//!!!could be nice to have a version that writes to a stream and to a string
public static void DebugReportCollection(VaccineAsString[] vaccineAsStringCollection)
{
for (int iVaccineAsString = 0; iVaccineAsString < vaccineAsStringCollection.Length; ++iVaccineAsString)
{
VaccineAsString aVaccineAsString = vaccineAsStringCollection[iVaccineAsString];
Debug.WriteLine(string.Format("{0}\t{1}", iVaccineAsString, aVaccineAsString.String));
}
}
public Component MakePatchAComponent(Patch aPatch)
{
RemovePatchFromTables(aPatch);
VaccineAsString.AddComponent(aPatch.PatchPattern());
Component aComponent = Component.GetInstance(aPatch);
Components.AddNew(aComponent);
UpdateComponentTables(aComponent);
return(aComponent);
}
private static List <PatchPattern> PatchPatternCollection(VaccineAsString vaccineUncompressed)
{
List <PatchPattern> rg = new List <PatchPattern>();
PatchPatternFactory aPatchPatternFactory = PatchPatternFactory.GetFactory("strings");
foreach (string componentAsString in vaccineUncompressed.NiceStringCollection())
{
PatchPattern patchPattern = aPatchPatternFactory.GetInstance(componentAsString);
rg.Add(patchPattern);
}
return(rg);
}
static public VaccineAsString GetInstance(int maximumWindowLength, string name)
{
VaccineAsString aVaccineAsString = new VaccineAsString();
aVaccineAsString.Border = new string('_', (int)maximumWindowLength); //!!!Using _____ of varying length now seems not so good. How about using newlines?
aVaccineAsString.String = string.Format("{0}", aVaccineAsString.Border);
aVaccineAsString.NumberOfComponents = 0;
aVaccineAsString.TotalNumberOfAminoAcids = 0;
aVaccineAsString.Name = name;
return(aVaccineAsString);
}
override public void FirstVaccine(PatchTable patchTable)
{
PatchTable = patchTable;
VaccineAsString = VaccineAsString.GetInstance(patchTable.MaxPatchLength, Name);
PointsInPatchTable = 0.0;
foreach (Patch aPatch in patchTable.SortedPatchCollection)
{
PointsInPatchTable += aPatch.Weight;
UnusedPatches.AddNew(aPatch);
}
Patch patchBest = patchTable.SortedPatchCollection[0];
MakePatchAComponent(patchBest);
}
internal static VaccineAsString GetInstanceFromNice(string name, string nice)
{
string[] components = nice.Split(',');
int max = 0;
foreach (string component in components)
{
max = Math.Max(max, component.Length);
}
VaccineAsString aVaccineAsString = VaccineAsString.GetInstance(max, name);
foreach (string component in components)
{
aVaccineAsString.AddComponent(component);
}
return(aVaccineAsString);
}
public override double DupScore(Dictionary <PatchPattern, Patch> patchPaternToPatch, VaccineAsString vaccine)
{
double score = 0.0;
foreach (string component in vaccine.NiceStringCollection())
{
foreach (Patch aPatch in patchPaternToPatch.Values)
{
if (aPatch.PatchPattern().IsMatch(component))
{
score += aPatch.Weight;
}
}
}
return(score);
}
public override double Score(Dictionary <PatchPattern, Patch> patchPaternToPatch, VaccineAsString vaccineAsString)
{
double score = 0.0;
foreach (Patch aPatch in patchPaternToPatch.Values)
{
if (aPatch.PatchPattern().IsMatch(vaccineAsString.String))
{
score += aPatch.Weight;
}
}
return(score);
}
public abstract double DupScore(Dictionary <PatchPattern, Patch> patchPaternToPatch, VaccineAsString vaccine);
public double Score(VaccineAsString vaccineAsString)
{
return(PatchTableScorer.Score(PatchPatternToPatch, vaccineAsString));
}
internal double DupScore(VaccineAsString vaccine)
{
return(PatchTableScorer.DupScore(PatchPatternToPatch, vaccine));
}
internal static PatchTable GetInstanceWithUniformWeightByLength(VaccineAsString vaccineUncompressed)
{
return(GetInstanceWithUniformWeightByLength(PatchPatternCollection(vaccineUncompressed)));
}