//public static KeepSpecificRows GetInstance()
//{
// List<KeepSpecificRow> keepList = new List<KeepSpecificRow>();
// //// this is the list of associations that have q < 0.01 in Gag Within gene.
// //keepList.Add(KeepSpecificRow.GetInstance(2134, "P", 2146, "L"));
// //keepList.Add(KeepSpecificRow.GetInstance(2134, "L", 2146, "P"));
// //keepList.Add(KeepSpecificRow.GetInstance(2146, "P", 2134, "L"));
// //keepList.Add(KeepSpecificRow.GetInstance(2146, "L", 2134, "P"));
// //keepList.Add(KeepSpecificRow.GetInstance(1957, "I", 1990, "L"));
// //keepList.Add(KeepSpecificRow.GetInstance(1990, "L", 1957, "I"));
// //keepList.Add(KeepSpecificRow.GetInstance(2215, "K", 2227, "D"));
// //keepList.Add(KeepSpecificRow.GetInstance(1579, "K", 1306, "A"));
// //keepList.Add(KeepSpecificRow.GetInstance(1957, "V", 1990, "I"));
// //keepList.Add(KeepSpecificRow.GetInstance(1306, "A", 1579, "K"));
// //keepList.Add(KeepSpecificRow.GetInstance(1591, "M", 1579, "K"));
// //keepList.Add(KeepSpecificRow.GetInstance(1579, "K", 1591, "M"));
// //keepList.Add(KeepSpecificRow.GetInstance(1591, "M", 1306, "A"));
// //keepList.Add(KeepSpecificRow.GetInstance(2206, "P", 2182, "F"));
// //keepList.Add(KeepSpecificRow.GetInstance(1591, "L", 1579, "R"));
// //keepList.Add(KeepSpecificRow.GetInstance(2227, "D", 2215, "K"));
// //keepList.Add(KeepSpecificRow.GetInstance(1306, "A", 1591, "M"));
// //keepList.Add(KeepSpecificRow.GetInstance(1471, "I", 1531, "T"));
// //keepList.Add(KeepSpecificRow.GetInstance(1579, "R", 1591, "L"));
// //keepList.Add(KeepSpecificRow.GetInstance(2206, "P", 2176, "F"));
// //keepList.Add(KeepSpecificRow.GetInstance(2206, "P", 2215, "K"));
// //keepList.Add(KeepSpecificRow.GetInstance(2239, "E", 2224, "E"));
// //keepList.Add(KeepSpecificRow.GetInstance(2224, "E", 2239, "E"));
// //keepList.Add(KeepSpecificRow.GetInstance(2215, "G", 2206, "G"));
// //keepList.Add(KeepSpecificRow.GetInstance(2206, "G", 2215, "G"));
// //keepList.Add(KeepSpecificRow.GetInstance(1531, "T", 1471, "I"));
// //keepList.Add(KeepSpecificRow.GetInstance(2176, "Q", 2170, "Q"));
// //keepList.Add(KeepSpecificRow.GetInstance(2170, "Q", 2176, "Q"));
// //keepList.Add(KeepSpecificRow.GetInstance(2212, "P", 2185, "E"));
// //keepList.Add(KeepSpecificRow.GetInstance(2185, "E", 2212, "P"));
// //keepList.Add(KeepSpecificRow.GetInstance(895, "W", 889, "I"));
// //keepList.Add(KeepSpecificRow.GetInstance(904, "R", 889, "I"));
// //keepList.Add(KeepSpecificRow.GetInstance(904, "R", 895, "W"));
// //keepList.Add(KeepSpecificRow.GetInstance(901, "C", 889, "I"));
// return GetInstance(keepList);
//}
public static KeepSpecificRows GetInstance(string semiColonDelimitedRows)
{
string[] rowDefs = semiColonDelimitedRows.Split(';');
SpecialFunctions.CheckCondition(rowDefs.Length > 0);
List <KeepSpecificRow> rows = new List <KeepSpecificRow>(rowDefs.Length);
foreach (string row in rowDefs)
{
rows.Add(KeepSpecificRow.GetInstance(row));
}
return(GetInstance(rows));
}
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));
}
}