public override System.Collections.ArrayList HlaToLength4(LanlEpitope aLanlEpitope)
{
ArrayList rg = new ArrayList();
rg.Add(aLanlEpitope.HlaToLength);
return(rg);
}
public override ArrayList HlaToLength4(LanlEpitope aLanlEpitope)
{
Debug.Fail("Need code");
ArrayList rg = new ArrayList();
rg.Add(aLanlEpitope.HlaToLength);
return(rg);
}
public override ArrayList HlaToLength4(LanlEpitope aLanlEpitope)
{
throw new Exception("The commented out version of this code requires an implict set of HLAs");
//ArrayList rg = new ArrayList();
//foreach (HlaToLength hlaToLength4 in FourDigitPossiblities(aLanlEpitope.HlaToLength))
//{
// rg.Add(hlaToLength4);
//}
//return rg;
}
static public void DumpCollection(string fileSuffix, HlaResolution hlaResolution, ArrayList lanlEpitopeCollection)
{
string sOutputFile = string.Format(@"LanlEpitopeCollection{0}{1}.New.txt", fileSuffix, hlaResolution.ShortName);
using (StreamWriter streamwriterOutputFile = File.CreateText(sOutputFile))
{
LanlEpitope.WriteHeaderLine(streamwriterOutputFile);
foreach (LanlEpitope aLanlEpitope in lanlEpitopeCollection)
{
aLanlEpitope.WriteLine(streamwriterOutputFile);
}
}
}
static private ArrayList MakeOneLonger(LanlEpitope modelLanlEpitope)
{
ArrayList rgExpanded = new ArrayList();
for (int iPos = 0; iPos <= modelLanlEpitope.Epitope.Length; ++iPos)
{
LanlEpitope aLanlEpitope = new LanlEpitope();
aLanlEpitope.Epitope = AddCharToString(modelLanlEpitope.Epitope, iPos, "#");
aLanlEpitope.ProteinPositionNotCanonical = modelLanlEpitope.ProteinPositionNotCanonical;
aLanlEpitope.SpeciesPattern = modelLanlEpitope.SpeciesPattern;
aLanlEpitope.HlaToLength = modelLanlEpitope.HlaToLength;
aLanlEpitope.CaseWeight = 1.0 / ((double)modelLanlEpitope.Epitope.Length + 1.0);
aLanlEpitope.Source = modelLanlEpitope;
aLanlEpitope.Operator = string.Format("I{0}", iPos + 1);
rgExpanded.Add(aLanlEpitope);
}
return(rgExpanded);
}
// static private void AddToHashtable(LanlEpitope aLanlEpitope, ref Hashtable rgExpanded)
// {
// if (rgExpanded.ContainsKey(aLanlEpitope.Epitope))
// {
// LanlEpitope previous = (LanlEpitope) rgExpanded[aLanlEpitope.Epitope];
// previous.CaseWeight += aLanlEpitope.CaseWeight;
//
// }
// else
// {
// rgExpanded.Add(aLanlEpitope.Epitope, aLanlEpitope);
// }
// }
static private ArrayList MakeOneLongerAtE1(LanlEpitope modelLanlEpitope)
{
Debug.Assert(modelLanlEpitope.Epitope.Length == 8);
ArrayList rgExpanded = new ArrayList();
int iPos = 0;
LanlEpitope aLanlEpitope = new LanlEpitope();
aLanlEpitope.Epitope = AddCharToString(modelLanlEpitope.Epitope, iPos, "#");
aLanlEpitope.ProteinPositionNotCanonical = modelLanlEpitope.ProteinPositionNotCanonical;
aLanlEpitope.SpeciesPattern = modelLanlEpitope.SpeciesPattern;
aLanlEpitope.HlaToLength = modelLanlEpitope.HlaToLength;
aLanlEpitope.CaseWeight = 1.0;
aLanlEpitope.Source = modelLanlEpitope;
aLanlEpitope.Operator = string.Format("I{0}", iPos + 1);
rgExpanded.Add(aLanlEpitope);
return(rgExpanded);
}
static private ArrayList MakeOneShorterAt4thTo8th(LanlEpitope modelLanlEpitope)
{
Debug.Assert(modelLanlEpitope.Epitope.Length == 10);
ArrayList rgExpanded = new ArrayList();
for (int iPos = 3; iPos <= 8; ++iPos)
{
LanlEpitope aLanlEpitope = new LanlEpitope();
aLanlEpitope.Epitope = RemoveCharFromString(modelLanlEpitope.Epitope, iPos);
aLanlEpitope.ProteinPositionNotCanonical = modelLanlEpitope.ProteinPositionNotCanonical;
aLanlEpitope.SpeciesPattern = modelLanlEpitope.SpeciesPattern;
aLanlEpitope.HlaToLength = modelLanlEpitope.HlaToLength;
aLanlEpitope.CaseWeight = 1.0 / 6.0;
aLanlEpitope.Source = modelLanlEpitope;
aLanlEpitope.Operator = string.Format("D{0}", iPos + 1);
rgExpanded.Add(aLanlEpitope);
}
return(rgExpanded);
}
static public ArrayList GetLanlCollection(string fileSuffix, HlaResolution hlaResolution)
{
//Load up known epitopes
ArrayList lanlEpitopeCollection = new ArrayList();
if (fileSuffix == "ignore")
{
return(lanlEpitopeCollection);
}
string sInputFileName = LanlFile(fileSuffix, hlaResolution);
Dictionary <string, bool> rgSeenIt = new Dictionary <string, bool>();
using (StreamReader streamreaderInputFile = Predictor.OpenResource(sInputFileName))
{
string sLine = streamreaderInputFile.ReadLine();
SpecialFunctions.CheckCondition(sLine == PreferedHeader || sLine == @"Epitope,Protein,Hxb2locstart,Hxb2locend,Species,HLA" || sLine == @"Epitope,Protein,Hxb2locstart,Hxb2locend,Species,Hla,length"); //!!!raise error
while ((sLine = streamreaderInputFile.ReadLine()) != null)
{
if (sLine == "")
{
continue;
}
string[] rgField = sLine.Split(',', '\t');
SpecialFunctions.CheckCondition(rgField.Length == 7 || rgField.Length == 6); //!!!raise error
string aaSequence = rgField[0];
SpecialFunctions.CheckCondition(aaSequence.IndexOf('?') < 0); //!!!raise error
if (rgField.Length == 7)
{
int iLength = int.Parse(rgField[6]);
SpecialFunctions.CheckCondition(aaSequence.Length == iLength); //!!!raise error
}
string hlaCollection = rgField[5];
SpecialFunctions.CheckCondition(hlaCollection != ""); //!!!raise error
string species = rgField[4];
if (species.IndexOf("human") < 0)
{
Debug.WriteLine("Skipping non-human epitope: " + species);
continue;
}
foreach (HlaToLength aHlaToLength in HlaCollection(hlaCollection, hlaResolution))
{
LanlEpitope aLanlEpitope = new LanlEpitope();
aLanlEpitope.Epitope = aaSequence; //!!!const
string sProtein = rgField[1]; //!!!const
int aa1 = int.Parse(rgField[2]); //!!!could raise error //!!!const
aLanlEpitope.ProteinPositionNotCanonical = new ProteinPosition(sProtein, aa1);
//!!!add an assert about the species pattern being one that we can work with
aLanlEpitope.SpeciesPattern = "human";
//!!!would be good to assert that this matches pattern - no "HLA*" or " "
aLanlEpitope.HlaToLength = aHlaToLength;
string key = aLanlEpitope.Key();
if (!rgSeenIt.ContainsKey(key))
{
rgSeenIt.Add(key, true);
lanlEpitopeCollection.Add(aLanlEpitope);
}
}
}
}
LanlEpitope.ReportNormalizedInputWithNoDup(lanlEpitopeCollection, fileSuffix, hlaResolution);
lanlEpitopeCollection = FilterAndDuplicateAccordingToSuffix(lanlEpitopeCollection, fileSuffix);
DumpCollection(fileSuffix, hlaResolution, lanlEpitopeCollection);
return(lanlEpitopeCollection);
}
abstract public System.Collections.ArrayList HlaToLength4(LanlEpitope aLanlEpitope);
