/**
* getPeptidesForProteinAtConfidenceLevel.
*
* @param protein a {@link com.compomics.thermo_msf_parser_API.lowmeminstance.model.ProteinLowMem}
* object.
* @param msfFile a {@link com.compomics.thermo_msf_parser_API.lowmeminstance.model.MsfFile}
* object.
* @param confidenceLevel a int.
* @return a {@link java.util.List} object.
*/
public List<PeptideLowMem> getPeptidesForProteinAtConfidenceLevel(
ProteinLowMem protein, MsfFile msfFile, int confidenceLevel) {
List<PeptideLowMem> foundPeptides = new ArrayList<PeptideLowMem>();
counter = 0;
try {
Statement stat = null;
try {
stat = msfFile.getConnection().createStatement();
if (msfFile.getVersion() == MsfVersion.VERSION1_2) {
ResultSet rs =
stat.executeQuery(
"select peptides.PeptideID as PeptideID,ConfidenceLevel,Sequence,TotalIonsCount,MatchedIonsCount,Annotation,ProcessingNodeNumber, s.*, FileID as file from spectrumheaders as s, masspeaks, Peptides,Spectra as sp,(select PeptideID as ID from PeptidesProteins where ProteinID ="
+ protein.getProteinID()
+ ") as pepid where pepid.ID = peptides.PeptideID and masspeaks.masspeakid = s.masspeakid and s.SpectrumID = peptides.SpectrumID and sp.UniqueSpectrumID = s.UniqueSpectrumID and ConfidenceLevel = "
+ confidenceLevel
+ "order by peptides.PeptideID");
while (rs.next()) {
PeptideLowMem lPeptide =
new PeptideLowMem(
rs.getInt("PeptideID"),
rs.getInt("SpectrumID"),
rs.getInt("ConfidenceLevel"),
rs.getString("Sequence"),
rs.getInt("TotalIonsCount"),
rs.getInt("MatchedIonsCount"),
rs.getString("Annotation"),
rs.getInt("ProcessingNodeNumber"),
msfFile.getAminoAcids());
// iScoreType.addScoresToPeptide(lPeptide,protein.getConnection());
lPeptide.setParentSpectrum(
new SpectrumLowMem(
rs.getInt("SpectrumID"),
rs.getInt("UniqueSpectrumID"),
rs.getInt("MassPeakID"),
rs.getInt("LastScan"),
rs.getInt("FirstScan"),
rs.getInt("ScanNumbers"),
rs.getInt("Charge"),
rs.getDouble("RetentionTime"),
rs.getDouble("Mass"),
rs.getInt("ScanEventID")));
// TODO make initializer with fileID argument)
lPeptide.getParentSpectrum().setFileId(rs.getInt("file"));
// lPeptide.getParentSpectrum().setZippedSpectrumXML(rs.getBytes("Spectra"));
// TODO check speed of this
Statement customStat = msfFile.getConnection().createStatement();
ResultSet customRs =
customStat.executeQuery(
"select * from CustomDataPeptides where PeptideID = "
+ lPeptide.getPeptideId());
while (customRs.next()) {
lPeptide.addCustomDataField(
customRs.getInt("FieldID"), customRs.getString("FieldValue"));
}
customRs.close();
customStat.close();
foundPeptides.add(lPeptide);
counter++;
}
rs.close();
} else {
ResultSet rs =
stat.executeQuery(
"select peptides.PeptideID as peptideid,ConfidenceLevel,Sequence,TotalIonsCount,MatchedIonsCount,Annotation,MissedCleavages,UniquePeptideSequenceID,ProcessingNodeNumber, s.*,FileID as file from spectrumheaders as s, masspeaks, Peptides ,Spectra as sp,(select PeptideID as ID from PeptidesProteins where ProteinID ="
+ protein.getProteinID()
+ ") as pepid where pepid.ID = peptides.PeptideID and masspeaks.masspeakid = s.masspeakid and s.SpectrumID = peptides.SpectrumID and sp.UniqueSpectrumID = s.UniqueSpectrumID and ConfidenceLevel = "
+ confidenceLevel
+ " order by peptides.PeptideID");
while (rs.next()) {
PeptideLowMem lPeptide =
new PeptideLowMem(
rs.getInt("PeptideID"),
rs.getInt("SpectrumID"),
rs.getInt("ConfidenceLevel"),
rs.getString("Sequence"),
rs.getInt("TotalIonsCount"),
rs.getInt("MatchedIonsCount"),
rs.getString("Annotation"),
rs.getInt("ProcessingNodeNumber"),
msfFile.getAminoAcids());
lPeptide.setMissedCleavage(rs.getInt("MissedCleavages"));
lPeptide.setUniquePeptideSequenceId(rs.getInt("UniquePeptideSequenceID"));
lPeptide.setParentSpectrum(
new SpectrumLowMem(
rs.getInt("SpectrumID"),
rs.getInt("UniqueSpectrumID"),
rs.getInt("MassPeakID"),
rs.getInt("LastScan"),
rs.getInt("FirstScan"),
rs.getInt("ScanNumbers"),
rs.getInt("Charge"),
rs.getDouble("RetentionTime"),
rs.getDouble("Mass"),
rs.getInt("ScanEventID")));
// TODO make initializer with fileID argument)
lPeptide.getParentSpectrum().setFileId(rs.getInt("file"));
Statement customStat = msfFile.getConnection().createStatement();
ResultSet customRs =
customStat.executeQuery(
"select * from CustomDataPeptides where PeptideID = "
+ lPeptide.getPeptideId());
while (customRs.next()) {
lPeptide.addCustomDataField(
customRs.getInt("FieldID"), customRs.getString("FieldValue"));
}
customRs.close();
customStat.close();
foundPeptides.add(lPeptide);
counter++;
}
rs.close();
}
} finally {
if (stat != null) {
stat.close();
}
}
} catch (SQLException ex) {
logger.error(ex);
}
return foundPeptides;
}
