Example usage for com.google.common.collect Range span

List of usage examples for com.google.common.collect Range span

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Introduction

In this page you can find the example usage for com.google.common.collect Range span.

Prototype

public Range<C> span(Range<C> other)

Source Link

Document

Returns the minimal range that #encloses encloses both this range and other .

Usage

From source file:edu.mit.streamjit.impl.compiler2.Storage.java

/**
 * Returns a range spanning the indices written in this storage during an
 * execution of the given schedule. (Note that, as a span, not every
 * contained index will be written.) The returned range will be
 * {@link Range#canonical(com.google.common.collect.DiscreteDomain) canonical}.
 * The range is not cached so as to be responsive to changes in output index
 * functions./* ww  w.j  ava2  s. com*/
 * @param externalSchedule the schedule
 * @return a range spanning the indices written during the given schedule
 * under the current index functions
 * @see #writeIndices(java.util.Map)
 */
public Range<Integer> writeIndexSpan(Map<ActorGroup, Integer> externalSchedule) {
    Range<Integer> range = null;
    for (Actor a : upstream()) {
        //just the first and last iteration
        int maxIteration = a.group().schedule().get(a) * externalSchedule.get(a.group()) - 1;
        if (maxIteration >= 0)
            for (int iteration : new int[] { 0, maxIteration }) {
                ImmutableSortedSet<Integer> writes = a.writes(this, iteration);
                Range<Integer> writeRange = writes.isEmpty() ? range
                        : Range.closed(writes.first(), writes.last());
                range = range == null ? writeRange : range.span(writeRange);
            }
    }
    range = (range != null ? range : Range.closedOpen(0, 0));
    return range.canonical(DiscreteDomain.integers());
}

From source file:net.sf.mzmine.project.impl.RawDataFileImpl.java

public @Nonnull Range<Double> getDataRTRange(int msLevel) {

    // check if we have this value already cached
    Range<Double> rtRange = dataRTRange.get(msLevel);
    if (rtRange != null)
        return rtRange;

    // find the value
    for (Scan scan : scans.values()) {

        // ignore scans of other ms levels
        if ((msLevel != 0) && (scan.getMSLevel() != msLevel))
            continue;

        if (rtRange == null)
            rtRange = Range.singleton(scan.getRetentionTime());
        else/*from w w w  .j  a  v a2  s  . com*/
            rtRange = rtRange.span(Range.singleton(scan.getRetentionTime()));

    }

    // cache the value
    if (rtRange != null)
        dataRTRange.put(msLevel, rtRange);
    else
        rtRange = Range.singleton(0.0);

    return rtRange;

}

From source file:net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.Gap.java

public void noMoreOffers() {

    // Check peak that was last constructed
    if (currentPeakDataPoints != null) {
        checkCurrentPeak();//from w ww . j  av a  2s  .c  om
        currentPeakDataPoints = null;
    }

    // If we have best peak candidate, construct a SimpleChromatographicPeak
    if (bestPeakDataPoints != null) {

        double area = 0, height = 0, mz = 0, rt = 0;
        int scanNumbers[] = new int[bestPeakDataPoints.size()];
        DataPoint finalDataPoint[] = new DataPoint[bestPeakDataPoints.size()];
        Range<Double> finalRTRange = null, finalMZRange = null, finalIntensityRange = null;
        int representativeScan = 0;

        // Process all datapoints
        for (int i = 0; i < bestPeakDataPoints.size(); i++) {

            GapDataPoint dp = bestPeakDataPoints.get(i);

            if (i == 0) {
                finalRTRange = Range.singleton(dp.getRT());
                finalMZRange = Range.singleton(dp.getMZ());
                finalIntensityRange = Range.singleton(dp.getIntensity());
            } else {
                assert finalRTRange != null && finalMZRange != null && finalIntensityRange != null;
                finalRTRange = finalRTRange.span(Range.singleton(dp.getRT()));
                finalMZRange = finalMZRange.span(Range.singleton(dp.getMZ()));
                finalIntensityRange = finalIntensityRange.span(Range.singleton(dp.getIntensity()));
            }

            scanNumbers[i] = bestPeakDataPoints.get(i).getScanNumber();
            finalDataPoint[i] = new SimpleDataPoint(dp.getMZ(), dp.getIntensity());
            mz += bestPeakDataPoints.get(i).getMZ();

            // Check height
            if (bestPeakDataPoints.get(i).getIntensity() > height) {
                height = bestPeakDataPoints.get(i).getIntensity();
                rt = bestPeakDataPoints.get(i).getRT();
                representativeScan = bestPeakDataPoints.get(i).getScanNumber();
            }

            // Skip last data point
            if (i == bestPeakDataPoints.size() - 1)
                break;

            // X axis interval length
            double rtDifference = (bestPeakDataPoints.get(i + 1).getRT() - bestPeakDataPoints.get(i).getRT())
                    * 60d;

            // intensity at the beginning and end of the interval
            double intensityStart = bestPeakDataPoints.get(i).getIntensity();
            double intensityEnd = bestPeakDataPoints.get(i + 1).getIntensity();

            // calculate area of the interval
            area += (rtDifference * (intensityStart + intensityEnd) / 2);

        }

        // Calculate average m/z value
        mz /= bestPeakDataPoints.size();

        // Find the best fragmentation scan, if available
        int fragmentScan = ScanUtils.findBestFragmentScan(rawDataFile, finalRTRange, finalMZRange);

        SimpleFeature newPeak = new SimpleFeature(rawDataFile, mz, rt, height, area, scanNumbers,
                finalDataPoint, FeatureStatus.ESTIMATED, representativeScan, fragmentScan, finalRTRange,
                finalMZRange, finalIntensityRange);

        // Fill the gap
        peakListRow.addPeak(rawDataFile, newPeak);
    }

}

From source file:net.sf.mzmine.modules.rawdatamethods.peakpicking.targetedpeakdetection.Gap.java

public void noMoreOffers() {

    // Check peak that was last constructed
    if (currentPeakDataPoints != null) {
        checkCurrentPeak();/*from   ww w.j  a  va 2 s. c om*/
        currentPeakDataPoints = null;
    }

    // If we have best peak candidate, construct a SimpleChromatographicPeak
    if (bestPeakDataPoints != null) {

        double area = 0, height = 0, mz = 0, rt = 0;
        int scanNumbers[] = new int[bestPeakDataPoints.size()];
        DataPoint finalDataPoint[] = new DataPoint[bestPeakDataPoints.size()];
        Range<Double> finalRTRange = null, finalMZRange = null, finalIntensityRange = null;
        int representativeScan = 0;

        // Process all datapoints
        for (int i = 0; i < bestPeakDataPoints.size(); i++) {

            GapDataPoint dp = bestPeakDataPoints.get(i);

            if (i == 0) {
                finalRTRange = Range.singleton(dp.getRT());
                finalMZRange = Range.singleton(dp.getMZ());
                finalIntensityRange = Range.singleton(dp.getIntensity());
            } else {
                assert finalRTRange != null && finalMZRange != null && finalIntensityRange != null;
                finalRTRange = finalRTRange.span(Range.singleton(dp.getRT()));
                finalMZRange = finalMZRange.span(Range.singleton(dp.getMZ()));
                finalIntensityRange = finalIntensityRange.span(Range.singleton(dp.getIntensity()));
            }

            scanNumbers[i] = bestPeakDataPoints.get(i).getScanNumber();
            finalDataPoint[i] = new SimpleDataPoint(dp.getMZ(), dp.getIntensity());
            mz += bestPeakDataPoints.get(i).getMZ();

            // Check height
            if (bestPeakDataPoints.get(i).getIntensity() > height) {
                height = bestPeakDataPoints.get(i).getIntensity();
                rt = bestPeakDataPoints.get(i).getRT();
                representativeScan = bestPeakDataPoints.get(i).getScanNumber();
            }

            // Skip last data point
            if (i == bestPeakDataPoints.size() - 1) {
                break;
            }

            // X axis interval length
            double rtDifference = bestPeakDataPoints.get(i + 1).getRT() - bestPeakDataPoints.get(i).getRT();

            // Convert the RT scale to seconds
            rtDifference *= 60d;

            // intensity at the beginning and end of the interval
            double intensityStart = bestPeakDataPoints.get(i).getIntensity();
            double intensityEnd = bestPeakDataPoints.get(i + 1).getIntensity();

            // calculate area of the interval
            area += (rtDifference * (intensityStart + intensityEnd) / 2);

        }

        // Calculate average m/z value
        mz /= bestPeakDataPoints.size();

        // Find the best fragmentation scan, if available
        int fragmentScan = ScanUtils.findBestFragmentScan(rawDataFile, finalRTRange, finalMZRange);

        // Is intensity above the noise level?
        if (height >= noiseLevel) {
            SimpleFeature newPeak = new SimpleFeature(rawDataFile, mz, rt, height, area, scanNumbers,
                    finalDataPoint, FeatureStatus.ESTIMATED, representativeScan, fragmentScan, finalRTRange,
                    finalMZRange, finalIntensityRange);

            // Fill the gap
            peakListRow.addPeak(rawDataFile, newPeak);
        }
    }

}

From source file:net.sf.mzmine.util.components.PeakSummaryComponent.java

public void actionPerformed(ActionEvent e) {

    String command = e.getActionCommand();

    if (command.equals("SHOW")) {

        String visualizerType = (String) comboShow.getSelectedItem();
        int[] indexesRow = peaksInfoList.getSelectedRows();
        Feature[] selectedPeaks = new Feature[indexesRow.length];
        RawDataFile[] dataFiles = new RawDataFile[indexesRow.length];
        Range<Double> rtRange = null, mzRange = null;
        for (int i = 0; i < indexesRow.length; i++) {
            selectedPeaks[i] = listElementModel.getElementAt(indexesRow[i]);
            dataFiles[i] = selectedPeaks[i].getDataFile();

            if ((rtRange == null) || (mzRange == null)) {
                rtRange = dataFiles[i].getDataRTRange(1);
                mzRange = selectedPeaks[i].getRawDataPointsMZRange();
            } else {
                rtRange = rtRange.span(dataFiles[i].getDataRTRange(1));
                mzRange = mzRange.span(selectedPeaks[i].getRawDataPointsMZRange());
            }/*from   w w w .j  av a 2  s  .  c o  m*/
        }

        if (dataFiles.length == 0) {
            return;
        }

        if (visualizerType.equals("Chromatogram")) {

            // Label best peak with preferred identity.
            final Feature bestPeak = row.getBestPeak();
            final PeakIdentity peakIdentity = row.getPreferredPeakIdentity();
            final Map<Feature, String> labelMap = new HashMap<Feature, String>(1);
            if (bestPeak != null && peakIdentity != null) {

                labelMap.put(bestPeak, peakIdentity.getName());
            }

            ScanSelection scanSelection = new ScanSelection(rtRange, 1);

            TICVisualizerModule.showNewTICVisualizerWindow(dataFiles, selectedPeaks, labelMap, scanSelection,
                    TICPlotType.BASEPEAK, mzRange);
            return;

        } else if (visualizerType.equals("Mass spectrum")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i],
                        selectedPeaks[i].getRepresentativeScanNumber());
            }
        } else if (visualizerType.equals("Peak in 2D")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                Range<Double> peakRTRange = selectedPeaks[i].getRawDataPointsRTRange();
                Range<Double> peakMZRange = selectedPeaks[i].getRawDataPointsMZRange();
                final double rtLen = peakRTRange.upperEndpoint() - peakRTRange.lowerEndpoint();
                Range<Double> localRTRange = Range.closed(Math.max(0, peakRTRange.lowerEndpoint() - rtLen),
                        peakRTRange.upperEndpoint() + rtLen);

                final double mzLen = peakMZRange.upperEndpoint() - peakMZRange.lowerEndpoint();
                Range<Double> localMZRange = Range.closed(Math.max(0, peakMZRange.lowerEndpoint() - mzLen),
                        peakMZRange.upperEndpoint() + mzLen);
                TwoDVisualizerModule.show2DVisualizerSetupDialog(dataFiles[i], localMZRange, localRTRange);
            }
        } else if (visualizerType.equals("Peak in 3D")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                Range<Double> peakRTRange = selectedPeaks[i].getRawDataPointsRTRange();
                Range<Double> peakMZRange = selectedPeaks[i].getRawDataPointsMZRange();
                final double rtLen = peakRTRange.upperEndpoint() - peakRTRange.lowerEndpoint();
                Range<Double> localRTRange = Range.closed(Math.max(0, peakRTRange.lowerEndpoint() - rtLen),
                        peakRTRange.upperEndpoint() + rtLen);
                final double mzLen = peakMZRange.upperEndpoint() - peakMZRange.lowerEndpoint();
                Range<Double> localMZRange = Range.closed(Math.max(0, peakMZRange.lowerEndpoint() - mzLen),
                        peakMZRange.upperEndpoint() + mzLen);
                ThreeDVisualizerModule.setupNew3DVisualizer(dataFiles[i], localMZRange, localRTRange);
            }
        } else if (visualizerType.equals("MS/MS")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                int scanNumber = selectedPeaks[i].getMostIntenseFragmentScanNumber();
                if (scanNumber > 0) {
                    SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], scanNumber);
                } else {
                    JFrame frame = (JFrame) SwingUtilities.getAncestorOfClass(JFrame.class, this);
                    MZmineCore.getDesktop().displayMessage(frame, "There is no fragment for the mass "
                            + MZmineCore.getConfiguration().getMZFormat().format(selectedPeaks[i].getMZ())
                            + "m/z in the current raw data.");
                    return;
                }
            }

        } else if (visualizerType.equals("Isotope pattern")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                IsotopePattern ip = selectedPeaks[i].getIsotopePattern();
                if (ip == null) {
                    return;
                }
                SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i],
                        selectedPeaks[i].getMostIntenseFragmentScanNumber(), ip);

            }
        }
        return;
    }

    if (command.equals("CHANGE")) {
        int indexRow = peaksInfoList.getSelectedRow();
        if (indexRow == -1) {
            return;
        }
        Feature selectedPeak = listElementModel.getElementAt(indexRow);
        ManualPeakPickerModule.runManualDetection(selectedPeak.getDataFile(), row, null, null);

        return;
    }

}

From source file:net.sf.mzmine.modules.visualization.peaklisttable.PeakListTablePopupMenu.java

@Override
public void actionPerformed(final ActionEvent e) {

    final Object src = e.getSource();

    if (deleteRowsItem.equals(src)) {

        final int[] rowsToDelete = table.getSelectedRows();

        final int[] unsortedIndexes = new int[rowsToDelete.length];
        for (int i = rowsToDelete.length - 1; i >= 0; i--) {

            unsortedIndexes[i] = table.convertRowIndexToModel(rowsToDelete[i]);
        }//from w  w w.  ja v  a  2  s.co m

        // sort row indexes and start removing from the last
        Arrays.sort(unsortedIndexes);

        // delete the rows starting from last
        for (int i = unsortedIndexes.length - 1; i >= 0; i--) {
            peakList.removeRow(unsortedIndexes[i]);
        }

        // Notify the GUI that peaklist contents have changed
        updateTableGUI();
    }

    if (plotRowsItem.equals(src)) {

        final int[] selectedTableRows = table.getSelectedRows();

        final PeakListRow[] selectedRows = new PeakListRow[selectedTableRows.length];
        for (int i = 0; i < selectedTableRows.length; i++) {

            selectedRows[i] = peakList.getRow(table.convertRowIndexToModel(selectedTableRows[i]));
        }

        IntensityPlotModule.showIntensityPlot(MZmineCore.getProjectManager().getCurrentProject(), peakList,
                selectedRows);
    }

    if (showXICItem.equals(src) && allClickedPeakListRows.length != 0) {

        // Map peaks to their identity labels.
        final Map<Feature, String> labelsMap = new HashMap<Feature, String>(allClickedPeakListRows.length);

        final RawDataFile selectedDataFile = clickedDataFile == null
                ? allClickedPeakListRows[0].getBestPeak().getDataFile()
                : clickedDataFile;

        Range<Double> mzRange = null;
        final List<Feature> selectedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
        for (final PeakListRow row : allClickedPeakListRows) {

            for (final Feature peak : row.getPeaks()) {
                if (mzRange == null) {
                    mzRange = peak.getRawDataPointsMZRange();
                } else {
                    mzRange = mzRange.span(peak.getRawDataPointsMZRange());
                }
            }

            final Feature filePeak = row.getPeak(selectedDataFile);
            if (filePeak != null) {

                selectedPeaks.add(filePeak);

                // Label the peak with the row's preferred identity.
                final PeakIdentity identity = row.getPreferredPeakIdentity();
                if (identity != null) {
                    labelsMap.put(filePeak, identity.getName());
                }
            }
        }

        ScanSelection scanSelection = new ScanSelection(selectedDataFile.getDataRTRange(1), 1);

        TICVisualizerModule.showNewTICVisualizerWindow(new RawDataFile[] { selectedDataFile },
                selectedPeaks.toArray(new Feature[selectedPeaks.size()]), labelsMap, scanSelection,
                TICPlotType.BASEPEAK, mzRange);
    }

    if (showXICSetupItem.equals(src) && allClickedPeakListRows.length != 0) {

        // Map peaks to their identity labels.
        final Map<Feature, String> labelsMap = new HashMap<Feature, String>(allClickedPeakListRows.length);

        final RawDataFile[] selectedDataFiles = clickedDataFile == null ? peakList.getRawDataFiles()
                : new RawDataFile[] { clickedDataFile };

        Range<Double> mzRange = null;
        final ArrayList<Feature> allClickedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
        final ArrayList<Feature> selectedClickedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
        for (final PeakListRow row : allClickedPeakListRows) {

            // Label the peak with the row's preferred identity.
            final PeakIdentity identity = row.getPreferredPeakIdentity();

            for (final Feature peak : row.getPeaks()) {

                allClickedPeaks.add(peak);
                if (peak.getDataFile() == clickedDataFile) {
                    selectedClickedPeaks.add(peak);
                }

                if (mzRange == null) {
                    mzRange = peak.getRawDataPointsMZRange();
                } else {
                    mzRange = mzRange.span(peak.getRawDataPointsMZRange());
                }

                if (identity != null) {
                    labelsMap.put(peak, identity.getName());
                }
            }
        }

        ScanSelection scanSelection = new ScanSelection(selectedDataFiles[0].getDataRTRange(1), 1);

        TICVisualizerModule.setupNewTICVisualizer(
                MZmineCore.getProjectManager().getCurrentProject().getDataFiles(), selectedDataFiles,
                allClickedPeaks.toArray(new Feature[allClickedPeaks.size()]),
                selectedClickedPeaks.toArray(new Feature[selectedClickedPeaks.size()]), labelsMap,
                scanSelection, mzRange);
    }

    if (show2DItem.equals(src)) {

        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {

            TwoDVisualizerModule.show2DVisualizerSetupDialog(showPeak.getDataFile(), getPeakMZRange(showPeak),
                    getPeakRTRange(showPeak));
        }
    }

    if (show3DItem.equals(src)) {

        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {

            ThreeDVisualizerModule.setupNew3DVisualizer(showPeak.getDataFile(), getPeakMZRange(showPeak),
                    getPeakRTRange(showPeak));
        }
    }

    if (manuallyDefineItem.equals(src)) {

        ManualPeakPickerModule.runManualDetection(clickedDataFile, clickedPeakListRow, peakList, table);
    }

    if (showSpectrumItem.equals(src)) {

        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {

            SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(),
                    showPeak.getRepresentativeScanNumber(), showPeak);
        }
    }

    if (showMSMSItem.equals(src)) {

        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {

            final int scanNumber = showPeak.getMostIntenseFragmentScanNumber();
            if (scanNumber > 0) {
                SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), scanNumber);
            } else {
                MZmineCore.getDesktop().displayMessage(window,
                        "There is no fragment for "
                                + MZmineCore.getConfiguration().getMZFormat().format(showPeak.getMZ())
                                + " m/z in the current raw data.");
            }
        }
    }

    if (showIsotopePatternItem.equals(src)) {

        final Feature showPeak = getSelectedPeak();
        if (showPeak != null && showPeak.getIsotopePattern() != null) {

            SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(),
                    showPeak.getRepresentativeScanNumber(), showPeak.getIsotopePattern());
        }
    }

    if (formulaItem != null && formulaItem.equals(src)) {

        FormulaPredictionModule.showSingleRowIdentificationDialog(clickedPeakListRow);
    }

    if (dbSearchItem != null && dbSearchItem.equals(src)) {

        OnlineDBSearchModule.showSingleRowIdentificationDialog(clickedPeakListRow);
    }

    if (nistSearchItem != null && nistSearchItem.equals(src)) {

        NistMsSearchModule.singleRowSearch(peakList, clickedPeakListRow);
    }

    if (addNewRowItem.equals(src)) {

        // find maximum ID and add 1
        int newID = 1;
        for (final PeakListRow row : peakList.getRows()) {
            if (row.getID() >= newID) {
                newID = row.getID() + 1;
            }
        }

        // create a new row
        final PeakListRow newRow = new SimplePeakListRow(newID);
        ManualPeakPickerModule.runManualDetection(peakList.getRawDataFiles(), newRow, peakList, table);

    }

    if (showPeakRowSummaryItem.equals(src)) {

        PeakSummaryVisualizerModule.showNewPeakSummaryWindow(clickedPeakListRow);
    }

    if (exportIsotopesItem.equals(src)) {
        IsotopePatternExportModule.exportIsotopePattern(clickedPeakListRow);
    }

    if (exportMSMSItem.equals(src)) {
        MSMSExportModule.exportMSMS(clickedPeakListRow);
    }

    if (clearIdsItem.equals(src)) {

        // Delete identities of selected rows.
        for (final PeakListRow row : allClickedPeakListRows) {

            // Selected row index.
            for (final PeakIdentity id : row.getPeakIdentities()) {

                // Remove id.
                row.removePeakIdentity(id);
            }
        }

        // Update table GUI.
        updateTableGUI();
    }

    if (copyIdsItem.equals(src) && allClickedPeakListRows.length > 0) {

        final PeakIdentity id = allClickedPeakListRows[0].getPreferredPeakIdentity();
        if (id != null) {

            copiedId = (PeakIdentity) id.clone();
        }
    }

    if (pasteIdsItem.equals(src) && copiedId != null) {

        // Paste identity into selected rows.
        for (final PeakListRow row : allClickedPeakListRows) {

            row.setPreferredPeakIdentity((PeakIdentity) copiedId.clone());
        }

        // Update table GUI.
        updateTableGUI();
    }
}

From source file:edu.mit.streamjit.impl.compiler2.Storage.java

/**
 * Compute this storage's steady-state throughput and capacity.
 * @param externalSchedule the external schedule
 *//*  w  ww . jav a 2 s  .com*/
public void computeSteadyStateRequirements(Map<ActorGroup, Integer> externalSchedule) {
    Range<Integer> readIndices = readIndexSpan(externalSchedule);
    Range<Integer> writeIndices = writeIndexSpan(externalSchedule);
    assert readIndices.isEmpty() == writeIndices.isEmpty() : readIndices + " " + writeIndices;
    //We need to know the count of indices, so we can't just use the span
    //here.  There may be a lot of indices so writeIndices will use a lot of
    //memory.  But we know (assume) there are no overwrites, so we'll count.
    this.throughput = 0;
    for (Actor a : upstream()) {
        int iterations = a.group().schedule().get(a) * externalSchedule.get(a.group());
        for (int output = 0; output < a.outputs().size(); ++output)
            if (a.outputs().get(output).equals(this))
                this.throughput += iterations * a.push(output).max();
    }
    this.steadyStateCapacity = ContiguousSet.create(readIndices.span(writeIndices), DiscreteDomain.integers())
            .size();
}

From source file:net.sf.mzmine.modules.projectmethods.projectload.version_2_3.PeakListOpenHandler_2_3.java

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
 *      java.lang.String, java.lang.String)
 *//*from w w w  .  j  av a2  s . co m*/
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {

    if (canceled)
        throw new SAXException("Parsing canceled");

    // <NAME>
    if (qName.equals(PeakListElementName_2_3.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading peak list: " + name);
        peakListName = name;
    }

    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_3.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }

    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_3.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_3.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException(
                    "Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }

    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_3.SCAN_ID.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        scanNumbers = new int[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                scanNumbers[i] = dataInputStream.readInt();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <REPRESENTATIVE_SCAN>
    if (qName.equals(PeakListElementName_2_3.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName.equals(PeakListElementName_2_3.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_3.MZ.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        masses = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                masses[i] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_3.HEIGHT.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        intensities = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                intensities[i] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <PEAK>
    if (qName.equals(PeakListElementName_2_3.PEAK.getElementName())) {

        DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
        Range<Double> peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
        RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);

        if (dataFile == null)
            throw new SAXException("Error in project: data file " + peakColumnID + " not found");

        for (int i = 0; i < numOfMZpeaks; i++) {

            Scan sc = dataFile.getScan(scanNumbers[i]);
            double retentionTime = sc.getRetentionTime();

            double mz = masses[i];
            double intensity = intensities[i];

            if ((peakRTRange == null) || (peakIntensityRange == null)) {
                peakRTRange = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            if (mz > 0.0) {
                mzPeaks[i] = new SimpleDataPoint(mz, intensity);
                if (peakMZRange == null)
                    peakMZRange = Range.singleton(mz);
                else
                    peakMZRange = peakMZRange.span(Range.singleton(mz));
            }
        }

        FeatureStatus status = FeatureStatus.valueOf(peakStatus);

        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status,
                representativeScan, fragmentScan, peakRTRange, peakMZRange, peakIntensityRange);

        peak.setCharge(currentPeakCharge);

        if (currentIsotopes.size() > 0) {
            SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
                    currentIsotopes.toArray(new DataPoint[0]), currentIsotopePatternStatus,
                    currentIsotopePatternDescription);
            peak.setIsotopePattern(newPattern);
            currentIsotopes.clear();
        }

        buildingRow.addPeak(dataFile, peak);

    }

    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_3.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }

    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_3.PEAK_IDENTITY.getElementName())) {
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }

    // <ROW>
    if (qName.equals(PeakListElementName_2_3.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }

    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_3.ISOTOPE.getElementName())) {
        String text = getTextOfElement();
        String items[] = text.split(":");
        double mz = Double.valueOf(items[0]);
        double intensity = Double.valueOf(items[1]);
        DataPoint isotope = new SimpleDataPoint(mz, intensity);
        currentIsotopes.add(isotope);
    }

    if (qName.equals(PeakListElementName_2_3.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }

    if (qName.equals(PeakListElementName_2_3.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }

}

From source file:net.sf.mzmine.modules.projectmethods.projectload.version_2_5.PeakListOpenHandler_2_5.java

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
 *      java.lang.String, java.lang.String)
 *///from   w w  w.  j  a va  2  s .c  o m
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {

    if (canceled)
        throw new SAXException("Parsing canceled");

    // <NAME>
    if (qName.equals(PeakListElementName_2_5.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading peak list: " + name);
        peakListName = name;
    }

    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_5.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }

    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_5.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_5.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException(
                    "Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }

    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_5.SCAN_ID.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        scanNumbers = new int[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                scanNumbers[i] = dataInputStream.readInt();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <REPRESENTATIVE_SCAN>
    if (qName.equals(PeakListElementName_2_5.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName.equals(PeakListElementName_2_5.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_5.MZ.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        masses = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                masses[i] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_5.HEIGHT.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        intensities = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                intensities[i] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <PEAK>
    if (qName.equals(PeakListElementName_2_5.PEAK.getElementName())) {

        DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
        Range<Double> peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
        RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);

        if (dataFile == null)
            throw new SAXException("Error in project: data file " + peakColumnID + " not found");

        for (int i = 0; i < numOfMZpeaks; i++) {

            Scan sc = dataFile.getScan(scanNumbers[i]);
            double retentionTime = sc.getRetentionTime();

            double mz = masses[i];
            double intensity = intensities[i];

            if ((peakRTRange == null) || (peakIntensityRange == null)) {
                peakRTRange = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            if (mz > 0.0) {
                mzPeaks[i] = new SimpleDataPoint(mz, intensity);
                if (peakMZRange == null)
                    peakMZRange = Range.singleton(mz);
                else
                    peakMZRange = peakMZRange.span(Range.singleton(mz));
            }
        }

        FeatureStatus status = FeatureStatus.valueOf(peakStatus);

        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status,
                representativeScan, fragmentScan, peakRTRange, peakMZRange, peakIntensityRange);

        peak.setCharge(currentPeakCharge);

        if (currentIsotopes.size() > 0) {
            SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
                    currentIsotopes.toArray(new DataPoint[0]), currentIsotopePatternStatus,
                    currentIsotopePatternDescription);
            peak.setIsotopePattern(newPattern);
            currentIsotopes.clear();
        }

        buildingRow.addPeak(dataFile, peak);

    }

    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_5.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }

    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_5.PEAK_IDENTITY.getElementName())) {
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }

    // <ROW>
    if (qName.equals(PeakListElementName_2_5.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }

    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_5.ISOTOPE.getElementName())) {
        String text = getTextOfElement();
        String items[] = text.split(":");
        double mz = Double.valueOf(items[0]);
        double intensity = Double.valueOf(items[1]);
        DataPoint isotope = new SimpleDataPoint(mz, intensity);
        currentIsotopes.add(isotope);
    }

    if (qName.equals(PeakListElementName_2_5.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }

    if (qName.equals(PeakListElementName_2_5.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }

}

From source file:net.sf.mzmine.modules.projectmethods.projectload.version_2_0.PeakListOpenHandler_2_0.java

/**
 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
 *      java.lang.String, java.lang.String)
 *//*from  www. j  ava2  s .  c om*/
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {

    if (canceled)
        throw new SAXException("Parsing canceled");

    // <NAME>
    if (qName.equals(PeakListElementName_2_0.PEAKLIST_NAME.getElementName())) {
        name = getTextOfElement();
        logger.info("Loading peak list: " + name);
        peakListName = name;
    }

    // <PEAKLIST_DATE>
    if (qName.equals(PeakListElementName_2_0.PEAKLIST_DATE.getElementName())) {
        dateCreated = getTextOfElement();
    }

    // <QUANTITY>
    if (qName.equals(PeakListElementName_2_0.QUANTITY.getElementName())) {
        String text = getTextOfElement();
        totalRows = Integer.parseInt(text);
    }

    // <RAW_FILE>
    if (qName.equals(PeakListElementName_2_0.RAWFILE.getElementName())) {
        rawDataFileID = getTextOfElement();
        RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
        if (dataFile == null) {
            throw new SAXException(
                    "Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
        }
        currentPeakListDataFiles.add(dataFile);
    }

    // <SCAN_ID>
    if (qName.equals(PeakListElementName_2_0.SCAN_ID.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        scanNumbers = new int[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                scanNumbers[i] = dataInputStream.readInt();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <REPRESENTATIVE_SCAN>
    if (qName.equals(PeakListElementName_2_0.REPRESENTATIVE_SCAN.getElementName())) {
        representativeScan = Integer.valueOf(getTextOfElement());
    }

    // <FRAGMENT_SCAN>

    if (qName.equals(PeakListElementName_2_0.FRAGMENT_SCAN.getElementName())) {
        fragmentScan = Integer.valueOf(getTextOfElement());
    }

    // <MASS>
    if (qName.equals(PeakListElementName_2_0.MZ.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        masses = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                masses[i] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <HEIGHT>
    if (qName.equals(PeakListElementName_2_0.HEIGHT.getElementName())) {

        byte[] bytes = Base64.decodeToBytes(getTextOfElement());
        // make a data input stream
        DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
        intensities = new double[numOfMZpeaks];
        for (int i = 0; i < numOfMZpeaks; i++) {
            try {
                intensities[i] = (double) dataInputStream.readFloat();
            } catch (IOException ex) {
                throw new SAXException(ex);
            }
        }
    }

    // <PEAK>
    if (qName.equals(PeakListElementName_2_0.PEAK.getElementName())) {

        DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
        Range<Double> peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
        RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);

        if (dataFile == null)
            throw new SAXException("Error in project: data file " + peakColumnID + " not found");

        for (int i = 0; i < numOfMZpeaks; i++) {

            Scan sc = dataFile.getScan(scanNumbers[i]);
            double retentionTime = sc.getRetentionTime();

            double mz = masses[i];
            double intensity = intensities[i];

            if ((peakRTRange == null) || (peakIntensityRange == null)) {
                peakRTRange = Range.singleton(retentionTime);
                peakIntensityRange = Range.singleton(intensity);
            } else {
                peakRTRange = peakRTRange.span(Range.singleton(retentionTime));
                peakIntensityRange = peakIntensityRange.span(Range.singleton(intensity));
            }
            if (mz > 0.0) {
                mzPeaks[i] = new SimpleDataPoint(mz, intensity);
                if (peakMZRange == null)
                    peakMZRange = Range.singleton(mz);
                else
                    peakMZRange = peakMZRange.span(Range.singleton(mz));
            }
        }

        FeatureStatus status = FeatureStatus.valueOf(peakStatus);

        SimpleFeature peak = new SimpleFeature(dataFile, mass, rt, height, area, scanNumbers, mzPeaks, status,
                representativeScan, fragmentScan, peakRTRange, peakMZRange, peakIntensityRange);

        peak.setCharge(currentPeakCharge);

        if (currentIsotopes.size() > 0) {
            SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
                    currentIsotopes.toArray(new DataPoint[0]), currentIsotopePatternStatus,
                    currentIsotopePatternDescription);
            peak.setIsotopePattern(newPattern);
            currentIsotopes.clear();
        }

        buildingRow.addPeak(dataFile, peak);

    }

    // <IDENTITY_PROPERTY>
    if (qName.equals(PeakListElementName_2_0.IDPROPERTY.getElementName())) {
        identityProperties.put(identityPropertyName, getTextOfElement());
    }

    // <PEAK_IDENTITY>
    if (qName.equals(PeakListElementName_2_0.PEAK_IDENTITY.getElementName())) {
        String content = getTextOfElement();
        if (identityProperties.get(PeakIdentity.PROPERTY_NAME) == null)
            identityProperties.put(PeakIdentity.PROPERTY_NAME, content);
        SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
        buildingRow.addPeakIdentity(identity, preferred);
    }

    // <ROW>
    if (qName.equals(PeakListElementName_2_0.ROW.getElementName())) {
        buildingPeakList.addRow(buildingRow);
        buildingRow = null;
        parsedRows++;
    }

    // <ISOTOPE>
    if (qName.equals(PeakListElementName_2_0.ISOTOPE.getElementName())) {
        String text = getTextOfElement();
        String items[] = text.split(":");
        double mz = Double.valueOf(items[0]);
        double intensity = Double.valueOf(items[1]);
        DataPoint isotope = new SimpleDataPoint(mz, intensity);
        currentIsotopes.add(isotope);
    }

    if (qName.equals(PeakListElementName_2_0.METHOD_NAME.getElementName())) {
        String appliedMethod = getTextOfElement();
        appliedMethods.add(appliedMethod);
    }

    if (qName.equals(PeakListElementName_2_0.METHOD_PARAMETERS.getElementName())) {
        String appliedMethodParam = getTextOfElement();
        appliedMethodParameters.add(appliedMethodParam);
    }

}