//查看一个序列中的是否包含修饰，返回蛋白protein中的modification修饰列表的索引位置
private static void update_protein_modification(Protein protein, ObservableCollection <PSM> psms)
{
List <Protein_Mod> modification = new List <Protein_Mod>();
for (int i = 0; i < protein.psm_index.Count; ++i)
{
string mod_sits = psms[protein.psm_index[i]].Mod_sites;
List <string> mods = Modification.get_modSites_list(mod_sits);
for (int p = 0; p < mods.Count; ++p)
{
Protein_Mod mod_tmp = new Protein_Mod(mods[p]);
int index = modification.IndexOf(mod_tmp);
if (index == -1)
{
modification.Add(mod_tmp);
}
else
{
++modification[index].mod_count;
}
}
}
modification.Sort();
protein.modification = modification;
}
public bool Equals(Protein_Mod other)
{
if (other == null)
{
return(false);
}
return(this.modification.Equals(other.modification)); // && this.mod_index.Equals(other.mod_index)
}
int IComparable.CompareTo(Object obj)
{
Protein_Mod temp = (Protein_Mod)obj;
if (this.mod_count < temp.mod_count)
{
return(1);
}
else if (this.mod_count > temp.mod_count)
{
return(-1);
}
return(0);
}
public override bool Equals(object obj)
{
if (obj == null)
{
return(false);
}
Protein_Mod temp = obj as Protein_Mod;
if (temp == null)
{
return(false);
}
else
{
return(Equals(temp));
}
}
public static List <Protein_Modification> get_modSites_list(int start, int peptide_length, string modStr, Protein protein)
{
List <Protein_Modification> mods = new List <Protein_Modification>();
string[] all_mod = modStr.Split(';');
for (int i = 0; i < all_mod.Length - 1; ++i)
{
string[] one_mod = all_mod[i].Split(',');
int peptide_index = int.Parse(one_mod[0]);
if (peptide_index == 0)
{
peptide_index = 1;
}
else if (peptide_index == peptide_length + 1)
{
peptide_index = peptide_length;
}
string mod_name = one_mod[1].Split('#')[0];
Protein_Mod mod_tmp = new Protein_Mod(mod_name);
mods.Add(new Protein_Modification(start + peptide_index - 1, protein.modification.IndexOf(mod_tmp)));
}
return(mods);
}
