public void MakeAlignment(string alignFile)
{
List <string> toRemove = new List <string>();
if (molDic.Count == 0)
{
return;
}
if (molDic.Count == 1)
{
foreach (var item in molDic.Keys)
{
molDic[item].indexMol = new int[molDic[item].mol.Chains[0].chainSequence.Length];
for (int i = 0; i < molDic[item].indexMol.Length; i++)
{
molDic[item].indexMol[i] = i;
}
}
}
if (alignFile != null && alignFile.Length > 0)
{
Dictionary <string, string> al = Alignment.ReadAlignment(alignFile);
foreach (var item in molDic.Keys)
{
string ss;
if (al.ContainsKey(item))
{
ss = al[item];
molDic[item].indexMol = new int[ss.Length];
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
{
molDic[item].indexMol[j] = count++;
}
else
{
molDic[item].indexMol[j] = -1;
}
}
}
}
}
else
if (molDic.Count == 2)
{
using (MAlignment align = new MAlignment(refSeq.Length))
{
MAlignment.alignSeq alignRes;
List <string> molItems = new List <string>(molDic.Keys);
string str1, str2;
if (molDic[molItems[0]].mol.Chains[0].chainSequence.Length > molDic[molItems[1]].mol.Chains[0].chainSequence.Length)
{
str1 = molItems[0];
str2 = molItems[1];
}
else
{
str1 = molItems[1];
str2 = molItems[0];
}
alignRes = align.Align(molDic[str1].mol.Chains[0].chainSequence, molDic[str2].mol.Chains[0].chainSequence);
molDic[str1].indexMol = new int[alignRes.seq1.Length];
molDic[str2].indexMol = new int[alignRes.seq1.Length];
//string ss = align.Align(molDic[refStuctName].mol.Chains[0].chainSequence, molDic[item].mol.Chains[0].chainSequence).seq2;
string ss = alignRes.seq2;
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
{
molDic[str2].indexMol[j] = count++;
}
else
{
molDic[str2].indexMol[j] = -1;
}
}
ss = alignRes.seq1;
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
{
molDic[str1].indexMol[j] = count++;
}
else
{
molDic[str1].indexMol[j] = -1;
}
}
}
}
else
{
Settings set = new Settings();
set.Load();
int threadNumbers = set.numberOfCores;
//return;
auxFiles = new List <string> [threadNumbers];
resetEvents = new ManualResetEvent[threadNumbers];
List <string> allFiles = new List <string>(molDic.Keys);
for (int i = 0; i < threadNumbers; i++)
{
auxFiles[i] = new List <string>((i + 1) * molDic.Count / threadNumbers - i * molDic.Count / threadNumbers);
for (int j = i * allFiles.Count / threadNumbers; j < (i + 1) * allFiles.Count / threadNumbers; j++)
{
auxFiles[i].Add(allFiles[j]);
}
}
DebugClass.WriteMessage("Alignment start =" + threadNumbers);
//PDBSAlign(auxFiles)
for (int i = 0; i < threadNumbers; i++)
{
//PDBSAlign(auxFiles[i]);
Params p = new Params();
p.k = i;
resetEvents[p.k] = new ManualResetEvent(false);
ThreadPool.QueueUserWorkItem(new WaitCallback(PDBSAlign), (object)p);
// startProg = Task.Factory.StartNew(() => RunMakeProfiles(fileName,auxFiles,k));
// runnigTask[i] = startProg;
}
for (int i = 0; i < threadNumbers; i++)
{
resetEvents[i].WaitOne();
}
//WaitHandle.WaitAll(resetEvents);
DebugClass.WriteMessage("Alignment stop");
}
}
public void MakeAlignment(string alignFile)
{
List<string> toRemove = new List<string>();
if (molDic.Count == 0)
return;
if (molDic.Count == 1)
{
foreach (var item in molDic.Keys)
{
molDic[item].indexMol = new int[molDic[item].mol.Chains[0].chainSequence.Length];
for (int i = 0; i < molDic[item].indexMol.Length; i++)
molDic[item].indexMol[i] = i;
}
}
if (alignFile != null && alignFile.Length > 0)
{
Dictionary<string, string> al = Alignment.ReadAlignment(alignFile);
foreach (var item in molDic.Keys)
{
string ss;
if (al.ContainsKey(item))
{
ss = al[item];
molDic[item].indexMol = new int[ss.Length];
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
molDic[item].indexMol[j] = count++;
else
molDic[item].indexMol[j] = -1;
}
}
}
}
else
if (molDic.Count == 2)
{
using (MAlignment align = new MAlignment(refSeq.Length))
{
MAlignment.alignSeq alignRes;
List<string> molItems = new List<string>(molDic.Keys);
string str1, str2;
if (molDic[molItems[0]].mol.Chains[0].chainSequence.Length > molDic[molItems[1]].mol.Chains[0].chainSequence.Length)
{
str1 = molItems[0];
str2 = molItems[1];
}
else
{
str1 = molItems[1];
str2 = molItems[0];
}
alignRes = align.Align(molDic[str1].mol.Chains[0].chainSequence, molDic[str2].mol.Chains[0].chainSequence);
molDic[str1].indexMol = new int[alignRes.seq1.Length];
molDic[str2].indexMol = new int[alignRes.seq1.Length];
//string ss = align.Align(molDic[refStuctName].mol.Chains[0].chainSequence, molDic[item].mol.Chains[0].chainSequence).seq2;
string ss = alignRes.seq2;
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
molDic[str2].indexMol[j] = count++;
else
molDic[str2].indexMol[j] = -1;
}
ss = alignRes.seq1;
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
molDic[str1].indexMol[j] = count++;
else
molDic[str1].indexMol[j] = -1;
}
}
}
else
{
Settings set = new Settings();
set.Load();
int threadNumbers = set.numberOfCores;
auxFiles = new List<string>[threadNumbers];
resetEvents = new ManualResetEvent[threadNumbers];
List<string> allFiles = new List<string>(molDic.Keys);
for(int i=0;i<threadNumbers;i++)
{
auxFiles[i] = new List<string>((i + 1) * molDic.Count / threadNumbers - i * molDic.Count / threadNumbers);
for (int j = i * allFiles.Count / threadNumbers; j < (i + 1) * allFiles.Count / threadNumbers; j++)
auxFiles[i].Add(allFiles[j]);
}
DebugClass.WriteMessage("Alignment start =" + threadNumbers);
//PDBSAlign(auxFiles)
for (int i = 0; i < threadNumbers; i++)
{
//PDBSAlign(auxFiles[i]);
Params p = new Params();
p.k=i;
resetEvents[p.k] = new ManualResetEvent(false);
ThreadPool.QueueUserWorkItem(new WaitCallback(PDBSAlign), (object)p);
// startProg = Task.Factory.StartNew(() => RunMakeProfiles(fileName,auxFiles,k));
// runnigTask[i] = startProg;
}
for (int i = 0; i < threadNumbers; i++)
resetEvents[i].WaitOne();
//WaitHandle.WaitAll(resetEvents);
DebugClass.WriteMessage("Alignment stop");
}
}
public override void RunThreads(string fileName)
{
List<string> files = CheckFile(fileName);
if (files.Count == 0)
return;
//Task[] runnigTask = new Task[threadNumbers];
//Task startProg;
maxV = files.Count*2;
ReadPdbs(files);
if (pdbs.molDic.Count == 0)
return;
string aux = Path.GetDirectoryName(files[0]).TrimEnd(Path.DirectorySeparatorChar);
string refSeqFile = aux+".ref";
if(File.Exists(refSeqFile))
pdbs.ReadRefSeq(refSeqFile);
else
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(null);
if (contOne == null)
{
string molDicKey="";
foreach (var item in pdbs.molDic.Keys)
{
molDicKey = item;
break;
}
int len = pdbs.molDic[molDicKey].indexMol.Length;
contOne = new int[len * (len + 1) / 2];
contact = new byte[threadNumbers][];
contactToString=new char [threadNumbers][];
for(int i=0;i<threadNumbers;i++)
{
contact[i]=new byte [len * (len + 1) / 2];
contactToString[i]=new char [len * (len + 1)];
}
for (int i = 0; i < contOne.Length; i++)
contOne[i] =0;
for (int i = 0; i < threadNumbers; i++)
for (int j = 0; j < contOne.Length; j++)
contact[i][j] = 0;
}
auxFiles =new List<string>[threadNumbers];
List<string> allFiles = new List<string>(pdbs.molDic.Keys);
for (int i = 0; i < threadNumbers; i++)
{
auxFiles[i] = new List<string>((i + 1) * pdbs.molDic.Count / threadNumbers - i * pdbs.molDic.Count / threadNumbers);
for (int j = i * allFiles.Count / threadNumbers; j < (i + 1) * allFiles.Count / threadNumbers; j++)
auxFiles[i].Add(files[j]);
}
for (int i = 0; i < threadNumbers; i++)
{
Params p = new Params();
p.fileName = fileName;
p.k = i;
resetEvents[p.k] = new ManualResetEvent(false);
ThreadPool.QueueUserWorkItem(new WaitCallback(RunMakeProfiles), (object)p);
}
for (int i = 0; i < threadNumbers; i++)
resetEvents[i].WaitOne();
//JoinFiles(fileName);
CuttProfiles(fileName);
currentProgress = maxV;
}
