public static KeepTest <Dictionary <string, string> > GetInstance(string geneRanges)
{
List <KeepTest <Dictionary <string, string> > > geneList = new List <KeepTest <Dictionary <string, string> > >();
string[] genes = geneRanges.Split(',');
foreach (string gene in genes)
{
geneList.Add(KeepGene.GetInstance(gene));
}
return(Or <Dictionary <string, string> > .GetInstance(geneList));
}
public static KeepGene GetInstance(string geneRange)
{
KeepGene keepGene = new KeepGene();
string[] fields = geneRange.Split('-');
try
{
keepGene._start = int.Parse(fields[0]);
keepGene._stop = int.Parse(fields[1]);
}
catch
{
throw new FormatException(string.Format("Could not parse range {0}.", geneRange));
}
return(keepGene);
}
new public static KeepTest <Dictionary <string, string> > GetInstance(string inputDirectory,
string binarySeqFileName, string hlaFileName, string keepTestName, int merSize, Dictionary <int, string> pidToCaseName)
{
//!!!would be nice of classes could parse themselves
if (keepTestName.StartsWith(KeepEndOfGag.Prefix))
{
bool keepIt = bool.Parse(keepTestName.Substring(KeepEndOfGag.Prefix.Length));
return(KeepEndOfGag.GetInstance(keepIt));
}
else if (keepTestName.StartsWith(K1.Prefix))
{
int k1 = int.Parse(keepTestName.Substring(K1.Prefix.Length));
return(K1.GetInstance(k1));
}
//else if (keepTestName.StartsWith(K2.Prefix))
//{
// int k2 = int.Parse(keepTestName.Substring(K2.Prefix.Length));
// return K2.GetInstance(k2);
//}
else if (keepTestName.StartsWith(KeepNonOverlappingAA.Prefix))
{
return(KeepNonOverlappingAA.GetInstance());
}
else if (keepTestName.StartsWith(KeepGene.Prefix))
{
string geneRange = keepTestName.Substring(KeepGene.Prefix.Length);
return(KeepGene.GetInstance(geneRange));
}
else if (keepTestName.StartsWith(KeepSpecificRows.Prefix))
{
return(KeepSpecificRows.GetInstance(keepTestName.Substring(KeepSpecificRows.Prefix.Length)));
}
else if (keepTestName.StartsWith(KeepSpecificRow.Prefix))
{
return(KeepSpecificRow.GetInstance(keepTestName.Substring(KeepSpecificRow.Prefix.Length)));
}
else if (keepTestName.StartsWith(KeepSpecificGenes.Prefix))
{
return(KeepSpecificGenes.GetInstance(keepTestName.Substring(KeepSpecificGenes.Prefix.Length)));
}
else if (keepTestName.StartsWith(KeepOneOfAAPair.Prefix))
{
return(KeepOneOfAAPair.GetInstance());
}
else if (keepTestName.StartsWith(KeepAllButSamePosition.Prefix))
{
return(KeepAllButSamePosition.GetInstance());
}
else if (keepTestName.StartsWith(KeepAllButSameDeletion.Prefix))
{
return(KeepAllButSameDeletion.GetInstance());
}
else if (keepTestName.StartsWith(KeepNonTrivialRows.Prefix))
{
return(new KeepNonTrivialRows());
}
else if (keepTestName.StartsWith(KeepTestTemp.Prefix))
{
return(KeepTestTemp.GetInstance());
}
//else if (keepTestName.StartsWith(KeepPollockOneDirection.Prefix))
//{
// return KeepPollockOneDirection.GetInstance(keepTestName.Substring(KeepPollockOneDirection.Prefix.Length));
//}
//else if (keepTestName.StartsWith(KeepFisherOneDirection.Prefix))
//{
// return KeepFisherOneDirection.GetInstance(keepTestName.Substring(KeepFisherOneDirection.Prefix.Length));
//}
else if (keepTestName.StartsWith(KeepNonRare.Prefix))
{
return(KeepNonRare.GetInstance(keepTestName.Substring(KeepNonRare.Prefix.Length)));
}
else if (keepTestName.StartsWith(KeepPredictorTargetPairs.Prefix))
{
return(KeepPredictorTargetPairs.GetInstance(keepTestName.Substring(KeepPredictorTargetPairs.Prefix.Length)));
}
else if (keepTestName.StartsWith("JointGagPolTest"))
{
return(And <Dictionary <string, string> > .GetInstance(
//KeepRandom<Dictionary<string,string>>.GetInstance(0, 0.001), // how do we make it the same when we count and when we really run through it?
KeepOneOfAAPair.GetInstance(),
KeepNonOverlappingAA.GetInstance(),
KeepSpecificGenes.GetInstance(keepTestName.Substring("JointGagPolTest".Length))));
}
else
{
return(KeepTest <TRow> .GetInstance(inputDirectory, binarySeqFileName, null, keepTestName, merSize, pidToCaseName));
}
}