/*
* public static int TargetDecoyComparison(Protein left, Protein right)
* {
* if (left.Target)
* if (right.Target)
* return 0;
* else
* return -1;
* else
* if (right.Target)
* return 1;
* else
* return 0;
* }//*/
public IEnumerable <Peptide> Digest(Protease protease, int maximumMissedCleavages, InitiatorMethionineBehavior initiatorMethionineBehavior,
int?minimumPeptideLength, int?maximumPeptideLength, bool onTheFlyDecoy)
{
List <int> indices = protease.GetDigestionSiteIndices(this);
indices.Insert(0, -1);
indices.Add(Length - 1);
for (int missed_cleavages = 0; missed_cleavages <= maximumMissedCleavages; missed_cleavages++)
{
for (int i = 0; i < indices.Count - missed_cleavages - 1; i++)
{
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Cleave || indices[i] + 1 != 0 || this[0] != 'M')
{
Peptide peptide = new Peptide(this, indices[i] + 1, indices[i + missed_cleavages + 1], missed_cleavages);
if ((!minimumPeptideLength.HasValue || peptide.Length >= minimumPeptideLength.Value) &&
(!maximumPeptideLength.HasValue || peptide.Length <= maximumPeptideLength.Value))
{
yield return(peptide);
if (onTheFlyDecoy)
{
yield return(new Peptide(this, indices[i + missed_cleavages + 1], indices[i] + 1, missed_cleavages));
}
}
}
if (initiatorMethionineBehavior != InitiatorMethionineBehavior.Retain && indices[i] + 1 == 0 && this[0] == 'M')
{
Peptide peptide_without_initiator_methionine = new Peptide(this, indices[i] + 1 + 1, indices[i + missed_cleavages + 1], missed_cleavages);
if ((!minimumPeptideLength.HasValue || peptide_without_initiator_methionine.Length >= minimumPeptideLength.Value) &&
(!maximumPeptideLength.HasValue || peptide_without_initiator_methionine.Length <= maximumPeptideLength.Value))
{
yield return(peptide_without_initiator_methionine);
if (onTheFlyDecoy)
{
yield return(new Peptide(this, indices[i + missed_cleavages + 1], indices[i] + 1 + 1, missed_cleavages));
}
}
}
}
}
}
public DBOptions(string fasta, IConSol console = null)
{
if (console == null)
{
ConSole = new ConSolCommandLine();
}
else
{
ConSole = console;
}
//Create with default values
this.DecoyFusion = true;
this.FastaDatabaseFilepath = fasta;
this.MaximumPeptideMass = 10000;
ProteaseDictionary proteases = ProteaseDictionary.Instance;
this.DigestionEnzyme = proteases["no enzyme"]; // proteases["trypsin (no proline rule)"];
this.NoEnzymeSearch = true;
this.ToleratedMissedCleavages = 100; // 3;//determines the length of peptides with no-enzyme option
this.initiatorMethionineBehavior = InitiatorMethionineBehavior.Variable;
this.fixedModifications = new GraphML_List <Modification>();
this.variableModifications = new GraphML_List <Modification>();
this.maximumVariableModificationIsoforms = 1024;
this.MinimumPrecursorChargeState = 1;
this.MaximumPrecursorChargeState = 4;
this.MaximumNumberOfFragmentsPerSpectrum = 400;
//TODO Add precision to the precursor by reading MS part of file
this.precursorMassTolerance = new MassTolerance(0.005, MassToleranceUnits.Da);//2.1
//TODO Add precision to the product masses by reading corresponding MS part of raw file
this.productMassTolerance = new MassTolerance(0.005, MassToleranceUnits.Da);
this.PSMFalseDiscoveryRate = 0.25; // 0.05;
this.OutputFolder = @"C:\_IRIC\DATA\Test2"; //C:\Documents and Settings\ProteoAdmin\Desktop\AEffacer\Morpheus\Output";
this.MinimumPSMScore = 0.0001;
}