internal static PatchTable GetInstanceWithUniformWeightByLength(IList <PatchPattern> patchPatternCollection)
{
PatchTable patchTable = new PatchTable();
patchTable.PatchTableScorer = PatchTableScorer.GetInstance("normal");
int totalLength = 0;
foreach (PatchPattern patchPattern in patchPatternCollection)
{
totalLength += patchPattern.FullLength;
}
foreach (PatchPattern patchPattern in patchPatternCollection)
{
double weight = (double)patchPattern.FullLength / (double)totalLength;
patchTable.SetMaxPatchLength(patchPattern);
Patch aPatch = Patch.GetInstance(patchPattern, weight);
patchTable.Add(aPatch);
patchTable.CreateSortedArrays();
}
return(patchTable);
}
private Patch GetPatchFromCollection(PatchPattern patchPattern)
{
if (PatchPatternToPatch.ContainsKey(patchPattern))
{
return((Patch)PatchPatternToPatch[patchPattern]);
}
else
{
Patch aPatch = Patch.GetInstance(patchPattern, 0.0);
PatchPatternToPatch.Add(patchPattern, aPatch);
return(aPatch);
}
}
static public PatchTable GetInstanceFromFile(PatchPatternFactory patchPatternFactory,
TextReader patchTableTextReader, string scorerName)
{
PatchTable patchTable = new PatchTable();
patchTable.PatchTableScorer = PatchTableScorer.GetInstance(scorerName);
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(patchTableTextReader, "Patch\tWeight", false))
{
PatchPattern patchPattern = patchPatternFactory.GetInstance(row["Patch"]);
double weight = double.Parse(row["Weight"]);
patchTable.SetMaxPatchLength(patchPattern);
Patch patch = Patch.GetInstance(patchPattern, weight);
patchTable.Add(patch);
}
patchTable.CreateSortedArrays();
return(patchTable);
}
static public PatchTable GetInstance(Dictionary <string, double> patchToWeight, string protein, string vaccineCriteriaName)
{
PatchTable patchTable = new PatchTable();
patchTable.PatchTableScorer = PatchTableScorer.GetInstance("normal");
PatchPatternFactory patchPatternFactory = PatchPatternFactory.GetFactory("strings");
patchTable.PatchPatternToPatch = new Dictionary <PatchPattern, Patch>();
foreach (KeyValuePair <string, double> patchAndWeight in patchToWeight)
{
string patchAsString = patchAndWeight.Key;
double weight = patchAndWeight.Value;
PatchPattern patchPattern = patchPatternFactory.GetInstance(patchAsString);
Patch aPatch = Patch.GetInstance(patchPattern, weight);
patchTable.Add(aPatch);
}
patchTable.CreateSortedArrays();
return(patchTable);
}