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Add basic support for PCA with MALDI-TOF spectra.
Signed-off-by: Matthias Mailänder <[email protected]>
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....chemclipse.chromatogram.xxd.process.supplier.pca.ui.quickstart.SpectraTileDefinition.xml
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <scr:component xmlns:scr="http://www.osgi.org/xmlns/scr/v1.1.0" name="org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.ui.quickstart.SpectraTileDefinition"> | ||
| <service> | ||
| <provide interface="org.eclipse.chemclipse.ux.extension.ui.definitions.TileDefinition"/> | ||
| </service> | ||
| <implementation class="org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.ui.quickstart.SpectraTileDefinition"/> | ||
| </scr:component> |
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...pse/chromatogram/xxd/process/supplier/pca/ui/internal/wizards/SpectraFilesWizardPage.java
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| /******************************************************************************* | ||
| * Copyright (c) 2017, 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: | ||
| * Jan Holy - initial API and implementation | ||
| * Christoph Läubrich - change to new Wizard API | ||
| * Philip Wenig - get rid of JavaFX | ||
| * Matthias Mailänder - adapted for MALDI | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.ui.internal.wizards; | ||
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| import java.io.File; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.model.DataInputEntry; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.model.IDataInputEntry; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.preferences.PreferenceSupplier; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.ui.Activator; | ||
| import org.eclipse.chemclipse.model.types.DataType; | ||
| import org.eclipse.chemclipse.ux.extension.xxd.ui.wizards.InputEntriesWizard; | ||
| import org.eclipse.chemclipse.ux.extension.xxd.ui.wizards.InputWizardSettings; | ||
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| public class SpectraFilesWizardPage extends DataInputPageWizard { | ||
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| public SpectraFilesWizardPage() { | ||
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| super("DataInputFiles"); | ||
| setTitle("MALDI-TOF MS Input Files"); | ||
| setDescription("This wizard lets you select MALDI-TOF MS input files and set bulk group name."); | ||
| } | ||
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| @Override | ||
| protected void addFiles() { | ||
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| InputWizardSettings inputWizardSettings = InputWizardSettings.create(Activator.getDefault().getPreferenceStore(), PreferenceSupplier.N_INPUT_FILE, DataType.MALDI); | ||
| inputWizardSettings.setTitle("MALDI-TOF MS Input Files"); | ||
| inputWizardSettings.setDescription("This wizard lets you select several mass spectra input files."); | ||
| // | ||
| List<IDataInputEntry> dataInputEntries = new ArrayList<>(); | ||
| for(File file : InputEntriesWizard.openWizard(getShell(), inputWizardSettings).keySet()) { | ||
| dataInputEntries.add(new DataInputEntry(file.getAbsolutePath())); | ||
| } | ||
| // | ||
| addInputFiles(dataInputEntries); | ||
| update(); | ||
| } | ||
| } |
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...mclipse/chromatogram/xxd/process/supplier/pca/ui/internal/wizards/SpectraInputWizard.java
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| /******************************************************************************* | ||
| * Copyright (c) 2017, 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: | ||
| * Jan Holy - initial API and implementation | ||
| * Matthias Mailänder - adapted for MALDI | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.ui.internal.wizards; | ||
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| import java.util.List; | ||
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| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.core.IExtractionData; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.core.IFilterSettings; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.core.IPreprocessingSettings; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.core.PcaExtractionSpectra; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.extraction.SpectraExtractionSupport.ExtractionType; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.model.IAnalysisSettings; | ||
| import org.eclipse.chemclipse.chromatogram.xxd.process.supplier.pca.model.IDataInputEntry; | ||
| import org.eclipse.jface.wizard.Wizard; | ||
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| public class SpectraInputWizard extends Wizard implements IInputWizard { | ||
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| private SpectraSettingsWizardPage spectraSettingsWizardPage = new SpectraSettingsWizardPage(); | ||
| private SpectraFilesWizardPage spectraFilesWizardPage = new SpectraFilesWizardPage(); | ||
| private GroupNamesWizardPage groupNamesWizardPage = new GroupNamesWizardPage(); | ||
| private PreprocessingWizardPage preprocessingWizardPage = new PreprocessingWizardPage(); | ||
| private FilterWizardPage filterWizardPage = new FilterWizardPage(); | ||
| /* | ||
| * Will be created when finishing the report. | ||
| */ | ||
| private PcaExtractionSpectra pcaExtractionData; | ||
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| @Override | ||
| public void addPages() { | ||
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| addPage(spectraSettingsWizardPage); | ||
| addPage(spectraFilesWizardPage); | ||
| addPage(groupNamesWizardPage); | ||
| addPage(preprocessingWizardPage); | ||
| addPage(filterWizardPage); | ||
| } | ||
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| @Override | ||
| public IExtractionData getExtractionData() { | ||
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| return pcaExtractionData; | ||
| } | ||
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| @Override | ||
| public List<IDataInputEntry> getDataInputEntries() { | ||
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| return spectraFilesWizardPage.getUniqueDataInputEnties(); | ||
| } | ||
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| @Override | ||
| public IAnalysisSettings getAnalysisSettings() { | ||
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| return spectraSettingsWizardPage.getAnalysisSettings(); | ||
| } | ||
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| @Override | ||
| public IPreprocessingSettings getPreprocessingSettings() { | ||
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| return preprocessingWizardPage.getPreprocessingSettings(); | ||
| } | ||
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| @Override | ||
| public IFilterSettings getFilterSettings() { | ||
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| return filterWizardPage.getFilterSettings(); | ||
| } | ||
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| @Override | ||
| public boolean performFinish() { | ||
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| List<IDataInputEntry> dataInputs = getDataInputEntries(); | ||
| int massWindow = spectraSettingsWizardPage.getMassWindow(); | ||
| boolean useDefaultProperties = spectraSettingsWizardPage.isUseDefaultProperties(); | ||
| ExtractionType extractionType = spectraSettingsWizardPage.getExtractionType(); | ||
| int maximalNumberScans = spectraSettingsWizardPage.getMaximalNumberPeaks(); | ||
| pcaExtractionData = new PcaExtractionSpectra(massWindow, maximalNumberScans, dataInputs, extractionType, useDefaultProperties); | ||
| return true; | ||
| } | ||
| } |
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