private void Run()
{
string processName = "";
bool end = false;
toolStripButton1.Enabled = false;
ErrorBase.ClearErrors();
SetDataDirOptions();
do
{
GetProcessName gName = new GetProcessName(opt.clusterAlgorithm.ToString());
gName.ShowDialog();
if (gName.DialogResult == DialogResult.OK)
{
List <string> keys = new List <string>(manager.clOutput.Keys);
Dictionary <string, int> dic = new Dictionary <string, int>();
foreach (var item in keys)
{
string [] aux = item.Split('_');
string l = "";
for (int i = 0; i < aux.Length - 1; i++)
{
l += aux[i];
}
if (!dic.ContainsKey(l))
{
dic.Add(l, 1);
}
}
if (dic.ContainsKey(gName.name))
{
MessageBox.Show("Process name: " + gName.name + " already exists");
}
else
{
processName = gName.name;
end = true;
}
}
else
{
return;
}
}while (!end);
manager.mUpdate = upMessage;
try
{
TimeInterval.Start();
manager.RunJob(processName);
}
catch (Exception ex)
{
TimeInterval.Stop();
MessageBox.Show("Exception: " + ex.Message);
}
}
/* 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();
* PDBFiles pdbsNew = new PDBFiles();
* //Needed only for CATH
* string []cathFiles=Directory.GetFiles("F:\\CATH");
* Dictionary<string, Dictionary<string, string>> aux = new Dictionary<string, Dictionary<string, string>>();
* foreach(var item in cathFiles)
* {
* if(item.Contains("COMBS"))
* ReadCathFile(item, aux);
* }
*
*
*
* //-----------------------
*
*
* maxV = files.Count;
* bool test=false;
* try
* {
* foreach (var item in aux.Keys)
* {
* string strName;
*
* //if (!test && item.Contains("1vij"))
* test = true;
*
* if (!test)
* continue;
* //strName = pdbs.AddPDB(item, PDBMODE.CA_CB);
* strName = pdbs.AddPDB("F:\\cath_pdb\\"+item, PDBMODE.ONLY_CA,CHAIN_MODE.ALL);
*
* // if(aux.ContainsKey(pdbs.molDic))
*
* if (strName != null)
* {
* if (!aux.ContainsKey(strName))
* Console.WriteLine("UPS");
* List<Chain> toRemove = new List<Chain>();
* chainId.Clear();
* pdbsNew.molDic.Clear();
* MolData mol=new MolData();
* mol.mol = new Molecule();
* pdbsNew.molDic=new Dictionary<string,MolData>();
* pdbsNew.molDic.Add(strName,mol);
* char chStart = '0';
* foreach (var chains in aux[strName].Keys)
* {
* if (!chains.Contains("_"))
* continue;
* Console.WriteLine(chains);
* Chain cc=pdbs.molDic[strName].mol.CuttMoleculeToSEQ(aux[strName][chains], chains.Substring(0, 1)[0]);
* if(cc!=null)
* {
* cc.ChainIdentifier = chStart;
* chainId.Add(chStart, chains);
* chStart++;
* pdbsNew.molDic[strName].mol.Chains.Add(cc);
* }
* }
* if(pdbsNew.molDic[strName].mol.Chains.Count>0)
* MakeProfiles(strName, pdbsNew.molDic[strName], wr);
* }
* pdbs.molDic.Clear();
* currentProgress++;
* }
* }
* catch (Exception ex)
* {
* // wr.Close();
* throw new Exception(ex.Message);
* }
*
* wr.Close();
* currentProgress = maxV;
* return 0;
* }*/
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();
chunk = new float[dirSettings.numberOfCores][, ];
center = new float[dirSettings.numberOfCores][];
for (int i = 0; i < dirSettings.numberOfCores; i++)
{
chunk[i] = new float[fragBagLibrary[0].GetLength(0), fragBagLibrary[0].GetLength(1)];
center[i] = new float[3];
}
maxV = files.Count;
try
{
resetEvents = new ManualResetEvent[dirSettings.numberOfCores];
for (int i = 0; i < dirSettings.numberOfCores; i++)
{
resetEvents[i] = new ManualResetEvent(false);
}
foreach (var item in files)
{
string strName;
//strName = pdbs.AddPDB(item, PDBMODE.CA_CB);
if (dirSettings.mode == INPUTMODE.PROTEIN)
{
strName = pdbs.AddPDB(item, PDBMODE.ONLY_CA, CHAIN_MODE.ALL);
}
else
{
strName = pdbs.AddPDB(item, PDBMODE.ONLY_P, CHAIN_MODE.ALL);
}
// if(aux.ContainsKey(pdbs.molDic))
if (strName != null)
{
MakeProfiles(strName, pdbs.molDic[strName], wr);
}
pdbs.molDic.Clear();
ErrorBase.ClearErrors();
Interlocked.Increment(ref currentProgress);
}
}
catch (Exception ex)
{
// wr.Close();
throw new Exception(ex.Message);
}
wr.Close();
// currentProgress = maxV;
return(0);
}
