/**
* Constructor.
*
* @param exportFeatures the features to export in this section
* @param indexes indicates whether the line index should be written
* @param header indicates whether the table header should be written
* @param writer the writer which will write to the file
*/
public PsPeptideSection(
ArrayList<ExportFeature> exportFeatures,
boolean indexes,
boolean header,
ExportWriter writer) {
ArrayList<ExportFeature> psmFeatures = new ArrayList<ExportFeature>();
for (ExportFeature exportFeature : exportFeatures) {
if (exportFeature instanceof PsPeptideFeature) {
peptideFeatures.add((PsPeptideFeature) exportFeature);
} else if (exportFeature instanceof PsPsmFeature
|| exportFeature instanceof PsIdentificationAlgorithmMatchesFeature
|| exportFeature instanceof PsFragmentFeature) {
psmFeatures.add(exportFeature);
} else {
throw new IllegalArgumentException(
"Export feature of type " + exportFeature.getClass() + " not recognized.");
}
}
Collections.sort(peptideFeatures);
if (!psmFeatures.isEmpty()) {
psmSection = new PsPsmSection(psmFeatures, indexes, header, writer);
}
this.indexes = indexes;
this.header = header;
this.writer = writer;
}
/**
* Writes the title of the section.
*
* @throws IOException exception thrown whenever an error occurred while writing the file
*/
public void writeHeader() throws IOException {
if (indexes) {
writer.writeHeaderText("");
writer.addSeparator();
}
boolean firstColumn = true;
for (ExportFeature exportFeature : peptideFeatures) {
if (firstColumn) {
firstColumn = false;
} else {
writer.addSeparator();
}
writer.writeHeaderText(exportFeature.getTitle());
}
writer.newLine();
}