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Fixed #915 - Chromatogram Filter - Select Scan
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109 changes: 109 additions & 0 deletions
109
...ipse/chemclipse/chromatogram/xxd/filter/supplier/scanremover/core/FilterScanSelector.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2022 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 org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scanremover.core; | ||
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| import org.eclipse.chemclipse.chromatogram.filter.core.chromatogram.AbstractChromatogramFilter; | ||
| import org.eclipse.chemclipse.chromatogram.filter.result.ChromatogramFilterResult; | ||
| import org.eclipse.chemclipse.chromatogram.filter.result.ResultStatus; | ||
| import org.eclipse.chemclipse.chromatogram.filter.settings.IChromatogramFilterSettings; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scanremover.exceptions.FilterException; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scanremover.preferences.PreferenceSupplier; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scanremover.settings.FilterSettingsScanSelector; | ||
| import org.eclipse.chemclipse.model.core.IChromatogram; | ||
| import org.eclipse.chemclipse.model.core.IChromatogramOverview; | ||
| import org.eclipse.chemclipse.model.core.IScan; | ||
| import org.eclipse.chemclipse.model.selection.IChromatogramSelection; | ||
| import org.eclipse.chemclipse.model.support.RetentionIndexMap; | ||
| import org.eclipse.chemclipse.processing.core.IProcessingInfo; | ||
| import org.eclipse.chemclipse.processing.core.MessageType; | ||
| import org.eclipse.chemclipse.processing.core.ProcessingMessage; | ||
| import org.eclipse.core.runtime.IProgressMonitor; | ||
|
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| @SuppressWarnings("rawtypes") | ||
| public class FilterScanSelector extends AbstractChromatogramFilter { | ||
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| @SuppressWarnings("unchecked") | ||
| @Override | ||
| public IProcessingInfo applyFilter(IChromatogramSelection chromatogramSelection, IChromatogramFilterSettings chromatogramFilterSettings, IProgressMonitor monitor) { | ||
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| IProcessingInfo processingInfo = validate(chromatogramSelection, chromatogramFilterSettings); | ||
| if(!processingInfo.hasErrorMessages()) { | ||
| try { | ||
| if(chromatogramFilterSettings instanceof FilterSettingsScanSelector) { | ||
| FilterSettingsScanSelector settings = (FilterSettingsScanSelector)chromatogramFilterSettings; | ||
| selectScan(chromatogramSelection, settings, monitor); | ||
| processingInfo.addMessage(new ProcessingMessage(MessageType.INFO, "Select Scan", "The scan has been selected successfully.")); | ||
| processingInfo.setProcessingResult(new ChromatogramFilterResult(ResultStatus.OK, "Scan selection was successful.")); | ||
| chromatogramSelection.getChromatogram().setDirty(true); | ||
| } | ||
| } catch(FilterException e) { | ||
| processingInfo.addMessage(new ProcessingMessage(MessageType.WARN, "Select Scan", e.getMessage())); | ||
| processingInfo.setProcessingResult(new ChromatogramFilterResult(ResultStatus.EXCEPTION, e.getMessage())); | ||
| } | ||
| } | ||
| return processingInfo; | ||
| } | ||
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| @Override | ||
| public IProcessingInfo applyFilter(IChromatogramSelection chromatogramSelection, IProgressMonitor monitor) { | ||
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| FilterSettingsScanSelector filterSettings = PreferenceSupplier.getFilterSettingsScanSelector(); | ||
| return applyFilter(chromatogramSelection, filterSettings, monitor); | ||
| } | ||
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| private void selectScan(IChromatogramSelection chromatogramSelection, FilterSettingsScanSelector filterSettingsScanSelector, IProgressMonitor monitor) throws FilterException { | ||
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| IChromatogram chromatogram = chromatogramSelection.getChromatogram(); | ||
| int startScan = chromatogram.getScanNumber(chromatogramSelection.getStartRetentionTime()); | ||
| int stopScan = chromatogram.getScanNumber(chromatogramSelection.getStopRetentionTime()); | ||
| int scanNumber = getScanNumber(chromatogram, filterSettingsScanSelector); | ||
| // | ||
| if(scanNumber >= startScan && scanNumber <= stopScan) { | ||
| IScan scan = chromatogram.getScan(scanNumber); | ||
| chromatogramSelection.setSelectedScan(scan); | ||
| } else { | ||
| throw new FilterException("The scan is outside of the chromatogram selection range."); | ||
| } | ||
| } | ||
|
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| private int getScanNumber(IChromatogram chromatogram, FilterSettingsScanSelector filterSettingsScanSelector) { | ||
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| int scanNumber; | ||
| double value = filterSettingsScanSelector.getScanSelectorValue(); | ||
| switch(filterSettingsScanSelector.getScanSelectorOption()) { | ||
| case SCAN_NUMER: | ||
| scanNumber = (int)Math.round(value); | ||
| break; | ||
| case RETENTION_TIME_MS: | ||
| scanNumber = chromatogram.getScanNumber((int)Math.round(value)); | ||
| break; | ||
| case RETENTION_TIME_MIN: | ||
| scanNumber = chromatogram.getScanNumber((int)Math.round(value * IChromatogramOverview.MINUTE_CORRELATION_FACTOR)); | ||
| break; | ||
| case RETENTION_INDEX: | ||
| RetentionIndexMap retentionIndexMap = new RetentionIndexMap(); | ||
| retentionIndexMap.updateRetentionIndexMap(chromatogram); | ||
| int retentionTime = retentionIndexMap.getRetentionTime((int)Math.round(value)); | ||
| if(retentionTime > -1) { | ||
| scanNumber = chromatogram.getScanNumber(retentionTime); | ||
| } else { | ||
| scanNumber = -1; | ||
| } | ||
| break; | ||
| default: | ||
| scanNumber = -1; | ||
| break; | ||
| } | ||
| // | ||
| return scanNumber; | ||
| } | ||
| } |
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39 changes: 39 additions & 0 deletions
39
...pse/chemclipse/chromatogram/xxd/filter/supplier/scanremover/model/ScanSelectorOption.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2022 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 org.eclipse.chemclipse.chromatogram.xxd.filter.supplier.scanremover.model; | ||
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| import org.eclipse.chemclipse.support.text.ILabel; | ||
|
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| public enum ScanSelectorOption implements ILabel { | ||
| SCAN_NUMER("Scan Number"), // | ||
| RETENTION_TIME_MS("Retention Time [ms]"), // | ||
| RETENTION_TIME_MIN("Retention Time [min]"), // | ||
| RETENTION_INDEX("Retention Index"); // | ||
|
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| private String label = ""; | ||
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| private ScanSelectorOption(String label) { | ||
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| this.label = label; | ||
| } | ||
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| @Override | ||
| public String label() { | ||
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| return label; | ||
| } | ||
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| public static String[][] getOptions() { | ||
|
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| return ILabel.getOptions(values()); | ||
| } | ||
| } |
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