//reset search
void Reset_Inter.ResetSearch(SearchParam sp)
{
sp.Db_index = -1;
sp.setDatabase();
sp.Enzyme_index = 0;
sp.setEnzyme();
sp.Enzyme_Spec_index = 0;
sp.setEnzymeSpec();
sp.Cleavages = 3; //default
sp.Ptl.Tl_value = 20;
sp.Ptl.Isppm = 1;
sp.Ftl.Tl_value = 20;
sp.Ftl.Isppm = 1;
sp.Open_search = true;
sp.Fix_mods.Clear();
sp.Var_mods.Clear();
}
//read from pFind.pfd
void pFind_Inter.readpFind_pfd(string task_path, bool pParse, ref _Task _task)
{
try
{
File _file = _task.T_File;
SearchParam _search = _task.T_Search;
FilterParam _filter = _task.T_Filter;
QuantitationParam _quantitation = _task.T_Quantitation;
FileStream fst = new FileStream(task_path + "\\param\\pFind.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
string strLine = sr.ReadLine();
string subtitle = "";
#region
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine[0] == '#')
{
strLine = sr.ReadLine();
continue;
}
if (strLine.Length > 0 && strLine[0] == '[' && strLine[strLine.Length - 1] == ']')
{
subtitle = strLine;
}
else
{
#region [param]
if (subtitle.Equals("[param]"))
{
if (strLine.Length > 15 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("activation_type"))
{
_file.Instrument = strLine.Substring(strLine.LastIndexOf("=") + 1);
_file.setInstrument_index();
}
else if (strLine.Length > 5 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("mstol"))
{
_search.Ptl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 8 && strLine.Substring(0, 8).Equals("mstolppm"))
{
_search.Ptl.Isppm = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 7 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("msmstol"))
{
_search.Ftl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("msmstolppm"))
{
_search.Ftl.Isppm = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("temppepnum"))
{
_search.Search_advanced.Temppepnum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 6 && strLine.Substring(0, 6).Equals("pepnum"))
{
_search.Search_advanced.Pepnum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("selectpeak"))
{
_search.Search_advanced.Selectpeak = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 9 && strLine.Substring(0, 9).Equals("maxprolen"))
{
_search.Search_advanced.Maxprolen = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 7 && strLine.Substring(0, 7).Equals("maxspec"))
{
_search.Search_advanced.Maxspec = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > "IeqL".Length && strLine.Substring(0, "IeqL".Length).Equals("IeqL"))
{
_search.Search_advanced.IeqL = (strLine.Substring(strLine.LastIndexOf("=") + 1) == "1") ? true : false;
}
else if (strLine.Length > "npep".Length && strLine.Substring(0, "npep".Length).Equals("npep"))
{
_search.Search_advanced.NPeP = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > "maxdelta".Length && strLine.Substring(0, "maxdelta".Length).Equals("maxdelta"))
{
_search.Search_advanced.MAXDelta = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 9 && strLine.Substring(0, 9).Equals("selectmod"))
{
string tmpvar = strLine.Trim();
string tmpfix = sr.ReadLine().Trim();
if (tmpvar.Equals("selectmod="))
{
if (tmpfix.Equals("fixmod="))
{
//_search.Open_search = true;
}
_search.Var_mods.Clear();
}
else
{
tmpvar = tmpvar.Substring(strLine.LastIndexOf("=") + 1);
//_search.Open_search = false;
string[] tmpv = tmpvar.Split(';');
foreach (string c in tmpv)
{
if (c != "")
{
_search.Var_mods.Add(c);
}
}
}
if (tmpfix.Equals("fixmod="))
{
_search.Fix_mods.Clear();
}
else
{
tmpfix = tmpfix.Substring(tmpfix.LastIndexOf("=") + 1);
//_search.Open_search = false;
string[] tmpf = tmpfix.Split(';');
foreach (string c in tmpf)
{
if (c != null)
{
_search.Fix_mods.Add(c);
}
}
}
}
else if (strLine.Length > 6 && strLine.Substring(0, 6).Equals("maxmod"))
{
_search.Search_advanced.Maxmod = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 6 && strLine.Substring(0, 6).Equals("enzyme"))
{
_search.Enzyme = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Enzyme_index = _search.setEnzymeIndex();
}
else if (strLine.Length > 6 && strLine.Substring(0, 6).Equals("digest"))
{
int digestway = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
if (digestway == 3)
{
_search.Enzyme_Spec_index = 0;
}
else if (digestway > 0)
{
_search.Enzyme_Spec_index = 1;
}
else
{
_search.Enzyme_Spec_index = 2;
}
_search.setEnzymeSpec();
}
else if (strLine.Length > 13 && strLine.Substring(0, 13).Equals("max_clv_sites"))
{
_search.Cleavages = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
}
#endregion
#region [filter]
if (subtitle.Equals("[filter]"))
{
if (strLine.Length > 7 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("psm_fdr"))
{
_filter.Fdr.Fdr_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) * 100;
}
else if (strLine.Length > 12 && strLine.Substring(0, 8).Equals("psm_fdr_type"))
{
_filter.Fdr.IsPeptides = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("mass_lower"))
{
_filter.Pep_mass_range.Left_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("mass_upper"))
{
_filter.Pep_mass_range.Right_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 9 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("len_lower"))
{
_filter.Pep_length_range.Left_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 9 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("len_upper"))
{
_filter.Pep_length_range.Right_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 11 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pep_per_pro"))
{
_filter.Min_pep_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 7 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pro_fdr"))
{
_filter.Protein_Fdr = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) * 100;
}
}
#endregion
else if (subtitle.Equals("[engine]"))
{
if (strLine.Length > 4 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("open"))
{
_search.Open_search = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) == 1 ? true : false;
}
else if (strLine.Length > 12 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("open_tag_len"))
{
_search.Search_advanced.Open_tag_len = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 18 && strLine.Substring(0, 18).Equals("rest_tag_iteration"))
{
_search.Search_advanced.Rest_tag_iteration = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 12 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("rest_tag_len"))
{
_search.Search_advanced.Rest_tag_len = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 12 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("rest_mod_num"))
{
_search.Search_advanced.Rest_mod_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 15 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("salvo_iteration"))
{
_search.Search_advanced.Salvo_iteration = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 13 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("salvo_mod_num"))
{
_search.Search_advanced.Salvo_mod_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
}
#region file
else if (subtitle.Equals("[file]"))
{
if (strLine.Length > 9 && strLine.Substring(0, 9).Equals("fastapath"))
{
string db_path = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (db_path.Trim().Length > 0)
{
DB db = new DB();
db.Db_path = db_path;
if (ConfigHelper.ReDBmap.Contains(db.Db_path))
{
db.Db_name = ConfigHelper.ReDBmap[db.Db_path].ToString();
_search.Db = db;
_search.Db_index = _search.setDatabaseIndex();
}
else //the database is damaged
{
_search.Db_index = -1;
_search.Db = db;
}
}
else //when new a task
{
_search.Db_index = -1;
_search.Db = new DB();
}
#region Todo
//当不存在指定数据库时
#endregion
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("outputpath"))
{
string tpath = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (tpath.Trim().Length > 0)
{
if (task_path.EndsWith("\\"))
{
task_path = task_path.Substring(0, task_path.Length - 1);
}
_task.Path = task_path + "\\";
_task.Task_name = task_path.Substring(task_path.LastIndexOf("\\") + 1);
sr.ReadLine();
}
}
}
#endregion
#region [datalist]
else if (subtitle.Equals("[datalist]"))
{
//if (strLine.Length > 7 && strLine.Substring(0, 7).Equals("msmsnum") && (!pParse))
//{
// #region
// //默认：raw经处理后统一用PF2，只要是MGF文件，则必定是用户添加的
// #endregion
// //if new a task, then dtnum=0
// int msmsnum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
// _file.Data_file_list.Clear();
// for (int i = 0; i < msmsnum; i++)
// {
// strLine = sr.ReadLine().Trim();
// if (strLine.Length > 8 && strLine.Substring(0, 8).Equals("msmspath"))
// {
// string filep = strLine.Substring(strLine.LastIndexOf("=") + 1);
// if (filep.Substring(filep.LastIndexOf(".") + 1).Equals("mgf") || filep.Substring(filep.LastIndexOf(".") + 1).Equals("MGF"))
// {
// _file.File_format_index = (int)FormatOptions.MGF;
// _file.File_format = "mgf";
// }
// if (System.IO.File.Exists(filep))
// {
// _file.Data_file_list.Add(new _FileInfo(filep));
// }
// else
// {
// System.Windows.MessageBox.Show("\"" + filep + "\" does not exist.");
// }
// }
// }
//}
}
#endregion
#region Todo quant
else if (subtitle.Equals("[quant]"))
{
if (strLine.Length > 5 && strLine.Substring(0, 5).Equals("quant"))
{
string qt = strLine.Substring(strLine.LastIndexOf("=") + 1);
string[] lb = qt.Split('|');
int lbcount = lb.GetUpperBound(0);
int lbnum = int.Parse(lb[0]);
#region 如果是MGF文件怎么办
#endregion
//labeling
if (lbnum == 1 && (lb[1].Equals("none") || lb[1].Equals("None")))
{
_quantitation.Quantitation_type = (int)Quant_Type.Labeling_None;
_quantitation.Labeling.Multiplicity = 1;
_quantitation.Labeling.Multiplicity_index = 0;
_quantitation.Labeling.Medium_label.Add(lb[1]);
}
else
{
_quantitation.Quantitation_type = (int)Quant_Type.Labeling_SILAC; //if 15N, it will be changed in pQuant_Read
_quantitation.Labeling.Multiplicity = lbnum;
_quantitation.Labeling.Multiplicity_index = lbnum - 1;
if (lbnum == 1)
{
/*
* string[] lbs = lb[1].Split(',');
* foreach (string c in lbs)
* {
* if (c.Trim() != ""&&c.ToLower()!="none")
* {
* _quantitation.Labeling.Medium_label.Add(c.Trim());
* }
* }*/
_quantitation.Labeling.Medium_label.Add(lb[1]);
}
else if (lbnum == 2)
{
if (lb[1].Equals(ConfigHelper.N15_label) || lb[2].Equals(ConfigHelper.N15_label))
{
_quantitation.Quantitation_type = (int)Quant_Type.Labeling_15N;
}
_quantitation.Labeling.Light_label.Add(lb[1]);
_quantitation.Labeling.Heavy_label.Add(lb[2]);
}
else if (lbnum == 3)
{
_quantitation.Labeling.Light_label.Add(lb[1]);
_quantitation.Labeling.Medium_label.Add(lb[2]);
_quantitation.Labeling.Heavy_label.Add(lb[3]);
}
}
}
}
#endregion
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}