net.openchrom.chromatogram.msd.identifier.supplier.cdk.ui.internal.handlers.DeleteIdentificationsChromatogramRunnable.java Source code

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Here is the source code for net.openchrom.chromatogram.msd.identifier.supplier.cdk.ui.internal.handlers.DeleteIdentificationsChromatogramRunnable.java

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/*******************************************************************************
 * Copyright (c) 2013, 2017 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:
 * Dr. Philip Wenig - initial API and implementation
 *******************************************************************************/
package net.openchrom.chromatogram.msd.identifier.supplier.cdk.ui.internal.handlers;

import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;

import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.model.identifier.ILibraryInformation;
import org.eclipse.chemclipse.model.targets.IPeakTarget;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IChromatogramPeakMSD;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.core.identifier.massspectrum.IMassSpectrumTarget;
import org.eclipse.chemclipse.msd.model.core.selection.ChromatogramSelectionMSD;
import org.eclipse.chemclipse.msd.model.core.selection.IChromatogramSelectionMSD;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.jface.operation.IRunnableWithProgress;
import org.eclipse.swt.widgets.Display;

public class DeleteIdentificationsChromatogramRunnable implements IRunnableWithProgress {

    private IChromatogramSelectionMSD chromatogramSelection;

    public DeleteIdentificationsChromatogramRunnable(IChromatogramSelectionMSD chromatogramSelection) {
        this.chromatogramSelection = chromatogramSelection;
    }

    @Override
    public void run(IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {

        try {
            monitor.beginTask("SMILES calculator", IProgressMonitor.UNKNOWN);
            /*
             * Scans
             */
            IChromatogramMSD chromatogram = chromatogramSelection.getChromatogramMSD();
            int startScan = chromatogram.getScanNumber(chromatogramSelection.getStartRetentionTime());
            int stopScan = chromatogram.getScanNumber(chromatogramSelection.getStopRetentionTime());
            /*
             * Scans
             */
            for (int scan = startScan; scan <= stopScan; scan++) {
                IScan supplierScan = chromatogram.getScan(scan);
                if (supplierScan instanceof IScanMSD) {
                    IScanMSD scanMSD = (IScanMSD) supplierScan;
                    /*
                     * Scan
                     */
                    if (scanMSD.getTargets().size() > 0) {
                        deleteTargets(scanMSD);
                    }
                    /*
                     * Optimized Scan.
                     */
                    IScanMSD optimizedMassSpectrum = scanMSD.getOptimizedMassSpectrum();
                    if (optimizedMassSpectrum != null) {
                        if (optimizedMassSpectrum.getTargets().size() > 0) {
                            deleteTargets(scanMSD);
                        }
                    }
                }
            }
            /*
             * Peaks
             */
            List<IChromatogramPeakMSD> peaks = chromatogramSelection.getChromatogramMSD()
                    .getPeaks(chromatogramSelection);
            deleteTargets(peaks);
            /*
             * Fire an update.
             */
            updateSelection();
        } finally {
            monitor.done();
        }
    }

    private void deleteTargets(IScanMSD scanMSD) {

        /*
         * Get the targets for each peak.
         */
        List<IMassSpectrumTarget> targets = scanMSD.getTargets();
        List<IMassSpectrumTarget> targetsToDelete = new ArrayList<IMassSpectrumTarget>();
        for (IMassSpectrumTarget target : targets) {
            /*
             * Check if the peak is a peak identification entry.
             */
            if (target instanceof IMassSpectrumTarget) {
                ILibraryInformation libraryInformation = ((IMassSpectrumTarget) target).getLibraryInformation();
                if (libraryInformation.getSmiles().equals("")) {
                    targetsToDelete.add(target);
                }
            }
        }
        /*
         * Delete each marked entry in the selected peak.
         */
        scanMSD.removeTargets(targetsToDelete);
    }

    private void deleteTargets(List<IChromatogramPeakMSD> peaks) {

        for (IChromatogramPeakMSD peak : peaks) {
            /*
             * Get the targets for each peak.
             */
            List<IPeakTarget> targets = peak.getTargets();
            List<IPeakTarget> targetsToDelete = new ArrayList<IPeakTarget>();
            for (IPeakTarget target : targets) {
                /*
                 * Check if the peak is a peak identification entry.
                 */
                if (target instanceof IPeakTarget) {
                    ILibraryInformation libraryInformation = ((IPeakTarget) target).getLibraryInformation();
                    if (libraryInformation.getSmiles().equals("")) {
                        targetsToDelete.add(target);
                    }
                }
            }
            /*
             * Delete each marked entry in the selected peak.
             */
            peak.removeTargets(targetsToDelete);
        }
    }

    // ---------------------------------------------------------private methods
    /*
     * Updates the selection using the GUI thread.
     */
    private void updateSelection() {

        Display.getDefault().asyncExec(new Runnable() {

            @Override
            public void run() {

                if (chromatogramSelection instanceof ChromatogramSelectionMSD) {
                    ((ChromatogramSelectionMSD) chromatogramSelection).update(false);
                }
            }
        });
    }
    // ---------------------------------------------------------private methods
}