public void readFileAndGenerate(boolean onlyUniquePeptides, ISpectrumDataFilter... filters) {
@SuppressWarnings("UnusedDeclaration")
int numberProcessed = 0;
@SuppressWarnings("UnusedDeclaration")
double lastRetentionTime = 0;
@SuppressWarnings("UnusedDeclaration")
int numberUnProcessed = 0;
try {
LineNumberReader rdr = new LineNumberReader(new FileReader(m_File));
String line = rdr.readLine();
while (line != null) {
if (line.contains("<spectrum_query")) {
String retention_time_sec = XMLUtil.extractAttribute(line, "retention_time_sec");
scan_id = XMLUtil.extractAttribute(line, "start_scan");
if (retention_time_sec == null) {
lastRetentionTime = 0;
} else {
try {
lastRetentionTime = Double.parseDouble(retention_time_sec.trim());
} catch (NumberFormatException e) {
lastRetentionTime = 0;
}
}
}
//noinspection StatementWithEmptyBody,StatementWithEmptyBody
if (line.contains("<search_result")) {
String[] searchHitLines = readSearchHitLines(line, rdr);
// System.out.println(line);
boolean processed =
handleSearchHit(searchHitLines, lastRetentionTime, onlyUniquePeptides, filters);
if (processed) {
for (int i = 0; i < searchHitLines.length; i++) {
@SuppressWarnings("UnusedDeclaration")
String searchHitLine = searchHitLines[i];
}
numberProcessed++;
} else numberUnProcessed++;
}
line = rdr.readLine();
}
//noinspection UnnecessaryReturnStatement
return;
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public static IdentifiedPSM processPeptide(final String line, double retentionTime, String id) {
String peptide = XMLUtil.extractAttribute(line, "peptide");
if (peptide == null) throw new IllegalArgumentException("bad line " + line);
Polypeptide polypeptide = Polypeptide.fromString(peptide);
polypeptide.setRetentionTime(retentionTime);
return new IdentifiedPSM(id, polypeptide);
}
public static IProtein processProtein(final String line) {
String peptide = XMLUtil.extractAttribute(line, "protein_descr");
if (peptide == null) throw new IllegalArgumentException("bad line " + line);
return Protein.getProtein(peptide, "", "", null);
}