use of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.ProteinSection in project mzmine2 by mzmine.
the class MascotParserUtils method parsePeptideInfo.
/*
* String "info" is divided into three sections by ";", which the first one is peptide, second
* protein and third is peptide terminals.
*
* Peptide section must have 11 elements: missed cleavages, peptide mass, delta mass, number of
* matched ions, aa sequence, peaks used from ion 1, variable modifications (binary code), ion
* score, ion series, peaks used from ions2, peaks used from ion 3
*
* Protein section must have 5 elements: accesion name, frame number, start, stop and multiplicity
*
* Peptide terminal section must have 2 elements; left aa, right aa of the sequence
*
* Example=' 1,743.428955,0.000893,5,KGAAQLR,25,000001000,27.19,0002001000000000000 ,0,0;
* "SPBC839.04":0:23:29:1,"SPBC2F12.07c":0:23:29:1,"SPAC1F7.13c":0:23:29:1; R,T:R,T:R,T '
*/
public static Peptide[] parsePeptideInfo(int queryNumber, String info, double mass, double massExpected, int precursorCharge, PeptideIdentityDataFile pepDataFile, double identityThreshold, boolean isTopScore) {
String[] tokens = info.split(";");
String peptideSection = tokens[0];
String proteinSection = tokens[1];
String terminalSection = tokens[2];
// Terminals
tokens = terminalSection.split(":");
String[] peptideInfos = new String[tokens.length];
for (int i = 0; i < tokens.length; i++) {
peptideInfos[i] = peptideSection + "," + tokens[i];
}
// Proteins
tokens = proteinSection.split(",");
String[] proteinInfos = new String[tokens.length];
for (int i = 0; i < tokens.length; i++) {
proteinInfos[i] = tokens[i];
}
if (proteinInfos.length != peptideInfos.length)
return null;
Vector<Peptide> peptides = new Vector<Peptide>();
// Peptide
for (int pepIndex = 0; pepIndex < peptideInfos.length; pepIndex++) {
tokens = peptideInfos[pepIndex].split(",");
int missedCleavages = Integer.parseInt(tokens[0]);
double precursorMass = Double.parseDouble(tokens[1]);
double deltaMass = Double.parseDouble(tokens[2]);
String sequence = tokens[11] + tokens[4] + tokens[12];
String modSeries = tokens[6];
double ionScore = Double.parseDouble(tokens[7]);
if (ionScore >= identityThreshold)
continue;
Peptide peptide = new Peptide(queryNumber, sequence, ionScore, mass, massExpected, precursorCharge, precursorMass, deltaMass, missedCleavages, null, "Mascot", isTopScore);
HashMap<Integer, ModificationPeptide> modifications = new HashMap<Integer, ModificationPeptide>();
ModificationPeptide[] searchedMods = pepDataFile.getSearchedModifications();
// site.
for (int pos = 0; pos < modSeries.length(); pos++) {
if (modSeries.charAt(pos) == '1') {
char aa = sequence.charAt(pos);
for (int index = 0; index < searchedMods.length; index++) {
if (searchedMods[index].getSite() == aa) {
modifications.put(pos, searchedMods[index]);
}
}
}
}
peptide.setModifications(modifications);
// Ion serie
PeptideIonSerie peptideIonSerie = parseIonSeriesSignificance(tokens[8]);
peptide.setIonSeries(peptideIonSerie);
// Calculate fragmentation
PeptideFragmentation fragmentation = new PeptideFragmentation(peptide, pepDataFile);
peptide.setFragmentation(fragmentation);
// Protein info
ProteinSection section;
tokens = proteinInfos[pepIndex].split(":");
String sysname = tokens[0].replace("\"", "");
Protein protein = pepDataFile.getProtein(sysname);
if (protein == null)
protein = new Protein(sysname);
int startRegion = Integer.parseInt(tokens[2]);
int stopRegion = Integer.parseInt(tokens[3]);
int multiplicity = Integer.parseInt(tokens[4]);
section = new ProteinSection(startRegion, stopRegion, multiplicity);
// Link peptide and protein
peptide.setProtein(protein);
protein.addPeptide(peptide, section, isTopScore);
peptides.add(peptide);
}
return peptides.toArray(new Peptide[0]);
}
use of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.ProteinSection in project mzmine2 by mzmine.
the class ProteomeUtils method peptideToString.
/**
* Common utility method to be used as Peptide.toString() method
*
* @param Peptide Peptide to be converted to String
* @return String representation of the peptide
*/
public static String peptideToString(Peptide peptide) {
StringBuffer buf = new StringBuffer();
Format mzFormat = MZmineCore.getConfiguration().getMZFormat();
Protein protein = peptide.getProtein();
ProteinSection section;
section = protein.getSection(peptide);
buf.append(protein.getSysname() + ":" + section.getName() + "; " + protein.getHits() + " hits");
buf.append("\n" + peptide.getSequence());
buf.append("\nPeptideMz ");
buf.append(mzFormat.format(peptide.getMass()));
buf.append(" ;CalculatedMz ");
buf.append(mzFormat.format(peptide.getMassExpected()));
buf.append(" ;Score ");
buf.append(peptide.getIonScore());
buf.append(" \nCharge ");
buf.append(peptide.getPrecursorCharge());
buf.append(" ;FragmentScan ");
buf.append(peptide.getScan().getScanNumber());
return buf.toString();
}
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