private void AlignProfile(string protName, string profileName, List <byte> prof)
{
List <byte> ll = new List <byte>(prof.Count);
int m = 0;
if (align == null || align[profileName] == null || !align[profileName].ContainsKey(protName))
{
foreach (var item in prof)
{
ll.Add(item);
}
}
else
{
string alignProfile = align[profileName][protName];
for (int i = 0; i < alignProfile.Length; i++)
{
if (alignProfile[i] == '-')
{
ll.Add(0);
continue;
}
if (m < prof.Count)
{
ll.Add(prof[m++]);
}
else
{
ErrorBase.AddErrors("Profile " + profileName + " for " + protName + " seems to be incorect");
}
}
}
protInfo tmp = new protInfo();
if (r.profiles[profileName].ContainsKey(protName))
{
tmp = r.profiles[profileName][protName];
tmp.alignment = ll;
r.profiles[profileName][protName] = tmp;
}
}
public int GetProfileLength()
{
if (profiles == null || profiles.Count == 0)
{
return(0);
}
List <string> profName = new List <string>(profiles.Keys);
List <string> protName = new List <string>(profiles[profName[0]].Keys);
if (protName == null || protName.Count == 0)
{
return(0);
}
protInfo info = profiles[profName[0]][protName[0]];
return(info.alignment.Count);
}
public Dictionary <string, protInfo> ReadProfile(profileNode node)
{
string line;
bool flag = false;
protInfo profile;
Dictionary <string, protInfo> profList = new Dictionary <string, protInfo>();
string protName;
if (File.Exists(node.OutFileName))
{
StreamReader file = null;
try
{
file = new StreamReader(node.OutFileName);
line = file.ReadLine();
while (line != null)
{
if (line.Contains(">"))
{
string[] profState;
profile = new protInfo();
flag = true;
string [] nameTmp;
protName = line.Replace(">", "");
nameTmp = protName.Split(new char [] { '/', '\\' });
protName = nameTmp[nameTmp.Length - 1];
profile.sequence = file.ReadLine();
line = file.ReadLine();
profState = line.Split(' ');
profile.profile = new List <byte>(profState.Length);
foreach (var item in profState)
{
profile.profile.Add(node.GetCodedState(item));
}
if (profile.sequence.Length > 5 || profile.profile.Count != 0)
{
profList.Add(protName, profile);
}
line = file.ReadLine();
}
else
{
line = file.ReadLine();
}
}
}
finally
{
if (file != null)
{
file.Close();
}
}
if (!flag)
{
throw new Exception("Error: In the profile file: " + node.OutFileName + " could not find line that begins with > ");
}
}
return(profList);
}
public Dictionary <string, List <byte> > CombineProfiles(string protName, Dictionary <string, Dictionary <string, protInfo> > pr)
{
if (protCombineStates == null)
{
protCombineStates = new Dictionary <string, List <byte> >();
}
if (combine == profileCombination.JOIN_STATES)
{
List <string> profName = new List <string>(pr.Keys);
List <string> states = new List <string>(pr[profName[0]][protName].alignment.Count);
protInfo info = pr[profName[0]][protName];
for (int i = 0; i < info.alignment.Count; i++)
{
string currentState = "";
foreach (var profileName in pr.Keys)
{
byte cc = pr[profileName][protName].alignment[i];
if (cc == 0)
{
currentState = "0";
break;
}
currentState += cc.ToString();
}
states.Add(currentState);
}
if (states.Count > 0)
{
//return states;
if (protCombineStates.Count > 0)
{
List <string> keys = new List <string>(protCombineStates.Keys);
if (states.Count == protCombineStates[keys[0]].Count)
{
AddItemsCombineStates(protName, states);
}
else
{
ErrorBase.AddErrors("Wrong alignment: " + protName);
}
}
else
{
AddItemsCombineStates(protName, states);
}
}
}
else
{
List <string> profNames = new List <string>(pr.Keys);
for (int i = 0; i < profNames.Count; i++)
{
List <string> codes = new List <string>();
foreach (var code in pr[profNames[i]][protName].alignment)
{
if (code != 0)
{
codes.Add(code.ToString() + "_" + i);
}
else
{
codes.Add("0");
}
AddItemsCombineStates(protName, codes);
codes.Clear();
}
}
}
return(protCombineStates);
}