public GDT_TS(DCDFile dcd, string alignFile, bool flag, string refJuryProfile = null)
: base(dcd, alignFile, flag, PDBMODE.ONLY_CA, refJuryProfile)
{
order = true;
maxSimilarity = 100.0;
gdt = new GDT(dcd, alignFile, flag, refJuryProfile);
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
DCDReader readDCD = new DCDReader(dcd);
dirSettings.Load();
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont=readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}
while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
if(pdbs is ErrorBase)
AddErrors(pdbs.errors);
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
DCDReader readDCD = new DCDReader(dcd);
dirSettings.Load();
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont = readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
if (pdbs is ErrorBase)
{
AddErrors(pdbs.errors);
}
opt = new Optimization();
structNames = CheckAvailableStructures();
order = true;
}
protected Dictionary <string, int> CheckFile(DCDFile dcd)
{
Dictionary <string, int> dic = new Dictionary <string, int>();
if (File.Exists(GetProfileFileName(dcd)))
{
using (StreamReader rf = new StreamReader(GetProfileFileName(dcd)))
{
if (rf == null)
{
return(null);
}
string line = rf.ReadLine();
while (line != null)
{
if (line.Contains('>'))
{
line = line.Remove(0, 1);
dic.Add(line, 1);
}
line = rf.ReadLine();
}
rf.Close();
}
}
return(dic);
}
protected void InitMeasure(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
base.InitMeasure(dcd, alignFile, flag, refJuryProfile);
DCDReader readDCD = new DCDReader(dcd);
pdbs = new PDBFiles();
readDCD.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
int counter = 0;
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter wStream = new StreamWriter(mStream);
cont = readDCD.ReadAndSavePDB(wStream);
string name = "Model" + counter++;
mStream.Position = 0;
pdbs.AddPDB(mStream, allAtoms, name);
}while(cont);
readDCD.FinishDCDReading();
pdbs.FindReferenceSeq();
pdbs.MakeAlignment(alignFile);
structNames = CheckAvailableStructures();
atomDic = pdbs.MakeAllAtomsDic();
}
public HammingBase(DCDFile dcd, string alignFile, bool flag, string profileName, string refJuryProfile = null)
{
this.dcd = dcd;
this.alignFile = alignFile;
this.flag = flag;
this.profileName = profileName;
this.refJuryProfile = refJuryProfile;
}
public GDT_TS(DCDFile dcd, string alignFile, bool flag, string refJuryProfile = null)
: base(dcd, alignFile, flag, PDBMODE.ONLY_CA, refJuryProfile)
{
order = true;
maxSimilarity = 100.0;
gdt = new GDT(dcd, alignFile, flag, refJuryProfile);
}
public Rmsd(DCDFile dcd, string alignFile, bool flag, PDBMODE allAtoms, string refJuryProfile = null)
{
order = true;
dirSettings.Load();
this.dcd = dcd;
this.alignFile = alignFile;
this.flag = flag;
this.allAtoms = allAtoms;
this.refJuryProfile = refJuryProfile;
}
protected string GetProfileFileName(DCDFile dcd)
{
string[] aux;
string bDir = "";
aux = dcd.dcdFile.Split(Path.DirectorySeparatorChar);
if (set.profilesDir != null && set.profilesDir.Length > 0)
{
bDir = set.profilesDir + Path.DirectorySeparatorChar;
}
return(bDir + aux[aux.Length - 1] + "_" + profileName);
}
public static Dictionary <string, protInfo> GetProfile(profileNode node, DCDFile dcd)
{
profileNode n = GetNode(node.internalName);
if (n != null)
{
Type t = Type.GetType(internalList[n]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
return(c.GetProfile(node, null, dcd));
}
return(null);
}
public virtual void InitMeasure(DCDFile dcd, string alignFile, bool referenceFlag, string juryProfile = null)
{
this.alignFile = alignFile;
if (referenceFlag)
{
if (juryProfile.Length == 0 || !File.Exists(juryProfile))
{
throw new Exception("Profile for reference structure searching has been not defined or does not exist");
}
jury = new jury1D();
jury.PrepareJury(dcd, alignFile, juryProfile);
}
}
public void InitMeasure(DCDFile dcd, string alignFile, bool flag, string profileName, string refJuryProfile = null)
{
base.InitMeasure(dcd, alignFile, flag, refJuryProfile);
if (profileName != null)
{
currentProfile = profileName;
}
dirSettings.Load();
al = new Alignment();
al.Prepare(dcd, dirSettings, currentProfile);
InitHamming();
}
public void RunProfile(string name, DCDFile dcd)
{
profileNode node = GetNode(name);
if (node != null)
{
Type t = Type.GetType(internalList[node]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
c.CheckIfAvailable();
progressInfo = c;
c.Run(dcd);
progressInfo = null;
progress++;
}
}
// virtual public void RunThreads(string listFile);
abstract public void Run(DCDFile dcd);
abstract public Dictionary <string, protInfo> GetProfile(profileNode node, string listFile, DCDFile dcd);
protected string GetProfileFileName(DCDFile dcd)
{
string[] aux;
string bDir = "";
aux = dcd.dcdFile.Split(Path.DirectorySeparatorChar);
if (set.profilesDir != null && set.profilesDir.Length > 0)
bDir = set.profilesDir + Path.DirectorySeparatorChar;
return bDir+aux[aux.Length - 1] + "_" + profileName;
}
public override Dictionary<string, protInfo> GetProfile(profileNode node, string listFile,DCDFile dcd=null)
{
Dictionary<string, protInfo> dic = null;
StreamReader wr;
DebugClass.WriteMessage("start reading file" + listFile);
string useFile = listFile;
List<string> names = GetFileList(listFile);
if(names==null)
DebugClass.WriteMessage("After GetFileList null");
else
DebugClass.WriteMessage("After GetFileList "+names.Count);
maxV = names.Count;
Dictionary<string, int> dicNames = new Dictionary<string, int>(names.Count);
foreach (var item in names)
{
string[] aux = item.Split(Path.DirectorySeparatorChar);
if(!dicNames.ContainsKey(aux[aux.Length-1]))
dicNames.Add(aux[aux.Length-1], 0);
}
DebugClass.WriteMessage("After loop");
string[] dotFlag = names[0].Split('|');
bool flag = false;
if (dotFlag.Length == 2)
flag = true;
DebugClass.WriteMessage("Before profile");
if (dcd == null)
{
wr = new StreamReader(GetProfileFileName(listFile));
}
else
wr = new StreamReader(GetProfileFileName(dcd));
DebugClass.WriteMessage("start ddd reading");
protInfo info;
string line = wr.ReadLine();
string name="";
string seq="";
List<string> profile; ;
List<byte> newProfile = null;
string profileName;
if (node.ContainsState("H"))
profileName = ssProfile;
else
profileName = contactProfile;
//Check number of elements in file
int lineLength=0;
while (line != null)
{
if (lineLength < line.Length)
lineLength = line.Length;
line=wr.ReadLine();
}
wr.BaseStream.Position = 0;
wr.DiscardBufferedData();
profile = new List<string>(lineLength);
dic = new Dictionary<string, protInfo>(names.Count);
line=wr.ReadLine();
string remName="";
DebugClass.WriteMessage("Starrrrr");
while (line != null)
{
if (line[0]=='>')
{
if (name.Length > 0)
{
if (dicNames.ContainsKey(name))
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
//string newName = line;
//newName = newName.Remove(0, 1);
if (!dic.ContainsKey(remName))
dic.Add(remName, info);
else
ErrorBase.AddErrors("!!In the generated profile file structure " + remName + " exists more then once!!!\nOnly the first profile will be considered!");
currentProgress++;
}
}
name = line.Remove(0, 1);
remName = name;
if(name.Contains("|") && !flag)
{
string[] tmp = name.Split('|');
name = tmp[0];
}
}
if (dicNames.ContainsKey(name))
{
if (line.Contains(SEQprofile))
seq = line.Remove(0, SEQprofile.Length);
else
if (line.Contains(profileName))
{
//StringBuilder tmp = new StringBuilder(line);
line=line.Remove(0,profileName.Length);
//tmp = tmp.Remove(0, profileName.Length);
//StringBuilder tmp = new StringBuilder (line.Remove(0, profileName.Length));
string[] aux;
if(line.Contains(' '))
aux = line.Split(' ');
else
{
aux = new string[line.Length];
for (int i = 0; i < line.Length; i++)
aux[i] = line[i].ToString();
}
newProfile = CreateNewProfile(node, aux);
}
}
line = wr.ReadLine();
}
if (dicNames.ContainsKey(name))
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
dic.Add(remName, info);
}
wr.Close();
DebugClass.WriteMessage("Reading finished");
return dic;
}
public GDT(DCDFile dcd, string alignFile, bool flag, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
order = true;
maxSimilarity = 100.0;
}
public override void Run(DCDFile dcd)
{
DCDReader dcdReader = new DCDReader(null);
string modelName=null;
int counter = 0;
string fileName;
StreamWriter wr;
PDBFiles pdbs = new PDBFiles();
Dictionary<string,int> modelList=null;
fileName = GetProfileFileName(dcd);
if (File.Exists(fileName))
{
modelList = CheckFile(dcd);
wr = File.AppendText(fileName);
}
else
wr = new StreamWriter(fileName);
if (wr == null)
throw new Exception("Cannot open file: " + fileName);
dcdReader.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter write = new StreamWriter(mStream);
cont = dcdReader.ReadAndSavePDB(write);
modelName = "Model" + counter++;
if (modelList == null || modelList.ContainsKey(modelName))
continue;
mStream.Position = 0;
if (this.GetType() == typeof(ContactProfile))
pdbs.AddPDB(mStream, PDBMODE.ALL_ATOMS, modelName);
else
pdbs.AddPDB(mStream, PDBMODE.ONLY_CA, modelName);
if(pdbs.molDic.ContainsKey(modelName))
MakeProfiles(modelName,pdbs.molDic[modelName], wr);
}
while (cont);
dcdReader.FinishDCDReading();
wr.Close();
}
protected Dictionary<string,int> CheckFile(DCDFile dcd)
{
Dictionary<string, int> dic = new Dictionary<string, int>();
if (File.Exists(GetProfileFileName(dcd)))
{
using (StreamReader rf = new StreamReader(GetProfileFileName(dcd)))
{
if (rf == null)
return null;
string line = rf.ReadLine();
while (line != null)
{
if (line.Contains('>'))
{
line = line.Remove(0, 1);
dic.Add(line, 1);
}
line = rf.ReadLine();
}
rf.Close();
}
}
return dic;
}
abstract public Dictionary<string, protInfo> GetProfile(profileNode node, string listFile,DCDFile dcd);
public override void Run(DCDFile dcd)
{
throw new NotImplementedException();
}
public DCDReader(DCDFile dcdFile)
{
this.dcdFile = dcdFile;
}
public override Dictionary <string, protInfo> GetProfile(profileNode node, string fileName, DCDFile dcd)
{
Dictionary <string, protInfo> dic = new Dictionary <string, protInfo>();
StreamReader wr;
DebugClass.WriteMessage("profile" + fileName);
wr = new StreamReader(fileName);
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List <string> profile = new List <string>();
List <byte> newProfile = new List <byte>();
while (line != null)
{
if (line.Contains(">"))
{
if (name.Length > 0)
{
info = new protInfo();
info.sequence = null;
info.profile = newProfile;
if (dic.ContainsKey(name))
{
wr.Close();
throw new Exception("The nameof profile must be unique, name: " + name + " already exists in " + fileName);
}
dic.Add(name, info);
}
newProfile = new List <byte>();
name = line.Replace(">", "");
line = wr.ReadLine();
}
if (line != null && line.Contains(" profile "))
{
int index = line.IndexOf(" profile ");
if (index == -1)
{
wr.Close();
throw new Exception("Incorrect file format you have to have 'profile' word!");
}
string cLine = line.Remove(0, " profile ".Length + index);
cLine = Regex.Replace(cLine, @"\s+", " ");
if (line.Length == 0)
{
continue;
}
cLine = cLine.Trim();
string[] aux;
if (cLine.Contains(' '))
{
aux = cLine.Split(' ');
}
else
{
char[] charArray = cLine.ToCharArray();
aux = cLine.Select(x => x.ToString()).ToArray();
}
profile.Clear();
foreach (var item in aux)
{
profile.Add(item);
}
newProfile = new List <byte>();
for (int i = 0; i < profile.Count; i++)
{
if (node.ContainsState(profile[i].ToString()))
{
newProfile.Add(node.GetCodedState(node.states[profile[i].ToString()]));
}
else
if (profile[i].ToString() != "-" && profile[i].ToString() != "X")
{
throw new Exception("Unknow state " + profile[i].ToString() + " in " + node.profName + " profile!");
}
else
{
newProfile.Add(0);
}
}
}
line = wr.ReadLine();
}
if (newProfile.Count > 0)
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
dic.Add(name, info);
}
DebugClass.WriteMessage("number of profiles " + dic.Keys.Count);
wr.Close();
return(dic);
}
public void RunProfile(string name, DCDFile dcd)
{
profileNode node = GetNode(name);
if (node != null)
{
Type t = Type.GetType(internalList[node]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
c.CheckIfAvailable();
progressInfo = c;
c.Run(dcd);
progressInfo = null;
progress++;
}
}
public static Dictionary<string, protInfo> GetProfile(profileNode node, DCDFile dcd)
{
profileNode n = GetNode(node.internalName);
if (n != null)
{
Type t = Type.GetType(internalList[n]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
return c.GetProfile(node, null,dcd);
}
return null;
}
public GDT(DCDFile dcd, string alignFile, bool flag, string refJuryProfile = null)
: base(dcd, alignFile, flag, refJuryProfile)
{
order = true;
maxSimilarity = 100.0;
}
public CosineDistance(DCDFile dcd, string alignFile, bool flag, string profileName, string refJuryProfile = null)
: base(dcd, alignFile, flag, profileName, refJuryProfile)
{
}
public override void Run(DCDFile dcd)
{
DCDReader dcdReader = new DCDReader(null);
string modelName = null;
int counter = 0;
string fileName;
StreamWriter wr;
PDBFiles pdbs = new PDBFiles();
Dictionary <string, int> modelList = null;
fileName = GetProfileFileName(dcd);
if (File.Exists(fileName))
{
modelList = CheckFile(dcd);
wr = File.AppendText(fileName);
}
else
{
wr = new StreamWriter(fileName);
}
if (wr == null)
{
throw new Exception("Cannot open file: " + fileName);
}
dcdReader.DCDPrepareReading(dcd.dcdFile, dcd.pdbFile);
bool cont = true;
do
{
MemoryStream mStream = new MemoryStream();
StreamWriter write = new StreamWriter(mStream);
cont = dcdReader.ReadAndSavePDB(write);
modelName = "Model" + counter++;
if (modelList == null || modelList.ContainsKey(modelName))
{
continue;
}
mStream.Position = 0;
if (this.GetType() == typeof(ContactProfile))
{
pdbs.AddPDB(mStream, PDBMODE.ALL_ATOMS, modelName);
}
else
{
pdbs.AddPDB(mStream, PDBMODE.ONLY_CA, modelName);
}
if (pdbs.molDic.ContainsKey(modelName))
{
MakeProfiles(modelName, pdbs.molDic[modelName], wr);
}
}while (cont);
dcdReader.FinishDCDReading();
wr.Close();
}
// virtual public void RunThreads(string listFile);
abstract public void Run(DCDFile dcd);
public override Dictionary <string, protInfo> GetProfile(profileNode node, string listFile, DCDFile dcd = null)
{
Dictionary <string, protInfo> res = base.GetProfile(node, listFile, dcd);
/* StreamReader r = new StreamReader("sekw");
* string line = r.ReadLine();
* int []index = new int[399];
* int counter = 0;
* while (line != null)
* {
* index[counter] = Convert.ToInt32(line);
* line = r.ReadLine();
* counter++;
* }*/
int[] index = new int[20] {
0, 74, 57, 375, 343, 174, 33, 371, 227, 330, 9, 327, 141, 160, 256, 216, 138, 385, 51, 268
}; // for proteins
// int[] index = new int[29] { 21, 64, 29, 2, 33, 57, 77, 84, 14, 44, 81, 0, 90, 74, 30, 71, 76, 8, 48, 61,86,41,3,7,15,20,23,25,51};//for rna
List <string> keys = new List <string>(res.Keys);
foreach (var item in keys)
{
List <byte> newProfile = new List <byte>();
for (int i = 0; i < index.Length; i++)
{
newProfile.Add(res[item].profile[index[i]]);
}
protInfo xx = res[item];
xx.profile = newProfile;
res[item] = xx;
}
//res = RearangeColumnOrder(res);
// res = RearangeColumnOrder(res, "C:\\Projects\\listIndex");
res = ProfileStat.RearangeStates(res, 0.51);
return(res);
}
public override Dictionary <string, protInfo> GetProfile(profileNode node, string fileName, DCDFile dcd)
{
Dictionary <string, protInfo> dic = new Dictionary <string, protInfo>();
StreamReader wr;
DebugClass.WriteMessage("profile" + fileName);
wr = new StreamReader(fileName);
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List <string> profile = new List <string>();
List <byte> newProfile = new List <byte>();
while (line != null)
{
if (line.Contains(">"))
{
if (name.Length > 0)
{
info = new protInfo();
info.sequence = null;
info.profile = newProfile;
dic.Add(name, info);
}
name = line.Replace(">", "");
line = wr.ReadLine();
}
if (line.Contains(" profile "))
//if (line.Contains(node.profName+" "))
{
string[] aux;
aux = line.Split(' ');
node.profName = aux[0];
string cLine = line.Remove(0, (node.profName + " profile ").Length);
cLine = Regex.Replace(cLine, @"\s+", " ");
cLine = cLine.Trim();
if (cLine.Contains(' '))
{
aux = cLine.Split(' ');
}
else
{
char[] charArray = cLine.ToCharArray();
aux = cLine.Select(x => x.ToString()).ToArray();
}
profile.Clear();
foreach (var item in aux)
{
profile.Add(item);
}
newProfile = new List <byte>();
for (int i = 0; i < profile.Count; i++)
{
if (node.ContainsState(profile[i].ToString()))
{
newProfile.Add(node.GetCodedState(node.states[profile[i].ToString()]));
}
else
if (profile[i].ToString() != "-" && profile[i].ToString() != "X")
{
throw new Exception("Unknow state " + profile[i].ToString() + " in " + node.profName + " profile!");
}
else
{
newProfile.Add(0);
}
}
}
line = wr.ReadLine();
}
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
dic.Add(name, info);
DebugClass.WriteMessage("number of profiles " + dic.Keys.Count);
wr.Close();
return(dic);
}
public override void Run(DCDFile dcd)
{
throw new NotImplementedException();
}
public override Dictionary <string, protInfo> GetProfile(profileNode node, string listFile, DCDFile dcd = null)
{
Dictionary <string, protInfo> dic = null;
StreamReader wr;
DebugClass.WriteMessage("start reading file" + listFile);
string useFile = listFile;
List <string> names = GetFileList(listFile);
if (names == null)
{
DebugClass.WriteMessage("After GetFileList null");
}
else
{
DebugClass.WriteMessage("After GetFileList " + names.Count);
}
maxV = names.Count;
Dictionary <string, int> dicNames = new Dictionary <string, int>(names.Count);
foreach (var item in names)
{
string[] aux = item.Split(Path.DirectorySeparatorChar);
if (!dicNames.ContainsKey(aux[aux.Length - 1]))
{
dicNames.Add(aux[aux.Length - 1], 0);
}
}
DebugClass.WriteMessage("After loop");
string[] dotFlag = names[0].Split('|');
bool flag = false;
if (dotFlag.Length == 2)
{
flag = true;
}
DebugClass.WriteMessage("Before profile");
if (dcd == null)
{
wr = new StreamReader(GetProfileFileName(listFile));
}
else
{
wr = new StreamReader(GetProfileFileName(dcd));
}
DebugClass.WriteMessage("start ddd reading");
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List <string> profile;;
List <byte> newProfile = null;
string profileName;
if (node.ContainsState("H"))
{
profileName = ssProfile;
}
else
{
profileName = contactProfile;
}
//Check number of elements in file
int lineLength = 0;
while (line != null)
{
if (lineLength < line.Length)
{
lineLength = line.Length;
}
line = wr.ReadLine();
}
wr.BaseStream.Position = 0;
wr.DiscardBufferedData();
profile = new List <string>(lineLength);
dic = new Dictionary <string, protInfo>(names.Count);
line = wr.ReadLine();
string remName = "";
DebugClass.WriteMessage("Starrrrr");
while (line != null)
{
if (line[0] == '>')
{
if (name.Length > 0)
{
if (dicNames.ContainsKey(name))
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
//string newName = line;
//newName = newName.Remove(0, 1);
if (!dic.ContainsKey(remName))
{
dic.Add(remName, info);
}
else
{
ErrorBase.AddErrors("!!In the generated profile file structure " + remName + " exists more then once!!!\nOnly the first profile will be considered!");
}
currentProgress++;
}
}
name = line.Remove(0, 1);
remName = name;
if (name.Contains("|") && !flag)
{
string[] tmp = name.Split('|');
name = tmp[0];
}
}
if (dicNames.ContainsKey(name))
{
if (line.Contains(SEQprofile))
{
seq = line.Remove(0, SEQprofile.Length);
}
else
if (line.Contains(profileName))
{
//StringBuilder tmp = new StringBuilder(line);
line = line.Remove(0, profileName.Length);
//tmp = tmp.Remove(0, profileName.Length);
//StringBuilder tmp = new StringBuilder (line.Remove(0, profileName.Length));
string[] aux;
if (line.Contains(' '))
{
aux = line.Split(' ');
}
else
{
aux = new string[line.Length];
for (int i = 0; i < line.Length; i++)
{
aux[i] = line[i].ToString();
}
}
newProfile = CreateNewProfile(node, aux);
}
}
line = wr.ReadLine();
}
if (dicNames.ContainsKey(name))
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
dic.Add(remName, info);
}
wr.Close();
DebugClass.WriteMessage("Reading finished");
return(dic);
}
public CosineDistance(DCDFile dcd, string alignFile, bool flag, string profileName, string refJuryProfile = null)
:base(dcd, alignFile, flag, profileName, refJuryProfile)
{
}
public MaxSub(DCDFile dcd, string alignFile, bool flag, string refJuryProfile = null)
: base(dcd, alignFile, flag, PDBMODE.ONLY_CA, refJuryProfile)
{
order = true;
maxSimilarity = 0.0;
}
public override Dictionary<string, protInfo> GetProfile(profileNode node, string fileName, DCDFile dcd)
{
Dictionary<string, protInfo> dic = new Dictionary<string, protInfo>();
StreamReader wr;
DebugClass.WriteMessage("profile" + fileName);
wr = new StreamReader(fileName);
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List<string> profile = new List<string>();
List<byte> newProfile = new List<byte>();
while (line != null)
{
if (line.Contains(">"))
{
if (name.Length > 0)
{
info = new protInfo();
info.sequence = null;
info.profile = newProfile;
dic.Add(name, info);
}
name = line.Replace(">", "");
line = wr.ReadLine();
}
if (line.Contains(node.profName+" "))
{
string cLine=line.Remove(0, (node.profName+" profile ").Length);
cLine = Regex.Replace(cLine, @"\s+", " ");
cLine = cLine.Trim();
string[] aux;
if (cLine.Contains(' '))
aux = cLine.Split(' ');
else
{
char[] charArray = cLine.ToCharArray();
aux = cLine.Select(x => x.ToString()).ToArray();
}
profile.Clear();
foreach (var item in aux)
profile.Add(item);
newProfile = new List<byte>();
for (int i = 0; i < profile.Count; i++)
if (node.ContainsState(profile[i].ToString()))
newProfile.Add(node.GetCodedState(node.states[profile[i].ToString()]));
else
if(profile[i].ToString()!="-" && profile[i].ToString()!="X")
throw new Exception("Unknow state " + profile[i].ToString() + " in "+ node.profName + " profile!");
else
newProfile.Add(0);
}
line = wr.ReadLine();
}
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
dic.Add(name, info);
DebugClass.WriteMessage("number of profiles " + dic.Keys.Count);
wr.Close();
return dic;
}
public override Dictionary <string, protInfo> GetProfile(profileNode node, string fileName, DCDFile dcd = null)
{
Dictionary <string, protInfo> dic = new Dictionary <string, protInfo>();
currentProgress = 0;
if (!File.Exists(GetProfileFileName(fileName)))
{
throw new Exception("Profile rnaSS does not exists!");
}
string profileName;
if (node.ContainsState("+"))
{
profileName = LWprofile;
}
else
{
profileName = SSprofile;
}
StreamReader wr = new StreamReader(GetProfileFileName(fileName));
List <string> files = GetFileList(fileName);
maxV = files.Count;
Dictionary <string, int> dicFile = new Dictionary <string, int>();
foreach (var item in files)
{
string[] aux = item.Split(Path.DirectorySeparatorChar);
if (!dicFile.ContainsKey(aux[aux.Length - 1]))
{
dicFile.Add(aux[aux.Length - 1], 0);
}
}
protInfo info;
string line = wr.ReadLine();
string name = "";
string seq = "";
List <string> profile = new List <string>();
List <byte> newProfile = new List <byte>();
while (line != null)
{
if (line.Contains('>'))
{
if (name.Length > 0)
{
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
if (dicFile.ContainsKey(name))
{
if (!dic.ContainsKey(name))
{
dic.Add(name, info);
}
else
{
ErrorBase.AddErrors("There are two the same names " + name + " in the profile file " + GetProfileFileName(fileName));
}
}
currentProgress++;
}
name = line.Remove(0, 1);
}
if (line.Contains(SEQprofile))
{
seq = line.Remove(0, SEQprofile.Length);
}
if (line.Contains(profileName))
{
string tmp = line.Remove(0, profileName.Length);
string[] aux;
profile.Clear();
if (tmp.Contains(" "))
{
tmp = tmp.TrimEnd();
aux = tmp.Split(' ');
foreach (var item in aux)
{
profile.Add(item);
}
}
else
{
for (int i = 0; i < tmp.Length; i++)
{
profile.Add(tmp[i].ToString());
}
}
newProfile = new List <byte>();
for (int i = 0; i < profile.Count; i++)
{
if (node.ContainsState(profile[i].ToString()))
{
newProfile.Add(node.GetCodedState(node.states[profile[i].ToString()]));
}
else
if (profile[i].ToString() != "-" && profile[i].ToString() != "X")
{
throw new Exception("Unknow state: " + profile[i].ToString() + " in structure " + name + " in profile " + node.profName + " profile!");
}
else
{
newProfile.Add(0);
}
}
}
line = wr.ReadLine();
}
info = new protInfo();
info.sequence = seq;
info.profile = newProfile;
if (!dic.ContainsKey(name))
{
dic.Add(name, info);
}
else
{
ErrorBase.AddErrors("There are two the same names " + name + " in the profile file " + GetProfileFileName(fileName));
}
wr.Close();
currentProgress = maxV;
return(dic);
}