private static string LanlFileNormalizedOutput(string fileSuffix, HlaResolution hlaResolution)
{
SpecialFunctions.CheckCondition(fileSuffix == "Lanl"); //!!!raise error
string sInputFileName = string.Format(@"lanl-{0}digit.Normalized.new.txt", hlaResolution.ShortName); //!!!const
return(sInputFileName);
}
static public HlaToLength GetInstanceABMixed(string hlaPattern)
{
HlaToLength aHlaToLength = new HlaToLength();
aHlaToLength.HlaResolution = HlaResolution.ABMixed;
if (HlaResolution.TwoDigitHlaPatternIsOK(hlaPattern))
{
aHlaToLength._hlaClass = hlaPattern.Substring(0, 1);
aHlaToLength._hlaNumberToLength = int.Parse(hlaPattern.Substring(1));
SpecialFunctions.CheckCondition(aHlaToLength._hlaClass != "B" || aHlaToLength._hlaNumberToLength != 15); //!!!raise error
SpecialFunctions.CheckCondition(aHlaToLength._hlaClass != "A" || aHlaToLength._hlaNumberToLength != 68); //!!!raise error
}
else
{
HlaToLength hlaToLengthFour = GetInstanceFour(hlaPattern);
int twoDigits = hlaToLengthFour.TwoDigits();
if ((twoDigits == 15 && hlaToLengthFour.HlaClass == "B") || (twoDigits == 68 && hlaToLengthFour.HlaClass == "A"))
{
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = hlaToLengthFour._hlaNumberToLength;
}
else
{
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = twoDigits;
}
}
return(aHlaToLength);
}
static public HlaToLength GetInstance(string hlaPattern, HlaResolution hlaResolution)
{
HlaToLength aHlaToLength = hlaResolution.GetHlaLengthInstance(hlaPattern);
SpecialFunctions.CheckCondition(aHlaToLength != null);
return(aHlaToLength);
}
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 string LanlFile(string fileSuffix, HlaResolution hlaResolution)
{
SpecialFunctions.CheckCondition(fileSuffix == "ignore" || fileSuffix == "" || fileSuffix == "Old" || fileSuffix == "Lanl" || fileSuffix == "8910" || fileSuffix == "8910NoExpand" || fileSuffix == "8910SomeExpand" || fileSuffix == "8910Both"); //!!!raise error
string sInputFileName;
if (fileSuffix == "Old")
{
sInputFileName = string.Format(@"lanlOld.csv"); //!!!const
}
else
{
sInputFileName = string.Format(@"lanl-{0}digit.csv", hlaResolution.ShortName); //!!!const
}
return(sInputFileName);
}
static internal HlaToLength GetInstanceTwo(string hlaPattern)
{
HlaToLength aHlaToLength = new HlaToLength();
aHlaToLength.HlaResolution = HlaResolution.Two;
if (HlaResolution.TwoDigitHlaPatternIsOK(hlaPattern))
{
aHlaToLength._hlaClass = hlaPattern.Substring(0, 1);
aHlaToLength._hlaNumberToLength = int.Parse(hlaPattern.Substring(1));
}
else
{
HlaToLength hlaToLengthFour = GetInstanceFour(hlaPattern);
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = hlaToLengthFour.TwoDigits();
}
return(aHlaToLength);
}
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);
}
internal static void ReportNormalizedInputWithNoDup(ArrayList lanlEpitopeCollection, string fileSuffix, HlaResolution hlaResolution)
{
string outputFileName = LanlFileNormalizedOutput(fileSuffix, hlaResolution);
using (StreamWriter streamwriterOutputFile = File.CreateText(outputFileName))
{
streamwriterOutputFile.WriteLine(PreferedHeader);
foreach (LanlEpitope lanlEpitope in lanlEpitopeCollection)
{
string line = lanlEpitope.Key();
streamwriterOutputFile.WriteLine(line);
}
}
}
private static System.Collections.Generic.IEnumerable <HlaToLength> HlaCollection(string hlaCollection, HlaResolution hlaResolution)
{
foreach (string sHlaPattern in hlaCollection.Split('/'))
{
HlaToLength hlaToLength = HlaToLength.GetInstanceOrNull(sHlaPattern, hlaResolution);
SpecialFunctions.CheckCondition(hlaToLength != null); //!!!raise error
yield return(hlaToLength);
}
}
static public HlaToLength GetInstanceOrNull(string hlaPattern, HlaResolution hlaResolution)
{
return(hlaResolution.GetHlaLengthInstance(hlaPattern));
}
public HlaGroup PossibleHlaGroup()
{
return(HlaResolution.PossibleHlaGroup(this));
}
public override int GetHashCode()
{
return(_hlaNumberToLength.GetHashCode() ^ _hlaClass.GetHashCode() ^ HlaResolution.GetHashCode());
}
public string ToStringWithoutLeading0()
{
return(HlaResolution.HlaToLengthStringWithLeading0(this));
}
public override string ToString()
{
return(HlaResolution.HlaToLengthString(this));
}
static public HlaToLength GetInstanceOrNull(HlaGroup hlaGroup, HlaResolution hlaResolution)
{
HlaToLength hlaToLength = HlaToLength.GetInstanceOrNull(hlaGroup.ToString(), hlaResolution);
return(hlaToLength);
}
