/**
* Insert bar charts into the table.
*/
private void insertBarCharts() {
AnnotationPreferences annotationPreferences = peptideShakerGUI.getAnnotationPreferences();
PtmtableContent tempContent, tableContent = new PtmtableContent();
MSnSpectrum spectrum;
SpectrumMatch spectrumMatch;
SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
PTMFactory ptmFactory = PTMFactory.getInstance();
String ptmName = ptm.getName(), shortName = ptmFactory.getShortName(ptmName);
for (String spectrumKey : spectrumKeys) {
try {
spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
tempContent = PtmtableContent.getPTMTableContent(peptide, ptm, nPTM, spectrum, annotationPreferences.getIonTypes(),
annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value,
annotationPreferences.getFragmentIonAccuracy(), spectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()));
tempContent.normalize();
tableContent.addAll(tempContent);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
}
for (int aa = 0; aa < peptide.getSequence().length(); aa++) {
int column = 1;
for (int modCpt = 0; modCpt <= nPTM; modCpt++) {
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.A_ION)) {
setValueAt(tableContent.getQuantile(modCpt, PeptideFragmentIon.A_ION, aa + 1, 0.75), aa, column);
column++;
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.B_ION)) {
setValueAt(tableContent.getQuantile(modCpt, PeptideFragmentIon.B_ION, aa + 1, 0.75), aa, column);
column++;
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.C_ION)) {
setValueAt(tableContent.getQuantile(modCpt, PeptideFragmentIon.C_ION, aa + 1, 0.75), aa, column);
column++;
}
}
column++;
for (int modCpt = 0; modCpt <= nPTM; modCpt++) {
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.X_ION)) {
setValueAt(tableContent.getQuantile(modCpt, PeptideFragmentIon.X_ION, aa + 1, 0.75), aa, column);
column++;
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.Y_ION)) {
setValueAt(tableContent.getQuantile(modCpt, PeptideFragmentIon.Y_ION, aa + 1, 0.75), aa, column);
column++;
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.Z_ION)) {
setValueAt(tableContent.getQuantile(modCpt, PeptideFragmentIon.Z_ION, aa + 1, 0.75), aa, column);
column++;
}
}
}
// set the column renderers
for (int modCpt = 0; modCpt <= nPTM; modCpt++) {
String modification = "";
if (modCpt > 0) {
if (modCpt == 1) {
modification = " <" + shortName + ">";
} else {
modification = " <" + modCpt + shortName + ">";
}
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.A_ION)) {
try {
getColumn("a" + modification).setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, tableContent.getMaxIntensity(),
SpectrumPanel.determineFragmentIonColor(new PeptideFragmentIon(PeptideFragmentIon.A_ION), false)));
((JSparklinesBarChartTableCellRenderer) getColumn("a" + modification).getCellRenderer()).setMinimumChartValue(0);
} catch (IllegalArgumentException e) {
// do nothing
}
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.B_ION)) {
try {
getColumn("b" + modification).setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, tableContent.getMaxIntensity(),
SpectrumPanel.determineFragmentIonColor(new PeptideFragmentIon(PeptideFragmentIon.B_ION), false)));
((JSparklinesBarChartTableCellRenderer) getColumn("b" + modification).getCellRenderer()).setMinimumChartValue(0);
} catch (IllegalArgumentException e) {
// do nothing
}
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.C_ION)) {
try {
getColumn("c" + modification).setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, tableContent.getMaxIntensity(),
SpectrumPanel.determineFragmentIonColor(new PeptideFragmentIon(PeptideFragmentIon.C_ION), false)));
((JSparklinesBarChartTableCellRenderer) getColumn("c" + modification).getCellRenderer()).setMinimumChartValue(0);
} catch (IllegalArgumentException e) {
// do nothing
}
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.X_ION)) {
try {
getColumn("x" + modification).setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, tableContent.getMaxIntensity(),
SpectrumPanel.determineFragmentIonColor(new PeptideFragmentIon(PeptideFragmentIon.X_ION), false)));
((JSparklinesBarChartTableCellRenderer) getColumn("x" + modification).getCellRenderer()).setMinimumChartValue(0);
} catch (IllegalArgumentException e) {
// do nothing
}
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.Y_ION)) {
try {
getColumn("y" + modification).setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, tableContent.getMaxIntensity(),
SpectrumPanel.determineFragmentIonColor(new PeptideFragmentIon(PeptideFragmentIon.Y_ION), false)));
((JSparklinesBarChartTableCellRenderer) getColumn("y" + modification).getCellRenderer()).setMinimumChartValue(0);
} catch (IllegalArgumentException e) {
// do nothing
}
}
if (annotationPreferences.getFragmentIonTypes().contains(PeptideFragmentIon.Z_ION)) {
try {
getColumn("z" + modification).setCellRenderer(new JSparklinesBarChartTableCellRenderer(PlotOrientation.HORIZONTAL, tableContent.getMaxIntensity(),
SpectrumPanel.determineFragmentIonColor(new PeptideFragmentIon(PeptideFragmentIon.Z_ION), false)));
((JSparklinesBarChartTableCellRenderer) getColumn("z" + modification).getCellRenderer()).setMinimumChartValue(0);
} catch (IllegalArgumentException e) {