public NeoPsm(int scan, double expMass, InitialID nInfo, InitialID cInfo)
{
this.scanNumber = scan;
this.expMass = expMass;
this.nInfo = nInfo;
this.cInfo = cInfo;
this.candidates = new List <FusionCandidate>();
}
public static List <NeoPsm> ImportNeoPsms(string nFileName, string cFileName)
{
string[] nInput = File.ReadAllLines(nFileName);
string[] cInput = File.ReadAllLines(cFileName);
List <NeoPsm> psms = new List <NeoPsm>();
ParseHeader(nInput[0]);
List <InitialID> nAssignment = new List <InitialID>();
List <InitialID> cAssignment = new List <InitialID>();
for (int i = 1; i < nInput.Count(); i++)
{
string[] line = nInput[i].Split('\t').ToArray();
InitialID id = new InitialID(Convert.ToInt32(line[scanNumberIndex]), Convert.ToDouble(line[scanPrecursorMassIndex]), line[accessionIndex], line[fullIndex], line[matchedIonsIndex], line[scoreIndex]);
nAssignment.Add(id);
}
for (int i = 1; i < cInput.Count(); i++)
{
string[] line = cInput[i].Split('\t').ToArray();
InitialID id = new InitialID(Convert.ToInt32(line[scanNumberIndex]), Convert.ToDouble(line[scanPrecursorMassIndex]), line[accessionIndex], line[fullIndex], line[matchedIonsIndex], line[scoreIndex]);
cAssignment.Add(id);
}
//sort by scan number
List <InitialID> nAssignmentSorted = nAssignment.OrderBy(o => o.scanNumber).ToList();
List <InitialID> cAssignmentSorted = cAssignment.OrderBy(o => o.scanNumber).ToList();
//remove scans not found in both files
double maxCount = nAssignmentSorted.Count();
for (int i = 0; i < maxCount; i++)
{
if (i < cAssignmentSorted.Count())
{
if (nAssignmentSorted[i].scanNumber.Equals(cAssignmentSorted[i].scanNumber))
{
NeoPsm psm = new NeoPsm(nAssignmentSorted[i].scanNumber, nAssignmentSorted[i].expMass, nAssignmentSorted[i], cAssignmentSorted[i]);
psms.Add(psm);
continue;
}
else if (nAssignmentSorted[i].scanNumber < cAssignmentSorted[i].scanNumber) //no information was found for the b scan using y ions, so remove it
{
nAssignmentSorted.Remove(nAssignmentSorted[i]);
maxCount--;
i--;
}
else //no information was found for the y scan using b ions, so remove it
{
cAssignmentSorted.Remove(cAssignmentSorted[i]);
i--;
}
}
}
return(psms);
}