Examples with KovatsIndex net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex used on opensource projects

Example 1 with KovatsIndex

use of net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method loadFile.

/**
 * @return number of loaded files
 */
private int loadFile() {
    File lastFile = parameterSet.getParameter(KovatsIndexExtractionParameters.lastSavedFile).getValue();
    JFileChooser chooser = new JFileChooser();
    FileNameExtensionFilter ff = new FileNameExtensionFilter("Comma-separated values", "csv");
    chooser.addChoosableFileFilter(ff);
    chooser.setFileFilter(ff);
    if (lastFile != null)
        chooser.setSelectedFile(lastFile);
    chooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    chooser.setMultiSelectionEnabled(true);
    if (chooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) {
        File[] f = chooser.getSelectedFiles();
        TreeMap<KovatsIndex, Double> values = new TreeMap<>();
        // combine all
        for (File cf : f) {
            try {
                List<String> lines = Files.readLines(cf, StandardCharsets.UTF_8);
                for (String s : lines) {
                    String[] value = s.split(",");
                    try {
                        double time = Double.parseDouble(value[1]);
                        KovatsIndex ki = KovatsIndex.getByString(value[0]);
                        // average if already inserted
                        if (values.get(ki) != null) {
                            time = (time + values.get(ki)) / 2.0;
                            values.put(ki, time);
                        } else {
                            values.put(ki, time);
                        }
                    } catch (Exception e) {
                    // this try catch only identifies value columns
                    }
                }
                // set last file
                setLastFile(cf);
            } catch (IOException e) {
                logger.log(Level.WARNING, "Cannot read lines of " + cf.getAbsolutePath(), e);
            }
        }
        // all files are combined
        // to values component
        setValues(values);
        return f.length;
    }
    return 0;
}

Example 2 with KovatsIndex

use of net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method updateKovatsList.

/**
 * Update kuvats list min max
 */
private void updateKovatsList() {
    updateParameterSetFromComponents();
    try {
        int min = parameterSet.getParameter(KovatsIndexExtractionParameters.minKovats).getValue();
        int max = parameterSet.getParameter(KovatsIndexExtractionParameters.maxKovats).getValue();
        KovatsIndex[] newValues = KovatsIndex.getRange(min, max);
        KovatsIndex[] newSelected = Stream.of(newValues).filter(k -> ArrayUtils.contains(selectedKovats, k)).toArray(KovatsIndex[]::new);
        parameterSet.getParameter(KovatsIndexExtractionParameters.kovats).setChoices(newValues);
        parameterSet.getParameter(KovatsIndexExtractionParameters.kovats).setValue(newSelected);
        MultiChoiceComponent kovatsc = (MultiChoiceComponent) getComponentForParameter(KovatsIndexExtractionParameters.kovats);
        kovatsc.setChoices(newValues);
        kovatsc.setValue(newSelected);
        revalidate();
        repaint();
        handleKovatsSelectionChange();
        // update parameters again
        updateParameterSetFromComponents();
    } catch (Exception e) {
    }
}

Example 3 with KovatsIndex

use of net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method getCsvTable.

/**
 * GNPS GC MS formatted table (comma-separated)
 *
 * @param values
 *
 * @return
 */
private String getCsvTable(TreeMap<KovatsIndex, Double> values) {
    StringBuilder s = new StringBuilder();
    String nl = "\n";
    // header for GNPS
    // alkane name, num carbon(int), rt (seconds)
    s.append("Compound_Name,Carbon_Number,RT" + nl);
    DecimalFormat f = new DecimalFormat("0.##");
    for (Entry<KovatsIndex, Double> e : values.entrySet()) {
        s.append(e.getKey().getAlkaneName());
        s.append(",");
        s.append(String.valueOf(e.getKey().getNumCarbon()));
        s.append(",");
        // export rt in seconds for GNPS GC
        s.append(f.format(e.getValue() * 60.0));
        s.append(nl);
    }
    return s.toString();
}

Example 4 with KovatsIndex

use of net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method kovatsValuesChanged.

/**
 * replace markers
 */
private void kovatsValuesChanged() {
    // parse values
    if (parseValues() && chart != null) {
        // 
        chart.getChart().getXYPlot().clearDomainMarkers();
        if (markers == null)
            markers = new ArrayList<>();
        else
            markers.clear();
        for (Entry<KovatsIndex, Double> e : parsedValues.entrySet()) {
            ValueMarker marker = new ValueMarker(e.getValue(), ColorPalettes.getPositiveColor(MZmineCore.getConfiguration().getColorVision()), markerStroke);
            marker.setLabelOffset(new RectangleInsets(10, 0, 0, 0));
            marker.setLabelFont(new Font("Arial", Font.PLAIN, 12));
            marker.setLabelBackgroundColor(Color.WHITE);
            marker.setLabel(e.getKey().getShortName());
            chart.getChart().getXYPlot().addDomainMarker(marker);
            markers.add(marker);
        }
        revalidate();
        repaint();
    }
}

Example 5 with KovatsIndex

use of net.sf.mzmine.modules.tools.kovats.KovatsValues.KovatsIndex in project mzmine2 by mzmine.

the class KovatsIndexExtractionDialog method pickRetentionTimes.

/**
 * Peak picking to define Kovats index retention times
 */
private void pickRetentionTimes() {
    updateParameterSetFromComponents();
    XYDataset data = getData();
    if (data == null)
        return;
    int items = data.getItemCount(0);
    List<Double> results = new ArrayList<>();
    // auto set noiselevel to max/20 if 0
    if (Double.compare(noiseLevel, 0d) <= 0) {
        for (int i = 0; i < items; i++) {
            double intensity = data.getYValue(0, i);
            noiseLevel = Math.max(noiseLevel, intensity);
        }
        noiseLevel = noiseLevel / 20.0;
    }
    double max = 0;
    double startI = Double.MAX_VALUE;
    double maxRT = 0;
    for (int i = 0; i < items; i++) {
        double rt = data.getXValue(0, i);
        double intensity = data.getYValue(0, i);
        // find max
        if (intensity > max && intensity >= noiseLevel) {
            max = intensity;
            maxRT = rt;
        }
        // minimize startI above noiseLevel
        if (intensity >= noiseLevel && (intensity < startI)) {
            startI = intensity;
            max = 0;
            maxRT = rt;
        }
        // is peak?
        if (max / startI > ratioEdge && max / intensity > ratioEdge) {
            // add peak
            results.add(maxRT);
            max = 0;
            startI = intensity;
            maxRT = rt;
        }
    }
    // set rt values
    StringBuilder s = new StringBuilder();
    int i = 0;
    double lastRT = 1;
    for (KovatsIndex ki : selectedKovats) {
        double rt = i < results.size() ? results.get(i) : lastRT + 1;
        s.append(ki.name() + ":" + rtFormat.format(rt) + ",");
        i++;
        lastRT = rt;
    }
    valuesComponent.setText(s.toString());
    kovatsValuesChanged();
}