コード例 #1
0
        public override List <byte> CreateNewProfile(profileNode node, string[] profile)
        {
            List <byte> newProfile = new List <byte>(profile.Length);

            for (int i = 0; i < profile.Length; i++)
            {
                string state = profile[i];
                if (node.ContainsState(state))
                {
                    if (Convert.ToInt32(state, System.Globalization.CultureInfo.InvariantCulture) > 255)
                    {
                        state = "255";
                    }
                }
                if (node.ContainsState(state))
                {
                    newProfile.Add(node.GetCodedState(node.states[state], true));
                }
                else
                {
                    ErrorBase.AddErrors("Unknow state " + state + " in " + node.profName + " profile!");
                }
            }
            return(newProfile);
        }
コード例 #2
0
        public virtual List <byte> CreateNewProfile(profileNode node, string [] profile)
        {
            List <byte> newProfile = new List <byte>(profile.Length);

            for (int i = 0; i < profile.Length; i++)
            {
                string state = profile[i];
                if (node.ContainsState(state))
                {
                    newProfile.Add(node.GetCodedState(node.states[state]));
                }
                else
                {
                    ErrorBase.AddErrors("Unknow state " + state + " in " + node.profName + " profile!");
                }
            }
            return(newProfile);
        }
コード例 #3
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;
        }
コード例 #4
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;
                        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);
        }
コード例 #5
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(" 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);
        }
コード例 #6
0
        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);
        }
コード例 #7
0
        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);
        }
コード例 #8
0
        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;

        }
コード例 #9
0
        public virtual List<byte> CreateNewProfile(profileNode node,string [] profile)
        {
            List <byte>newProfile = new List<byte>(profile.Length);

            for (int i = 0; i < profile.Length; i++)
            {
                string state = profile[i];
                if (node.ContainsState(state))
                    newProfile.Add(node.GetCodedState(node.states[state]));
                else
                    ErrorBase.AddErrors("Unknow state " + state + " in " + node.profName + " profile!");
            }
            return newProfile;
        }