1 parent 9e19b33
commit 29597d2
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Showing 3 changed files with 18 additions and 1 deletion.
diff --git a/....eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/AbstractChromatogram.java b/....eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/AbstractChromatogram.java
@@ -42,6 +42,7 @@
 import org.eclipse.chemclipse.model.identifier.IIdentificationTarget;
 import org.eclipse.chemclipse.model.implementation.TripleQuadMethod;
 import org.eclipse.chemclipse.model.notifier.IChromatogramSelectionUpdateNotifier;
+import org.eclipse.chemclipse.model.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.model.processor.IChromatogramProcessor;
 import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
 import org.eclipse.chemclipse.model.signals.ITotalScanSignalExtractor;
@@ -1091,7 +1092,14 @@ public int getNumberOfPeaks() {
 	@Override
 	public void addPeak(T peak) {
 
-		if(peak.getPeakModel().getWidthByInflectionPoints() > 0) {
+		boolean addPeak = false;
+		if(PreferenceSupplier.isSkipPeakWidthCheck()) {
+			addPeak = true;
+		} else {
+			addPeak = peak.getPeakModel().getWidthByInflectionPoints() > 0;
+		}
+		//
+		if(addPeak) {
 			peaks.addPeak(peak);
 		}
 	}

diff --git a/...pse.chemclipse.model/src/org/eclipse/chemclipse/model/preferences/PreferenceSupplier.java b/...pse.chemclipse.model/src/org/eclipse/chemclipse/model/preferences/PreferenceSupplier.java
@@ -49,6 +49,8 @@ public class PreferenceSupplier implements IPreferenceSupplier {
 	public static final String DEF_BEST_TARGET_LIBRARY_FIELD = LibraryField.NAME.name();
 	public static final String P_ION_ROUND_METHOD = "ionRoundMethod"; // When changing this value, call clearCacheActiveIonRoundMethod.
 	public static final String DEF_ION_ROUND_METHOD = IonRoundMethod.DEFAULT.name();
+	public static final String P_SKIP_PEAK_WIDTH_CHECK = "skipPeakWidthCheck";
+	public static final boolean DEF_SKIP_PEAK_WIDTH_CHECK = false;
 	//
 	public static final String P_LIST_PATH_IMPORT = "listPathImport";
 	public static final String DEF_LIST_PATH_IMPORT = "";
@@ -100,6 +102,7 @@ public Map<String, String> getDefaultValues() {
 		defaultValues.put(P_USE_RETENTION_INDEX_QC, Boolean.toString(DEF_USE_RETENTION_INDEX_QC));
 		defaultValues.put(P_BEST_TARGET_LIBRARY_FIELD, DEF_BEST_TARGET_LIBRARY_FIELD);
 		defaultValues.put(P_ION_ROUND_METHOD, DEF_ION_ROUND_METHOD);
+		defaultValues.put(P_SKIP_PEAK_WIDTH_CHECK, Boolean.toString(DEF_SKIP_PEAK_WIDTH_CHECK));
 		defaultValues.put(P_LIST_PATH_IMPORT, DEF_LIST_PATH_IMPORT);
 		defaultValues.put(P_LIST_PATH_EXPORT, DEF_LIST_PATH_EXPORT);
 		defaultValues.put(P_SEPARATION_COLUMN_MAPPINGS, DEF_SEPARATION_COLUMN_MAPPINGS);
@@ -227,6 +230,11 @@ public static void setIonRoundMethod(IonRoundMethod ionRoundMethod) {
 		activeIonRoundMethod = ionRoundMethod;
 	}
 
+	public static boolean isSkipPeakWidthCheck() {
+
+		return getBoolean(P_SKIP_PEAK_WIDTH_CHECK, DEF_SKIP_PEAK_WIDTH_CHECK);
+	}
+
 	public static String getListPathImport() {
 
 		return getFilterPath(P_LIST_PATH_IMPORT, DEF_LIST_PATH_IMPORT);

diff --git a/...chemclipse.swt.ui/src/org/eclipse/chemclipse/swt/ui/preferences/PreferencePageSystem.java b/...chemclipse.swt.ui/src/org/eclipse/chemclipse/swt/ui/preferences/PreferencePageSystem.java
@@ -61,6 +61,7 @@ protected void createFieldEditors() {
 		addField(new BooleanFieldEditor(PreferenceSupplier.P_USE_RETENTION_INDEX_QC, "QC: Use Retention Index", getFieldEditorParent()));
 		addField(new ComboFieldEditor(PreferenceSupplier.P_BEST_TARGET_LIBRARY_FIELD, "Best Target", LibraryField.getOptions(), getFieldEditorParent()));
 		addField(new ComboFieldEditor(PreferenceSupplier.P_ION_ROUND_METHOD, "Ion Round Method", IonRoundMethod.getOptions(), getFieldEditorParent()));
+		addField(new BooleanFieldEditor(PreferenceSupplier.P_SKIP_PEAK_WIDTH_CHECK, "Skip Peak Width Check (Only enable this in edge cases!)", getFieldEditorParent()));
 		//
 		addField(new SpacerFieldEditor(getFieldEditorParent()));
 		addField(new DirectoryFieldEditor(PreferenceSupplier.P_LIST_PATH_IMPORT, "Mappings Import Folder", getFieldEditorParent()));