protected void InitMeasure(string dirName,string alignFile,bool flag,PDBMODE allAtoms,string refJuryProfile=null)
{
base.InitMeasure(dirName, alignFile, flag, refJuryProfile);
pdbs = new PDBFiles();
string[] files;
if(dirSettings.extension==null)
files = Directory.GetFiles(dirName);
else
files = Directory.GetFiles(dirName, dirSettings.extension);
if (files.Length == 0)
throw new Exception("In selected directory " + dirName + " there are no files with extesion " + dirSettings.extension);
maxV = files.Length;
string refSeqFile = dirName + ".ref";
pdbs.ReadRefSeq(refSeqFile);
currentV = 0;
pdbs.AddPDB(files, allAtoms,ref currentV);
if (pdbs.molDic.Keys.Count == 0)
throw new Exception("Non pdb files correctly read");
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
order = true;
atomDic = pdbs.MakeAllAtomsDic();
}
public override int Run(object processParams)
{
Dictionary<int, List<int>> contacts= new Dictionary<int, List<int>>();
string fileName = ((ThreadFiles)(processParams)).fileName;
List<string> files = threadingList[((ThreadFiles)(processParams)).threadNumber];// CheckFile(listFile);
if (files.Count == 0)
return 0;
StreamWriter wr;
if (File.Exists(fileName))
wr = File.AppendText(fileName);
else
wr = new StreamWriter(fileName);
if (wr == null)
throw new Exception("Cannot open file: " + fileName);
PDBFiles pdbs = new PDBFiles();
string refSeqFile = ((ThreadFiles)(processParams)) + ".ref";
pdbs.ReadRefSeq(refSeqFile);
maxV = files.Count;
try
{
foreach (var item in files)
{
string strName;
//strName = pdbs.AddPDB(item, PDBMODE.CA_CB);
if (this.GetType() == typeof(ContactProfile))
strName = pdbs.AddPDB(item, PDBMODE.ALL_ATOMS);
else
strName = pdbs.AddPDB(item, PDBMODE.ONLY_CA);
if(strName!=null)
MakeProfiles(strName,pdbs.molDic[strName], wr);
currentProgress++;
}
}
catch (Exception ex)
{
// wr.Close();
throw new Exception(ex.Message);
}
wr.Close();
currentProgress = maxV;
return 0;
}
