switch (column) {
case 0:
return row + 1;
case 1:
ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
String mainMatch = proteinMatch.getMainMatch();
return peptideShakerGUI.getDisplayFeaturesGenerator().addDatabaseLink(mainMatch);
case 2:
proteinMatch = identification.getProteinMatch(proteinKey);
String description = "";
try {
description = sequenceFactory.getHeader(proteinMatch.getMainMatch()).getSimpleProteinDescription();
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
return description;
case 3:
HashMap<Integer, Double> sequenceCoverage;
try {
sequenceCoverage = peptideShakerGUI.getIdentificationFeaturesGenerator().getSequenceCoverage(proteinKey);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
return Double.NaN;
}
Double sequenceCoverageConfident = 100 * sequenceCoverage.get(MatchValidationLevel.confident.getIndex());
Double sequenceCoverageDoubtful = 100 * sequenceCoverage.get(MatchValidationLevel.doubtful.getIndex());
Double sequenceCoverageNotValidated = 100 * sequenceCoverage.get(MatchValidationLevel.not_validated.getIndex()); //@TODO: this does not seem to be used?
double possibleCoverage = 100;
try {
possibleCoverage = 100 * peptideShakerGUI.getIdentificationFeaturesGenerator().getObservableCoverage(proteinKey);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
ArrayList<Double> doubleValues = new ArrayList<Double>();
doubleValues.add(sequenceCoverageConfident);
doubleValues.add(sequenceCoverageDoubtful);
doubleValues.add(sequenceCoverageNotValidated);
doubleValues.add(possibleCoverage - sequenceCoverageConfident - sequenceCoverageDoubtful - sequenceCoverageNotValidated);
ArrrayListDataPoints arrrayListDataPoints = new ArrrayListDataPoints(doubleValues, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumExceptLastNumber);
return arrrayListDataPoints;
case 4:
try {
proteinMatch = identification.getProteinMatch(proteinKey);
double nConfidentPeptides = peptideShakerGUI.getIdentificationFeaturesGenerator().getNConfidentPeptides(proteinKey);
double nDoubtfulPeptides = peptideShakerGUI.getIdentificationFeaturesGenerator().getNValidatedPeptides(proteinKey) - nConfidentPeptides;
doubleValues = new ArrayList<Double>();
doubleValues.add(nConfidentPeptides);
doubleValues.add(nDoubtfulPeptides);
doubleValues.add(proteinMatch.getPeptideCount() - nConfidentPeptides - nDoubtfulPeptides);
arrrayListDataPoints = new ArrrayListDataPoints(doubleValues, JSparklinesArrayListBarChartTableCellRenderer.ValueDisplayType.sumOfNumbers);
return arrrayListDataPoints;
} catch (Exception e) {
peptideShakerGUI.catchException(e);
return Double.NaN;