public override void AddInternalProfiles()
{
profileNode node = new profileNode();
node.profName = "SA CA";
node.internalName = "SA 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);
}
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;
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);
}
private void button2_Click(object sender, EventArgs e)
{
localNode.profName = textBox1.Text;
for (int i = 0; i < dataGridView1.Rows.Count; i++)
{
if (dataGridView1.Rows[i].Cells[0].Value != null && dataGridView1.Rows[i].Cells[1].Value != null)
{
localNode.AddStateItem((string)dataGridView1.Rows[i].Cells[0].Value, (string)dataGridView1.Rows[i].Cells[1].Value);
}
}
localNode.profWeights.Clear();
for (int i = 0; i < dataGridView2.Rows.Count; i++)
{
if (dataGridView2.Rows[i].Cells[0].Value != null && dataGridView2.Rows[i].Cells[1].Value != null)
{
string item1 = (string)dataGridView2.Rows[i].Cells[0].Value;
string item2 = (string)dataGridView2.Rows[i].Cells[1].Value;
if (localNode.profWeights.ContainsKey(item1))
{
if (localNode.profWeights[item1].ContainsKey(item2))
{
localNode.profWeights[item1].Remove(item2);
}
localNode.profWeights[item1].Add(item2, Convert.ToDouble(dataGridView2.Rows[i].Cells[2].Value.ToString()));
}
else
{
SerializableDictionary <string, double> ww = new SerializableDictionary <string, double>();
ww.Add(item2, Convert.ToDouble(dataGridView2.Rows[i].Cells[2].Value.ToString()));
localNode.profWeights.Add(item1, ww);
}
}
}
this.DialogResult = DialogResult.OK;
this.Close();
}
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 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);
}
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 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 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);
}