/*
* These are from the experiment and will be removed if you call reset on the
* graph
*/
public Peptide addPeptideFromIdentification(IDs id, double currentTime)
{
String peptideSequence = id.getPeptideSequence();
double peptideMass = id.getPeptideMass();
HashSet <String> parentProteinAccessions = id.getParentProteinAccessions();
Peptide pep;
if (containsPeptide(peptideSequence))
{
return(getPeptide(peptideSequence));
}
else
{
// Adds the peptide from the identification into the database
pep = new Peptide(peptideSequence, peptideMass, false);
// these peptides will be removed if reset() is called
SequenceToPeptide.Add(peptideSequence, pep);
peptides.Add(pep);
if (includeRetentionTime)
{
// TODO right now this takes the current time as the peak retention time...
// should we run it through RTCalc so we can better estimate our RT alignment?
// 2019-04-29 No, do not. Observed times are better than predicted
// pep.setRetentionTime(RetentionTimeUtil.convertDoubleToRetentionTime(rt,
// retentionTimeWindow,
// retentionTimeWindow));
RetentionTime rt = new RetentionTime(currentTime + retentionTimeWindow, retentionTimeWindow,
retentionTimeWindow, false);
pep.setRetentionTime(rt);
}
}
// update its parent proteins
foreach (String acc in parentProteinAccessions)
{
Protein parentProtein = AccesstionToProtein[acc];
if (parentProtein != null)
{
pep.addProtein(parentProtein);
}
else if (acc.Contains(GlobalVar.DecoyPrefix))
{
log.Info("WARNINGin Decoy parent protein for this peptide was not found!!");
log.Info(acc);
}
else
{
log.Warn("WARNINGin Non-decoy parent protein for this peptide was not found!!");
log.Warn(acc);
}
}
return(pep);
}
public void addPeptide(String reference, Peptide pep)
{
if (peptides.Keys.Contains(reference))
{
log.Debug("Peptide already exists");
}
else
{
peptides.Add(reference, pep);
}
}
public Protein addProteinFromIdentification(Peptide pep, HashSet <String> parentProteinAccessions)
{
// TODO
log.Error("Implementation for adding protein from identification not completed...");
return(null);
// foreach(String accessionin parentProteinAccessions) {
// Protein prot;
// if(!containsProtein(accession)) {
// prot = new Protein(accession, null);
// }
// }
}
public void printGraph()
{
log.Debug(ToString());
foreach (String acc in AccesstionToProtein.Keys)
{
Protein p = getProtein(acc);
log.Debug(p);
}
foreach (String seq in SequenceToPeptide.Keys)
{
Peptide pep = getPeptide(seq);
log.Debug(pep);
}
}
private void addPeptides(List <DigestedPeptide> digestedPeptideArray)
{
log.Debug("Adding peptides...");
foreach (DigestedPeptide dp in digestedPeptideArray)
{
String parentProteinAccession = dp.getAccession();
String peptideSequence = dp.getSequence();
double peptideMass = dp.getMass();
// Add digested peptide to the graph
Protein parentProtein = getProtein(parentProteinAccession);
Peptide pep;
if (containsPeptide(peptideSequence))
{
pep = getPeptide(peptideSequence);
}
else
{
// HERE is where you make the peptide objects!!
if (includeCarbamidoModification)
{
peptideMass = carbamidoModificationMass(peptideSequence, peptideMass);
}
pep = new Peptide(peptideSequence, peptideMass, true);
SequenceToPeptide.Add(peptideSequence, pep);
peptides.Add(pep);
}
if (parentProtein != null)
{
pep.addProtein(parentProtein);
}
else
{
log.Warn("WARNINGin Parent protein foreach this peptide was not found!!");
}
}
// add retention time information
setRetentionTimes();
peptides.Sort((Peptide x, Peptide y) => (y.getMass()).CompareTo(x.getMass()));
log.Debug("Done adding peptides.");
}
public bool Equals(Object o)
{
// If the object is compared with itself then return true
if (o == this)
{
return(true);
}
/*
* Check if o is an instance of Peptide or not "null instanceof [type]" also
* returns false
*/
if (!(o is Peptide))
{
return(false);
}
// typecast o to Complex so that we can compare data members
Peptide pep = (Peptide)o;
// Compare the data members and return accordingly
return(pep.getMass().CompareTo(this.getMass()) == 0 && this.getSequence().Equals(pep.getSequence()));
}