public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = ProfileName;
node.internalName = ProfileName;
InternalProfilesManager.AddNodeToList(node, typeof(UserDefinedProfile).FullName);
}
public bool CheckAccessibility(profileNode profile, INPUTMODE type)
{
Type t = Type.GetType(internalList[profile]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
if (c.destination.Contains(type))
{
return(true);
}
return(false);
}
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 static void AddNodeToList(profileNode node, string type)
{
profileNode nn = GetNode(node.internalName);
if (nn == null)
{
if (!internalList.ContainsKey(node))
{
internalList.Add(node, type);
SaveProfiles();
}
}
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = profileName;
node.internalName = profileName;
node.AddStateItem("0", "0");
node.AddStateItem("1", "1");
node.AddStateItem("2", "2");
node.AddStateItem("3", "3");
InternalProfilesManager.AddNodeToList(node, typeof(ContactMapProfileRNA).FullName);
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = profileName;
node.internalName = profileName;
for (int i = 0; i < 255; i++)
{
node.AddStateItem(i.ToString(), i.ToString(), true);
}
InternalProfilesManager.AddNodeToList(node, typeof(FragBagProfile).FullName);
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = profileName;
node.internalName = profileName;
node.AddStateItem("0", "0");
node.AddStateItem("1", "1");
node.AddStateItem("2", "2");
node.AddStateItem("3", "3");
InternalProfilesManager.AddNodeToList(node, typeof(ContactMapProfileRNA).FullName);
}
public void RunProfile(string name, string listFile)
{
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.RunThreads(listFile);
progressInfo = null;
progress++;
}
}
public InternalProfileForm(profileNode node,filterOPT filter,bool flag=true)
{
InitializeComponent();
if(filter==filterOPT.SIMILARITY)
{
button4.Visible = false;
button3.Visible = true;
}
else
{
button4.Visible = true;
button3.Visible = false;
}
if (node == null)
return;
if(node.internalName==UserDefinedProfile.ProfileName)
dataGridView1.Columns["Column1"].ReadOnly = false;
else
dataGridView1.Columns["Column1"].ReadOnly = flag;
localNode.profProgram = node.profProgram;
localNode.internalName = node.internalName;
textBox1.Text = node.profName;
if (node.GetNumberofStates()> 0)
{
dataGridView1.Rows.Add(node.GetNumberofStates());
int i = 0;
foreach (var item in node.states)
{
dataGridView1.Rows[i].Cells[0].Value = item.Key;
dataGridView1.Rows[i++].Cells[1].Value = item.Value;
}
foreach (var item in node.profWeights.Keys)
{
foreach (var item2 in node.profWeights[item].Keys)
{
dataGridView2.Rows.Add(1);
int index = dataGridView2.Rows.Count - 2;
dataGridView2.Rows[index].Cells[0].Value = item;
dataGridView2.Rows[index].Cells[1].Value = item2;
dataGridView2.Rows[index].Cells[2].Value = node.profWeights[item][item2].ToString();
}
}
}
}
public Dictionary <string, protInfo> GetProfile(profileNode node, string listFile)
{
profileNode n = GetNode(node.internalName);
if (n != null)
{
Type t = Type.GetType(internalList[n]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
progressInfo = c;
Dictionary <string, protInfo> res = c.GetProfile(node, listFile, null);
progressInfo = null;
progress++;
return(res);
}
return(null);
}
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);
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = "Contact";
node.internalName = "Contact";
for (int i = 0; i < 10; i++)
{
node.AddStateItem(i.ToString(), i.ToString());
}
//manager.AddNodeToList(node, "P");
node.AddStateItem("T", "T");
node.AddStateItem("C", "C");
node.AddStateItem("P", "P");
node.AddStateItem("H", "H");
node.AddStateItem("E", "E");
InternalProfilesManager.AddNodeToList(node, typeof(ContactProfile).FullName);
}
public ProfileDefinitionForm(profileNode profile)
{
InitializeComponent();
this.profile = profile;
textBox1.Text = profile.profName;
textBox2.Text = profile.profProgram;
textBox3.Text = profile.OutFileName;
if (profile.progParameters == null)
profile.progParameters = "input_file";
textBox4.Text = profile.progParameters;
checkBox1.Checked = profile.removeOutFile;
foreach (var item in profile.profWeights.Keys)
{
foreach (var item2 in profile.profWeights[item].Keys)
{
dataGridView1.Rows.Add();
dataGridView1.Rows[dataGridView1.Rows.Count-2].Cells[0].Value = item;
dataGridView1.Rows[dataGridView1.Rows.Count-2].Cells[1].Value = item2;
dataGridView1.Rows[dataGridView1.Rows.Count-2].Cells[2].Value = profile.profWeights[item][item2].ToString();
}
}
}
public ProfileDefinitionForm(profileNode profile)
{
InitializeComponent();
this.profile = profile;
textBox1.Text = profile.profName;
textBox2.Text = profile.profProgram;
textBox3.Text = profile.OutFileName;
if (profile.progParameters == null)
{
profile.progParameters = "input_file";
}
textBox4.Text = profile.progParameters;
checkBox1.Checked = profile.removeOutFile;
foreach (var item in profile.profWeights.Keys)
{
foreach (var item2 in profile.profWeights[item].Keys)
{
dataGridView1.Rows.Add();
dataGridView1.Rows[dataGridView1.Rows.Count - 2].Cells[0].Value = item;
dataGridView1.Rows[dataGridView1.Rows.Count - 2].Cells[1].Value = item2;
dataGridView1.Rows[dataGridView1.Rows.Count - 2].Cells[2].Value = profile.profWeights[item][item2].ToString();
}
}
}
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 void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = "RNA_SS";
node.internalName = "RNA_SS";
foreach (var item in SSList)
{
node.AddStateItem(item, item);
}
InternalProfilesManager.AddNodeToList(node, typeof(RNASSProfile).FullName);
node = new profileNode();
node.profName = "RNA_LW";
node.internalName = "RNA_LW";
foreach (var item in LWList)
{
node.AddStateItem(item, item);
}
InternalProfilesManager.AddNodeToList(node, typeof(RNASSProfile).FullName);
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = "SS";
node.internalName = "SS";
foreach (var item in SSList)
{
node.AddStateItem(item, item);
}
InternalProfilesManager.AddNodeToList(node, typeof(DsspInternalProfile).FullName);
node = new profileNode();
node.profName = "SA";
node.internalName = "SA";
for (int i = 0; i < 10; i++)
{
node.AddStateItem(i.ToString(), i.ToString());
}
InternalProfilesManager.AddNodeToList(node, typeof(DsspInternalProfile).FullName);
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = "Contact";
node.internalName = "Contact";
for (int i = 0; i < 10; i++)
node.AddStateItem(i.ToString(), i.ToString());
//manager.AddNodeToList(node, "P");
node.AddStateItem("T", "T");
node.AddStateItem("C", "C");
node.AddStateItem("P", "P");
node.AddStateItem("H", "H");
node.AddStateItem("E", "E");
InternalProfilesManager.AddNodeToList(node, typeof(ContactProfile).FullName);
}
public static ProfileTree AnalyseProfileFile(string fileName, SIMDIST similarityFlag, string internalName = null)
{
ProfileTree t = new ProfileTree();
StreamReader wr;
if (fileName == null || !File.Exists(fileName))
{
throw new Exception("File:" + fileName + " not exists");
}
wr = new StreamReader(fileName);
string line = wr.ReadLine();
Dictionary <string, Dictionary <string, int> > dic = new Dictionary <string, Dictionary <string, int> >();
while (line != null)
{
if (line.Contains(">"))
{
line = wr.ReadLine();
while (line != null && line[0] != '>')
{
if (line.Contains("profile") && !line.Contains("SEQ"))
{
string[] tmp = line.Split(new string[] { " profile " }, StringSplitOptions.None);
if (!dic.ContainsKey(tmp[0]))
{
dic.Add(tmp[0], new Dictionary <string, int>());
}
string[] aux;
if (tmp[1].Contains(" "))
{
aux = tmp[1].Split(' ');
}
else
{
aux = new string[tmp[1].Length];
for (int i = 0; i < tmp[1].Length; i++)
{
aux[i] = tmp[1][i].ToString();
}
}
foreach (var item in aux)
{
if (item != "-" && item != "")
{
if (!dic[tmp[0]].ContainsKey(item))
{
dic[tmp[0]].Add(item, 0);
}
}
}
}
line = wr.ReadLine();
}
}
else
{
line = wr.ReadLine();
}
}
wr.Close();
if (dic.Keys.Count == 0)
{
throw new Exception("File " + fileName + " is not valid Profile file!");
}
foreach (var item in dic)
{
profileNode node = new profileNode();
node.active = true;
if (internalName != null)
{
node.internalName = internalName;
}
else
{
node.internalName = "User defined profile";
}
node.profName = item.Key;
foreach (var itemK in item.Value)
{
node.AddStateItem(itemK.Key, itemK.Key);
}
node.profWeights = GenerateWeights(new List <string>(item.Value.Keys), similarityFlag);
t.AdddNode("/", node);
}
// t.pr
return(t);
}
public ProfileDefinitionForm()
{
InitializeComponent();
profile = new profileNode();
}
abstract public Dictionary <string, protInfo> GetProfile(profileNode node, string listFile, DCDFile dcd);
abstract public Dictionary<string, protInfo> GetProfile(profileNode node, string listFile,DCDFile dcd);
public Dictionary<string, protInfo> GetProfile(profileNode node,string listFile)
{
profileNode n=GetNode(node.internalName);
if (n != null)
{
Type t = Type.GetType(internalList[n]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
progressInfo = c;
Dictionary<string, protInfo> res = c.GetProfile(node, listFile, null);
progressInfo = null;
progress++;
return res;
}
return null;
}
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 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 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 static ProfileTree AnalyseProfileFile(string fileName, SIMDIST similarityFlag)
{
ProfileTree t = new ProfileTree();
StreamReader wr;
if (fileName == null || !File.Exists(fileName))
throw new Exception("File:" + fileName + " not exists");
wr = new StreamReader(fileName);
string line = wr.ReadLine();
Dictionary<string, Dictionary<string, int>> dic = new Dictionary<string, Dictionary<string, int>>();
while (line != null)
{
if (line.Contains(">"))
{
line = wr.ReadLine();
while (line != null && line[0] != '>')
{
if (line.Contains("profile") && !line.Contains("SEQ"))
{
string[] tmp = line.Split(new string[] { " profile " }, StringSplitOptions.None);
if (!dic.ContainsKey(tmp[0]))
dic.Add(tmp[0], new Dictionary<string, int>());
string[] aux;
if (tmp[1].Contains(" "))
aux = tmp[1].Split(' ');
else
{
aux = new string[tmp[1].Length];
for (int i = 0; i < tmp[1].Length; i++)
aux[i] = tmp[1][i].ToString();
}
foreach (var item in aux)
if (item != "-" && item!="")
if (!dic[tmp[0]].ContainsKey(item))
dic[tmp[0]].Add(item, 0);
}
line = wr.ReadLine();
}
}
else
line = wr.ReadLine();
}
wr.Close();
if (dic.Keys.Count == 0)
throw new Exception("File " + fileName + " is not valid Profile file!");
foreach (var item in dic)
{
profileNode node = new profileNode();
node.active = true;
node.internalName = "User defined profile";
node.profName = item.Key;
foreach (var itemK in item.Value)
node.AddStateItem(itemK.Key, itemK.Key);
node.profWeights = GenerateWeights(new List<string>(item.Value.Keys), similarityFlag);
t.AdddNode("/", node);
}
// t.pr
return t;
}
public bool CheckAccessibility(profileNode profile,INPUTMODE type)
{
Type t = Type.GetType(internalList[profile]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
if (c.destination.Contains(type))
return true;
return false;
}
public static void AddNodeToList(profileNode node,string type)
{
profileNode nn = GetNode(node.internalName);
if (nn==null)
{
if (!internalList.ContainsKey(node))
{
internalList.Add(node, type);
SaveProfiles();
}
}
}
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 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;
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = ProfileName;
node.internalName = ProfileName;
InternalProfilesManager.AddNodeToList(node, typeof(UserDefinedProfile).FullName);
}
public ProfileDefinitionForm()
{
InitializeComponent();
profile = new profileNode();
}
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 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;
}
private void EditProfile(string Path, bool edit, profileType type)
{
ProfileDefinitionForm profDef = null;
InternalProfileForm internalDef = null;
profileNode node = null;
profileNode newNode = null;
DialogResult res = DialogResult.Cancel;
if (edit)
{
node = treeProfiles.FindNode(Path);
if (node.internalName != null)
{
internalDef = new InternalProfileForm(node, filter);
res = internalDef.ShowDialog();
if (res == DialogResult.OK)
{
newNode = internalDef.localNode;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
else
{
profDef = new ProfileDefinitionForm(node);
res = profDef.ShowDialog();
if (res == DialogResult.OK)
{
newNode = profDef.profile;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
}
else
{
if (Path == null)
{
Path = "Profiles";
}
if (type == profileType.EXTERNAL)
{
profDef = new ProfileDefinitionForm();
res = profDef.ShowDialog();
if (res == DialogResult.OK)
{
node = profDef.profile;
node.internalName = null;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
else
{
Settings set = new Settings();
set.Load();
InternalProfilesManager manager = new InternalProfilesManager();
List <profileNode> validProfiles = new List <profileNode>();
foreach (var item in InternalProfilesManager.internalList.Keys)
{
if (manager.CheckAccessibility(item, set.mode))
{
validProfiles.Add(item);
}
}
ListInternal intr = new ListInternal(validProfiles);
res = intr.ShowDialog();
if (res == DialogResult.OK)
{
InternalProfileForm intForm;
profileNode localNode = InternalProfilesManager.GetNode(intr.selectedProfile);
if (localNode.profName.Contains("Load"))
{
intForm = new InternalProfileForm(localNode, filter, false);
}
else
{
intForm = new InternalProfileForm(localNode, filter);
}
res = intForm.ShowDialog();
if (res == DialogResult.OK)
{
node = intForm.localNode;
node.profProgram = intr.selectedProfile;
newNode = node;
toolSave.Enabled = true;
toolStripButton6.Enabled = true;
}
}
}
}
if (res == DialogResult.OK)
{
if (node != null && File.Exists(node.OutFileName))
{
File.Delete(node.OutFileName);
}
//profChanged = true;
if (!edit)
{
//profChanged = true;
Regex exp = new Regex("^/");
TreeNode nodeT;//= new TreeNode(profDef.profile.profName);
string nPath = "";
if (Path != null)
{
nPath = exp.Replace(Path, "");
}
if (profilesView.SelectedNode == null)
{
nodeT = profilesView.Nodes[0].Nodes.Add(node.profName);
profilesView.Nodes[0].Expand();
}
else
{
nodeT = profilesView.SelectedNode.Nodes.Add(node.profName);
profilesView.SelectedNode.Expand();
}
nodeT.Tag = newNode;
Regex exp2 = new Regex("^Profiles");
Path = exp2.Replace(Path, "");
treeProfiles.AdddNode(Path, node);
}
else
{
profilesView.SelectedNode.Text = node.profName;
treeProfiles.RemoveNode(Path);
Regex exp2 = new Regex("^Profiles");
Path = exp2.Replace(Path, "");
treeProfiles.AdddNode(ParentPath(Path), newNode);
node.CopyNode(newNode);
ShowTree();
}
}
}
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);
}
public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = "Contact CA";
node.internalName = "Contact CA";
for (int i = 0; i < 10; i++)
node.AddStateItem(i.ToString(), i.ToString());
InternalProfilesManager.AddNodeToList(node, typeof(CAProfiles).FullName);
node = new profileNode();
node.profName = "SS CA";
node.internalName = "SS CA";
node.AddStateItem("H", "H");
node.AddStateItem("J", "J");
node.AddStateItem("K", "K");
node.AddStateItem("L", "L");
node.AddStateItem("E", "E");
node.AddStateItem("R", "R");
node.AddStateItem("T", "T");
node.AddStateItem("Y", "Y");
node.AddStateItem("U", "U");
node.AddStateItem("N", "N");
InternalProfilesManager.AddNodeToList(node, typeof(CAProfiles).FullName);
}
