diff --git a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.csd.identifier/src/org/eclipse/chemclipse/chromatogram/csd/identifier/support/TargetBuilderCSD.java b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.csd.identifier/src/org/eclipse/chemclipse/chromatogram/csd/identifier/support/TargetBuilderCSD.java index bd660839be..6375e447fe 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.csd.identifier/src/org/eclipse/chemclipse/chromatogram/csd/identifier/support/TargetBuilderCSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.csd.identifier/src/org/eclipse/chemclipse/chromatogram/csd/identifier/support/TargetBuilderCSD.java @@ -15,6 +15,7 @@ import org.eclipse.chemclipse.csd.model.core.IPeakCSD; import org.eclipse.chemclipse.csd.model.core.IScanCSD; import org.eclipse.chemclipse.logging.core.Logger; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.exceptions.ReferenceMustNotBeNullException; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -31,12 +32,14 @@ public IIdentificationTarget setPeakTargetUnknown(IPeakCSD peakCSD, String ident IIdentificationTarget identificationTarget = null; try { - IScanCSD scan = peakCSD.getPeakModel().getPeakMaximum(); - ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(scan, targetUnknownSettings, ""); - IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality()); - identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult); - identificationTarget.setIdentifier(identifier); - peakCSD.getTargets().add(identificationTarget); + IScan scan = peakCSD.getPeakModel().getPeakMaximum(); + if(scan instanceof IScanCSD unknown) { + ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(unknown, targetUnknownSettings, ""); + IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality()); + identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult); + identificationTarget.setIdentifier(identifier); + peakCSD.getTargets().add(identificationTarget); + } } catch(ReferenceMustNotBeNullException e) { logger.warn(e); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.wsd.identifier/src/org/eclipse/chemclipse/chromatogram/wsd/identifier/support/TargetBuilderWSD.java b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.wsd.identifier/src/org/eclipse/chemclipse/chromatogram/wsd/identifier/support/TargetBuilderWSD.java index 4caf1bd4b5..29a8c3a3b6 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.wsd.identifier/src/org/eclipse/chemclipse/chromatogram/wsd/identifier/support/TargetBuilderWSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.wsd.identifier/src/org/eclipse/chemclipse/chromatogram/wsd/identifier/support/TargetBuilderWSD.java @@ -18,6 +18,7 @@ import java.util.List; import org.eclipse.chemclipse.logging.core.Logger; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.exceptions.ReferenceMustNotBeNullException; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -38,13 +39,15 @@ public IIdentificationTarget setPeakTargetUnknown(IPeakWSD peakWSD, String ident IIdentificationTarget identificationTarget = null; try { - IScanWSD scan = peakWSD.getPeakModel().getPeakMaximum(); - String traces = extractTraces(scan, targetUnknownSettings); - ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(scan, targetUnknownSettings, traces); - IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality()); - identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult); - identificationTarget.setIdentifier(identifier); - peakWSD.getTargets().add(identificationTarget); + IScan scan = peakWSD.getPeakModel().getPeakMaximum(); + if(scan instanceof IScanWSD unknown) { + String traces = extractTraces(unknown, targetUnknownSettings); + ILibraryInformation libraryInformation = UnknownTargetBuilder.getLibraryInformationUnknown(unknown, targetUnknownSettings, traces); + IComparisonResult comparisonResult = UnknownTargetBuilder.getComparisonResultUnknown(targetUnknownSettings.getMatchQuality()); + identificationTarget = new IdentificationTarget(libraryInformation, comparisonResult); + identificationTarget.setIdentifier(identifier); + peakWSD.getTargets().add(identificationTarget); + } } catch(ReferenceMustNotBeNullException e) { logger.warn(e); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.integrator.supplier.trapezoid/src/org/eclipse/chemclipse/chromatogram/xxd/integrator/supplier/trapezoid/processor/PeakIntegrator.java b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.integrator.supplier.trapezoid/src/org/eclipse/chemclipse/chromatogram/xxd/integrator/supplier/trapezoid/processor/PeakIntegrator.java index 60720c5c4f..8a529faece 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.integrator.supplier.trapezoid/src/org/eclipse/chemclipse/chromatogram/xxd/integrator/supplier/trapezoid/processor/PeakIntegrator.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.chromatogram.xxd.integrator.supplier.trapezoid/src/org/eclipse/chemclipse/chromatogram/xxd/integrator/supplier/trapezoid/processor/PeakIntegrator.java @@ -36,6 +36,7 @@ import org.eclipse.chemclipse.model.core.IMarkedTraces; import org.eclipse.chemclipse.model.core.IPeak; import org.eclipse.chemclipse.model.core.IPeakModel; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.implementation.IntegrationEntry; import org.eclipse.chemclipse.model.support.IntegrationConstraint; @@ -271,23 +272,25 @@ private List calculateIntegratedArea(IPeak peak, PeakIntegrat IPeakModelWSD peakModel = peakWSD.getPeakModel(); double integratedAreaTIC = calculateTICPeakArea(peak, baselineSupport, includeBackground, useAreaConstraint); - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); IIntegrationEntry integrationEntry; - if(!markedTraces.isEmpty() && !markedTraces.getTraces().contains(IMarkedTrace.TOTAL_SIGNAL_AS_INT)) { - Set wavelengths = markedTraces.getTraces(); - WavelengthPercentages wavelengthPercentages = new WavelengthPercentages(scan); - /* - * Calculate the percentage integrated area for each selected ion. - */ - for(Integer wavelength : wavelengths) { - float correctionFactor = wavelengthPercentages.getPercentage(wavelength) / WavelengthPercentages.MAX_PERCENTAGE; - double integratedArea = integratedAreaTIC * correctionFactor; - integrationEntry = new IntegrationEntry(wavelength, integratedArea * scaleFactor); + if(scan instanceof IScanWSD scanWSD) { + if(!markedTraces.isEmpty() && !markedTraces.getTraces().contains(IMarkedTrace.TOTAL_SIGNAL_AS_INT)) { + Set wavelengths = markedTraces.getTraces(); + WavelengthPercentages wavelengthPercentages = new WavelengthPercentages(scanWSD); + /* + * Calculate the percentage integrated area for each selected ion. + */ + for(Integer wavelength : wavelengths) { + float correctionFactor = wavelengthPercentages.getPercentage(wavelength) / WavelengthPercentages.MAX_PERCENTAGE; + double integratedArea = integratedAreaTIC * correctionFactor; + integrationEntry = new IntegrationEntry(wavelength, integratedArea * scaleFactor); + integrationEntries.add(integrationEntry); + } + } else { + integrationEntry = new IntegrationEntry(ISignal.TOTAL_INTENSITY, integratedAreaTIC * scaleFactor); integrationEntries.add(integrationEntry); } - } else { - integrationEntry = new IntegrationEntry(ISignal.TOTAL_INTENSITY, integratedAreaTIC * scaleFactor); - integrationEntries.add(integrationEntry); } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/AbstractPeakModelCSD.java b/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/AbstractPeakModelCSD.java index 5b1157d166..9c30e7dac7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/AbstractPeakModelCSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/AbstractPeakModelCSD.java @@ -25,16 +25,4 @@ protected AbstractPeakModelCSD(IScan peakMaximum, IPeakIntensityValues peakInten super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance); } - - @Override - public IScanCSD getPeakMaximum() { - - return (IScanCSD)super.getPeakMaximum(); - } - - @Override - public IScanCSD getPeakScan(int retentionTime) { - - return (IScanCSD)super.getPeakScan(retentionTime); - } } \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/IPeakModelCSD.java b/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/IPeakModelCSD.java index 89a8cb1929..32282a7314 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/IPeakModelCSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.csd.model/src/org/eclipse/chemclipse/csd/model/core/IPeakModelCSD.java @@ -15,10 +15,4 @@ import org.eclipse.chemclipse.model.core.IPeakModel; public interface IPeakModelCSD extends IPeakModel { - - @Override - IScanCSD getPeakMaximum(); - - @Override - IScanCSD getPeakScan(int retentionTime); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/IPeakModelFSD.java b/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/IPeakModelFSD.java index b208e4fa9f..6055f577c8 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/IPeakModelFSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/IPeakModelFSD.java @@ -15,10 +15,4 @@ import org.eclipse.chemclipse.model.core.IPeakModel; public interface IPeakModelFSD extends IPeakModel { - - @Override - IScanFSD getPeakMaximum(); - - @Override - IScanFSD getPeakScan(int retentionTime); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/implementation/AbstractPeakModelFSD.java b/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/implementation/AbstractPeakModelFSD.java index 9e0c82f6bc..280aa4ad86 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/implementation/AbstractPeakModelFSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.fsd.model/src/org/eclipse/chemclipse/fsd/model/core/implementation/AbstractPeakModelFSD.java @@ -13,7 +13,6 @@ package org.eclipse.chemclipse.fsd.model.core.implementation; import org.eclipse.chemclipse.fsd.model.core.IPeakModelFSD; -import org.eclipse.chemclipse.fsd.model.core.IScanFSD; import org.eclipse.chemclipse.model.core.IPeakIntensityValues; import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.exceptions.PeakException; @@ -27,16 +26,4 @@ protected AbstractPeakModelFSD(IScan peakMaximum, IPeakIntensityValues peakInten super(peakMaximum, peakIntensityValues, startBackgroundIntensity, stopBackgroundIntensity); } - - @Override - public IScanFSD getPeakMaximum() { - - return (IScanFSD)super.getPeakMaximum(); - } - - @Override - public IScanFSD getPeakScan(int retentionTime) { - - return (IScanFSD)super.getPeakScan(retentionTime); - } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractPeakModelMSD.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractPeakModelMSD.java index 51f06c763f..cb4148aed4 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractPeakModelMSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractPeakModelMSD.java @@ -54,16 +54,4 @@ public IPeakMassSpectrum getPeakMassSpectrum(int retentionTime) { } return null; } - - @Override - public IScanMSD getPeakMaximum() { - - return (IScanMSD)super.getPeakMaximum(); - } - - @Override - public IScanMSD getPeakScan(int retentionTime) { - - return (IScanMSD)super.getPeakScan(retentionTime); - } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IPeakModelMSD.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IPeakModelMSD.java index ee8a1fec3e..4efc08e650 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IPeakModelMSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IPeakModelMSD.java @@ -60,10 +60,4 @@ public interface IPeakModelMSD extends IPeakModel { * @return IMassSpectrum */ IPeakMassSpectrum getPeakMassSpectrum(int retentionTime); - - @Override - IScanMSD getPeakMaximum(); - - @Override - IScanMSD getPeakScan(int retentionTime); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/ExtendedPeakTracesUI.java b/chemclipse/plugins/org.eclipse.chemclipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/ExtendedPeakTracesUI.java index 7a072bdb54..c364446feb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/ExtendedPeakTracesUI.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.ux.extension.xxd.ui/src/org/eclipse/chemclipse/ux/extension/xxd/ui/swt/ExtendedPeakTracesUI.java @@ -23,6 +23,7 @@ import org.eclipse.chemclipse.logging.core.Logger; import org.eclipse.chemclipse.model.core.IChromatogramPeak; import org.eclipse.chemclipse.model.core.IPeak; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.msd.model.core.IPeakMSD; import org.eclipse.chemclipse.msd.model.core.IPeakModelMSD; import org.eclipse.chemclipse.msd.model.core.IScanMSD; @@ -441,14 +442,16 @@ private void deleteTraces(Display display, Set traces) { } } else if(peak instanceof IPeakWSD peakWSD) { IPeakModelWSD peakModelWSD = peakWSD.getPeakModel(); - IScanWSD scanWSD = peakModelWSD.getPeakMaximum(); - int maxDeleteTraces = scanWSD.getNumberOfScanSignals() - 1; - if(traces.size() >= maxDeleteTraces) { - MessageDialog.openInformation(display.getActiveShell(), CATEGORY, "It's not possible to delete all wavelengths."); - } else { - scanWSD.removeScanSignals(traces); - updatePeak(); - UpdateNotifierUI.update(display, peak); + IScan scan = peakModelWSD.getPeakMaximum(); + if(scan instanceof IScanWSD scanWSD) { + int maxDeleteTraces = scanWSD.getNumberOfScanSignals() - 1; + if(traces.size() >= maxDeleteTraces) { + MessageDialog.openInformation(display.getActiveShell(), CATEGORY, "It's not possible to delete all wavelengths."); + } else { + scanWSD.removeScanSignals(traces); + updatePeak(); + UpdateNotifierUI.update(display, peak); + } } } if(peak instanceof IChromatogramPeak chromatogramPeak) { diff --git a/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/AbtractPeakModelVSD.java b/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/AbtractPeakModelVSD.java index b9a8efd4be..b6189f83b4 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/AbtractPeakModelVSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/AbtractPeakModelVSD.java @@ -25,16 +25,4 @@ public AbtractPeakModelVSD(IScan peakMaximum, IPeakIntensityValues peakIntensity super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance); } - - @Override - public IScanVSD getPeakMaximum() { - - return (IScanVSD)super.getPeakMaximum(); - } - - @Override - public IScanVSD getPeakScan(int retentionTime) { - - return (IScanVSD)super.getPeakScan(retentionTime); - } } \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/IPeakModelVSD.java b/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/IPeakModelVSD.java index 300e75e630..f41295a0be 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/IPeakModelVSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.vsd.model/src/org/eclipse/chemclipse/vsd/model/core/IPeakModelVSD.java @@ -15,10 +15,4 @@ import org.eclipse.chemclipse.model.core.IPeakModel; public interface IPeakModelVSD extends IPeakModel { - - @Override - IScanVSD getPeakMaximum(); - - @Override - IScanVSD getPeakScan(int retentionTime); } \ No newline at end of file diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractChromatogramPeakWSD.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractChromatogramPeakWSD.java index e84a8a8ac3..769f1ed46e 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractChromatogramPeakWSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractChromatogramPeakWSD.java @@ -13,6 +13,7 @@ package org.eclipse.chemclipse.wsd.model.core; import org.eclipse.chemclipse.model.core.IChromatogram; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.exceptions.PeakException; public abstract class AbstractChromatogramPeakWSD extends AbstractPeakWSD implements IChromatogramPeakWSD { @@ -79,12 +80,14 @@ public float getPurity() { /* * Extracted is the unknown and genuine the reference scan. */ - IScanWSD peakScan = getPeakModel().getPeakMaximum(); - IScanWSD genuineScanWSD = chromatogram.getScan(getScanMax()); - if(genuineScanWSD != null) { - int numberOfSignals = genuineScanWSD.getNumberOfScanSignals(); - if(numberOfSignals != 0) { - purity = peakScan.getNumberOfScanSignals() / (float)numberOfSignals; + IScan peakScan = getPeakModel().getPeakMaximum(); + if(peakScan instanceof IScanWSD peakScanWSD) { + IScanWSD genuineScanWSD = chromatogram.getScan(getScanMax()); + if(genuineScanWSD != null) { + int numberOfSignals = genuineScanWSD.getNumberOfScanSignals(); + if(numberOfSignals != 0) { + purity = peakScanWSD.getNumberOfScanSignals() / (float)numberOfSignals; + } } } return purity; diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractPeakModelWSD.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractPeakModelWSD.java index 5d3fb473f9..4cf1fda7f1 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractPeakModelWSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/AbstractPeakModelWSD.java @@ -25,16 +25,4 @@ public AbstractPeakModelWSD(IScan peakMaximum, IPeakIntensityValues peakIntensit super(peakMaximum, peakIntensityValues, startBackgroundAbundance, stopBackgroundAbundance); } - - @Override - public IScanWSD getPeakMaximum() { - - return (IScanWSD)super.getPeakMaximum(); - } - - @Override - public IScanWSD getPeakScan(int retentionTime) { - - return (IScanWSD)super.getPeakScan(retentionTime); - } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/IPeakModelWSD.java b/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/IPeakModelWSD.java index 8a91226ae2..a99221cd42 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/IPeakModelWSD.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.wsd.model/src/org/eclipse/chemclipse/wsd/model/core/IPeakModelWSD.java @@ -15,10 +15,4 @@ import org.eclipse.chemclipse.model.core.IPeakModel; public interface IPeakModelWSD extends IPeakModel { - - @Override - IScanWSD getPeakMaximum(); - - @Override - IScanWSD getPeakScan(int retentionTime); } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1001.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1001.java index caf98156cb..90b0a56fe1 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1001.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1001.java @@ -31,6 +31,7 @@ import org.eclipse.chemclipse.csd.model.core.IScanCSD; import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format; import org.eclipse.core.runtime.IProgressMonitor; @@ -210,7 +211,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1002.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1002.java index 44347a53fe..15d3a4f085 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1002.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1002.java @@ -31,6 +31,7 @@ import org.eclipse.chemclipse.csd.model.core.IScanCSD; import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format; import org.eclipse.core.runtime.IProgressMonitor; @@ -209,7 +210,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1003.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1003.java index 7656b23c4b..4006bda365 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1003.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1003.java @@ -31,6 +31,7 @@ import org.eclipse.chemclipse.csd.model.core.IScanCSD; import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format; import org.eclipse.core.runtime.IProgressMonitor; @@ -211,7 +212,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1004.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1004.java index 878c076087..b18c29646f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1004.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1004.java @@ -31,6 +31,7 @@ import org.eclipse.chemclipse.csd.model.core.IScanCSD; import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format; import org.eclipse.core.runtime.IProgressMonitor; @@ -213,7 +214,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1005.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1005.java index 1943a99959..112e17f091 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1005.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1005.java @@ -32,6 +32,7 @@ import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.settings.Format; import org.eclipse.core.runtime.IProgressMonitor; @@ -242,7 +243,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getRetentionIndex()); // Retention Index dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1006.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1006.java index a2eabd0433..2f07aed450 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1006.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1006.java @@ -33,6 +33,7 @@ import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.support.model.SeparationColumnType; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.internal.support.RetentionIndexTypeSupport; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; @@ -258,7 +259,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal dataOutputStream.writeInt(scan.getRetentionTimeColumn1()); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1007.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1007.java index 8b471da05b..15cb00bbc4 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1007.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1007.java @@ -33,6 +33,7 @@ import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.support.model.SeparationColumnType; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.internal.support.RetentionIndexTypeSupport; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.preferences.PreferenceSupplier; @@ -258,7 +259,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal dataOutputStream.writeInt(scan.getRetentionTimeColumn1()); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1100.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1100.java index d11b4589a1..0d64383734 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1100.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1100.java @@ -34,6 +34,7 @@ import org.eclipse.chemclipse.model.baseline.IBaselineModel; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.quantitation.IInternalStandard; import org.eclipse.chemclipse.support.model.SeparationColumnType; import org.eclipse.chemclipse.xxd.converter.supplier.ocx.internal.support.RetentionIndexTypeSupport; @@ -270,7 +271,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal dataOutputStream.writeInt(scan.getRetentionTimeColumn1()); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java index d955e46033..e0932dea65 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java @@ -42,6 +42,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -321,7 +322,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java index c5f2f5cde7..5e705581a4 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java @@ -44,6 +44,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -321,7 +322,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java index daca9c8aa8..a6ae37982f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java @@ -45,6 +45,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -360,7 +361,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java index 41ba1cf583..3724dfa4ed 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java @@ -45,6 +45,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; import org.eclipse.chemclipse.model.identifier.ILibraryInformation; @@ -359,7 +360,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java index 5a0e1207cf..0afc305f7a 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java @@ -44,6 +44,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.quantitation.IInternalStandard; import org.eclipse.chemclipse.model.quantitation.IQuantitationEntry; import org.eclipse.chemclipse.model.ranges.TimeRange; @@ -351,7 +352,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java index 8bff8740a5..03e7c14916 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/csd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java @@ -44,6 +44,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.quantitation.IInternalStandard; import org.eclipse.chemclipse.model.quantitation.IQuantitationEntry; import org.eclipse.chemclipse.model.ranges.TimeRange; @@ -347,7 +348,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakCSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanCSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java index 45285e986f..3f1910cf65 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1300.java @@ -37,6 +37,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -353,7 +354,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakWSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java index 87a2f4768e..6f0c8099f4 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1301.java @@ -39,6 +39,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -353,7 +354,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakWSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java index 3d6c34f72d..bd0d0c00d3 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1400.java @@ -40,6 +40,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.core.ISignal; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; @@ -389,7 +390,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakWSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java index ad288dbc03..9796d0642f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1500.java @@ -40,6 +40,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.identifier.IComparisonResult; import org.eclipse.chemclipse.model.identifier.IIdentificationTarget; import org.eclipse.chemclipse.model.identifier.ILibraryInformation; @@ -388,7 +389,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakWSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java index 69c58d4e9e..0fe91643e7 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1501.java @@ -39,6 +39,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.quantitation.IInternalStandard; import org.eclipse.chemclipse.model.quantitation.IQuantitationEntry; import org.eclipse.chemclipse.model.ranges.TimeRange; @@ -380,7 +381,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakWSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal diff --git a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java index 270ce24466..c22c8b7cbb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.xxd.converter.supplier.ocx/src/org/eclipse/chemclipse/wsd/converter/supplier/ocx/internal/io/ChromatogramWriter_1502.java @@ -39,6 +39,7 @@ import org.eclipse.chemclipse.model.core.IChromatogram; import org.eclipse.chemclipse.model.core.IIntegrationEntry; import org.eclipse.chemclipse.model.core.IMethod; +import org.eclipse.chemclipse.model.core.IScan; import org.eclipse.chemclipse.model.quantitation.IInternalStandard; import org.eclipse.chemclipse.model.quantitation.IQuantitationEntry; import org.eclipse.chemclipse.model.ranges.TimeRange; @@ -379,7 +380,7 @@ private void writePeak(DataOutputStream dataOutputStream, IPeakWSD peak) throws dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStartRetentionTime())); // Start Background Abundance dataOutputStream.writeFloat(peakModel.getBackgroundAbundance(peakModel.getStopRetentionTime())); // Stop Background Abundance - IScanWSD scan = peakModel.getPeakMaximum(); + IScan scan = peakModel.getPeakMaximum(); dataOutputStream.writeInt(scan.getRetentionTime()); // Retention Time dataOutputStream.writeInt(scan.getRelativeRetentionTime()); dataOutputStream.writeFloat(scan.getTotalSignal()); // Total Signal