public void MyAlign(string alignFile)
{
bool test = false;
//Check if there is sequence that could be aligned
align = new Dictionary <string, Dictionary <string, string> >();
foreach (var item in r.profiles)
{
align.Add(item.Key, new Dictionary <string, string>());
if ((alignFile == null || alignFile.Length == 0))
{
refSeq = "";
foreach (var pp in item.Value)
{
if (pp.Value.profile == null)
{
throw new Exception("For " + pp.Key + " no profile has been found!");
}
if (refSeq == null || pp.Value.sequence.Length > refSeq.Length)
{
refSeq = pp.Value.sequence;
}
}
MAlignment al = new MAlignment(refSeq.Length);
foreach (var pp in item.Value)
{
if (pp.Value.sequence != null && refSeq.Length != pp.Value.sequence.Length)
{
string seq = (al.Align(refSeq, pp.Value.sequence)).seq2;
if (seq.Length > 0)
{
align[item.Key][pp.Key] = seq;
}
}
}
}
if (align.Count == 0)
{
throw new Exception("There is no alignment");
}
}
try
{
if (dirSettings.mode != INPUTMODE.USER_DEFINED)
{
AlignProfiles();
}
else
{
OmitAlignProfiles();
}
}
catch (Exception)
{
throw new Exception("Combining alignments went wrong!");
}
}
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");
}
}
private void PDBSAlign(object o)
{
Params p=(Params) o;
List<string> toRemove = new List<string>();
MAlignment align = new MAlignment(refSeq.Length);
DebugClass.WriteMessage("Started");
foreach (var item in auxFiles[p.k])
{
molDic[item].indexMol = new int[refSeq.Length];
MAlignment.alignSeq alignRes = align.Align(refSeq, molDic[item].mol.Chains[0].chainSequence);
if (alignRes.seq1.Contains('-'))
{
ErrorBase.AddErrors("Reference structure " + refStuctName + " cannot be used as reference to " + item + " structure because after alignment gaps to referense structure must be added what is not allowed");
toRemove.Add(item);
continue;
}
//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[item].indexMol[j] = count++;
else
molDic[item].indexMol[j] = -1;
}
}
DebugClass.WriteMessage("Almost done");
foreach (var item in toRemove)
molDic.Remove(item);
resetEvents[p.k].Set();
}
private void AddAlignment(string item)
{
MAlignment align = new MAlignment(molDic[refStuctName].mol.Chains[0].chainSequence.Length);
molDic[item].indexMol = new int[molDic[refStuctName].mol.Chains[0].chainSequence.Length];
string ss = align.Align(molDic[refStuctName].mol.Chains[0].chainSequence, molDic[item].mol.Chains[0].chainSequence).seq2;
for (int j = 0, count = 0; j < ss.Length; j++)
{
if (ss[j] != '-')
molDic[item].indexMol[j] = count++;
else
molDic[item].indexMol[j] = -1;
}
}
public void MyAlign(string alignFile)
{
bool test=false;
//Check if there is sequence that could be aligned
foreach (var item in r.profiles)
{
foreach (var pp in item.Value)
{
if (pp.Value.profile == null)
throw new Exception("No profile has been found!");
if (pp.Value.sequence == null || pp.Value.sequence.Length != pp.Value.profile.Count)
test = true;
break;
}
break;
}
if ((alignFile!=null && alignFile.Length > 0) || test)
{
// align = ReadAlignment(alignFile);
foreach (var item in r.profiles)
{
align = new Dictionary<string, string>(item.Value.Keys.Count);
foreach (var pp in item.Value)
{
string alignProf;
char []aux = new char[pp.Value.profile.Count];
for(int i=0;i<pp.Value.profile.Count;i++)
{
aux[i]= 'C';
}
alignProf = new string(aux);
align.Add(pp.Key, alignProf);
}
break;
}
}
else
{
foreach (var item in r.profiles)
{
foreach (var pp in item.Value)
{
if (refSeq==null || pp.Value.sequence.Length > refSeq.Length)
refSeq = pp.Value.sequence;
}
break;
}
MAlignment al = new MAlignment(refSeq.Length);
foreach (var item in r.profiles)
{
foreach (var pp in item.Value)
{
if (refSeq.Length != pp.Value.sequence.Length)
{
//Console.WriteLine(pp);
string seq = (al.Align(refSeq, pp.Value.sequence)).seq2;
if (seq.Length > 0)
align[pp.Key] = seq;
}
else
align[pp.Key] = refSeq;
}
break;
}
if (align.Count == 0)
throw new Exception("There is no alignment");
}
try
{
AlignProfiles();
}
catch (Exception ex)
{
throw new Exception("Combining alignments went wrong!");
}
}
public void AddStructureToAlignment(string protName,string profileName,ref protInfo profile)
{
MAlignment al = new MAlignment(refSeq.Length);
string resSeq = (al.Align(refSeq, profile.sequence)).seq2;
if (!align.ContainsKey(protName))
align.Add(protName, resSeq);
if(!r.profiles[profileName].ContainsKey(protName))
r.profiles[profileName].Add(protName,profile);
AlignProfile(protName, profileName, profile.profile);
profile.alignment = r.profiles[profileName][protName].alignment;
}
