public static IEnumerable <string> GreedyEpitomeEnumerable(string patchTableAsString)
{
//!!!Similar to other code
string scorerName = "normal";
PatchPatternFactory patchPatternFactory = PatchPatternFactory.GetFactory("strings");
VaccineMaker vaccineMaker = VaccineMaker.GetInstance("Greedy");
PatchTable patchTable = LoadPatchTable(patchTableAsString, scorerName, patchPatternFactory);
patchTable.Normalize();
AssertPointsTotalOne(patchTable);
//yield return VaccineMaker.DisplayHeaderString;
vaccineMaker.FirstVaccine(patchTable);
VaccineAsString vaccineAsString = null;
while (null != (vaccineAsString = vaccineMaker.VaccineAsString))
{
double rScoreOpt = patchTable.Score(vaccineAsString);
yield return(vaccineMaker.DisplayString(rScoreOpt));
vaccineMaker.ChangeToNext();
}
}
public static void MakeGreedyEpitomes(TextReader patchTableTextReader, TextWriter streamWriterOutputFile, int stopLength)
{
string scorerName = "normal";
PatchPatternFactory patchPatternFactory = PatchPatternFactory.GetFactory("strings");
VaccineMaker vaccineMaker = VaccineMaker.GetInstance("Greedy");
PatchTable patchTable = LoadPatchTable(patchTableTextReader, scorerName, patchPatternFactory);
patchTable.Normalize();
AssertPointsTotalOne(patchTable);
vaccineMaker.DisplayHeader(streamWriterOutputFile);
vaccineMaker.FirstVaccine(patchTable);
VaccineAsString vaccineAsString = null;
while (null != (vaccineAsString = vaccineMaker.VaccineAsString))
{
double rScoreOpt = patchTable.Score(vaccineAsString);
vaccineMaker.Display(streamWriterOutputFile, rScoreOpt);
streamWriterOutputFile.Flush();
if (vaccineAsString.TotalNumberOfAminoAcids > stopLength)
{
break;
}
vaccineMaker.ChangeToNext();
}
}