public List<int> RemoveDataBaseRedundancy(BlastObj obj, double removeAboveIdentiyTheshold, Boolean rebuildDatabase)
{
var l = new List<int>();
for (int i = 0; i < obj.entries.Count; i++)
{
if (obj.entries[i].blastFasta.giID == obj.queryFasta.giID)
continue;
if (obj.entries[i].Identity > removeAboveIdentiyTheshold)
{
for (int j = 0; j < this._fastaDBSet.Count; j++)
{
if (this._fastaDBSet[j].giID == obj.entries[i].blastFasta.giID)
{
l.Add(this._fastaDBSet[j].giID);
this._fastaDBSet.RemoveAt(j);
break;
}
}
}
}
if (rebuildDatabase)
this.CreateLocalBlastDatabase(this.command, this._blastType, this._fastaDBSet, this._fastaSetPath, true);
return l;
}
public BlastObj PerformBlast(String queryPath, bool includeWaitTime)
{
if (this._blastType == BlastType.Null)
return null;
this._lastQueryPath = queryPath;
var cs = LocalBlaster.BlastCommands[(int)this._blastType] +
@" -db " + this._localDBPath + @"\~tempLocalBlastDB" +
@" -query " + queryPath +
@" -out " + _outputPath + @"\~tempBlastOutput.txt";
this.command.RunCommandLine(cs, this._NCBIBlasteEXEPath); //C:\Ryan\ProteinProj\ProjectFiles\~tempLocalBlast.txt", NCBIExs);
if (includeWaitTime)
while (command.isRunning)
{ }
var bo = new BlastObj(queryPath, _outputPath + @"\~tempBlastOutput.txt");
/*
if (this._fastaDBSet != null)
for (int i = 0; i < bo.entries.Count; i++)
{
for (int j = 0; j < this._fastaDBSet.Count; j++)
{
if (bo.entries[i].blastFasta.giID == this._fastaDBSet[j].giID)
{
bo.entries[i].sourceFasta = this._fastaDBSet[j];
break;
}
if (j == this._fastaDBSet.Count - 1)
continue;
}
}*/
return bo;
}