private static Database databaseSetUp(String fasta_file_name)
{
FastaFile f = Loader.parseFasta(fasta_file_name);
DigestedFastaFile df = PerformDigestion.performDigest(f, GlobalVar.NUM_MISSED_CLEAVAGES);
int numberOfProteinsInFasta = f.getAccessionToFullSequence().Count;
int numberOfPeptidesInDigestedFasta = df.getDigestedPeptideArray().Count;
log.Info("Fasta file: " + fasta_file_name);
log.Info("Num missed cleavages: " + GlobalVar.NUM_MISSED_CLEAVAGES);
log.Info("Number of proteins: " + numberOfProteinsInFasta);
log.Info("Number of peptides: " + numberOfPeptidesInDigestedFasta);
log.Debug("Constructing graph...");
Database g;
if (GlobalVar.isSimulationForFeatureExtraction == true)
{
g = new Database(f, df, true, false);
}
else
{
g = new Database(f, df, true, true);
}
log.Debug(g);
return(g);
}
//depricated
public static String GenerateConcacenatedDecoyFasta_MimicCometInternal(String fastaFile, String outputFilePath)
{
StreamWriter sw = new StreamWriter(outputFilePath);
DigestedFastaFile df = PerformDigestion.performDigest(fastaFile, GlobalVar.NUM_MISSED_CLEAVAGES, false);
List <DigestedPeptide> targetSequences = df.getDigestedPeptideArray();
String line;
foreach (DigestedPeptide targetSeq in targetSequences)
{
//write the target sequence
line = ">" + targetSeq.getAccession();
sw.WriteLine(line);
line = targetSeq.getSequence();
sw.WriteLine(line);
//write the decoy sequence
line = ">" + GlobalVar.DecoyPrefix + targetSeq.getAccession();
sw.WriteLine(line);
line = ReverseSequence_keepCTerm(targetSeq.getSequence());
sw.WriteLine(line);
}
sw.Close();
return(outputFilePath);
}
public Database(FastaFile fastaFile, DigestedFastaFile digestedFastaFile, bool _includeCarbamidoModification,
bool _includeRetentionTime, double _retentionTimeWindow)
{
includeCarbamidoModification = _includeCarbamidoModification;
includeRetentionTime = _includeRetentionTime;
retentionTimeWindow = _retentionTimeWindow;
log.Debug("Constructing graph...");
SequenceToPeptide = new Dictionary <String, Peptide>();
peptides = new List <Peptide>();
AccesstionToProtein = fastaFile.getAccessionToFullSequence();
addPeptides(digestedFastaFile.getDigestedPeptideArray());
log.Debug("Done constructing graph.");
}