public Summary(File _file, SearchParam _search, FilterParam _filter, QuantitationParam _quantitation)
{
this.file = _file;
this.search = _search;
this.filter = _filter;
this.quantitation = _quantitation;
}
void Copy_Inter.QuantitaionCopy(QuantitationParam sq, QuantitationParam dq)
{
dq.Quantitation_type = sq.Quantitation_type;
Factory.Create_Copy_Instance().LabelingCopy(sq.Labeling, dq.Labeling);
Factory.Create_Copy_Instance().QuantAdvancedCopy(sq.Quant_advanced, dq.Quant_advanced);
Factory.Create_Copy_Instance().QuantInferenceCopy(sq.Quant_inference, dq.Quant_inference);
#region Todo
//Label Free
#endregion
}
//begin search
//void Run_Inter.StartSearchWork(_Task _task)
//{
// try
// {
// if (_task.Check_ok == false)
// {
// MessageBox.Show("The configuration is not completed!", "pFind", MessageBoxButton.OK, MessageBoxImage.Warning);
// }
// else
// {
// Factory.Create_Run_Instance().SaveParams(_task);
// Process process = new Process();
// process.StartInfo.UseShellExecute = false;
// process.StartInfo.CreateNoWindow = true;
// process.StartInfo.RedirectStandardOutput = true;
// process.StartInfo.RedirectStandardError = true;
// if (_task.T_File.File_format.Equals("raw"))
// {
// for (int i = 0; i < _task.T_File.Data_file_list.Count; i++)
// {
// string xtract = "-a -ms -m " + _task.T_File.Mz_decimal.ToString() + " -i " + _task.T_File.Intensity_decimal.ToString() + " \"" + _task.T_File.Data_file_list[i].FilePath.ToString() + "\"";
// process.StartInfo.FileName = "xtract.exe";
// process.StartInfo.Arguments = xtract;
// if (process.Start())
// {
// }
// process.WaitForExit();
// }
// process.StartInfo.FileName = "pParse.exe";
// process.StartInfo.Arguments = _task.Path + "param\\pParse.para";
// if (process.Start())
// {
// }
// process.WaitForExit();
// }
// process.StartInfo.FileName = "pFind.exe";
// process.StartInfo.Arguments = _task.Path + "param\\pFind.pfd";
// if (process.Start())
// {
// }
// process.WaitForExit();
// process.Close();
// }
// }
// catch (Exception ex)
// {
// Console.Write(ex.Message);
// System.Windows.MessageBox.Show("Sorry, there is something wrong with pFind!");
// }
//}
//check params of the task
bool Run_Inter.Check_Task(_Task _task)
{
File _file = _task.T_File;
SearchParam _sp = _task.T_Search;
FilterParam _fp = _task.T_Filter;
QuantitationParam _qp = _task.T_Quantitation;
//check file
if (_file.File_format_index != (int)FormatOptions.MGF && _file.File_format_index != (int)FormatOptions.RAW)
{
return(false);
}
if (_file.Data_file_list == null || _file.Data_file_list.Count == 0)
{
return(false);
}
#region Todo
//参数检查
#endregion
if (_file.Threshold.ToString() == "")
{
return(false);
}
//check search
if (_sp.Ptl.Tl_value.ToString() == "" || _sp.Ftl.Tl_value.ToString() == "")
{
return(false);
}
if (_sp.Db.Db_name == "null" || _sp.Db.Db_path == "null")
{
return(false);
}
//check filter
if (_fp.Fdr.Fdr_value.ToString() == "")
{
return(false);
}
if (_fp.Pep_mass_range.Left_value.ToString() == "" || _fp.Pep_mass_range.Right_value.ToString() == "" || _fp.Pep_mass_range.Left_value > _fp.Pep_mass_range.Right_value)
{
return(false);
}
if (_fp.Pep_length_range.Left_value.ToString() == "" || _fp.Pep_length_range.Right_value.ToString() == "" || _fp.Pep_length_range.Left_value > _fp.Pep_length_range.Right_value)
{
return(false);
}
if (_fp.Min_pep_num.ToString() == "")
{
return(false);
}
//check Quantitation
_task.Check_ok = true;
return(true);
}
//reset quantitation
void Reset_Inter.ResetQuantatition(QuantitationParam qp)
{
qp.Quantitation_type = (int)Quant_Type.Labeling_None;
qp.Labeling.Multiplicity_index = 0; //multiplicity=1
qp.Labeling.setMultiplicity();
#region Todo
//标记初始化
#endregion
qp.Labeling.Light_label.Clear();
qp.Labeling.Medium_label.Clear();
qp.Labeling.Medium_label.Add(ConfigHelper.labels[0]);
qp.Labeling.Heavy_label.Clear();
#region Todo
//Labelfree
#endregion
qp.Lf = new LabelFree();
qp.Quant_advanced.Number_scans_half_cmtg = 100;
qp.Quant_advanced.Ppm_for_calibration = 0.0;
qp.Quant_advanced.Ppm_half_win_accuracy_peak = 10.0;
qp.Quant_advanced.Number_hole_in_cmtg = 1; //index=1,value=2
qp.Quant_advanced.Type_same_start_end_between_evidence = 0;
qp.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.None;
}
//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);
}
}
//generate pFind.pfd
void pFind_Inter.pFind_write(_Task _task)
{
try
{
File _file = _task.T_File;
SearchParam _search = _task.T_Search;
FilterParam _filter = _task.T_Filter;
QuantitationParam _quantitation = _task.T_Quantitation;
StreamReader sr = new StreamReader(@"pFind.ini", Encoding.Default);
string strLine = sr.ReadLine();
string thread = "";
while (strLine != null)
{
if (strLine.Length > 6 && strLine.Substring(0, 6).Equals("thread"))
{
thread = strLine.Substring(strLine.LastIndexOf("=") + 1);
}
if (thread != "")
{
break;
}
strLine = sr.ReadLine();
}
string filepath = _task.Path + "param\\pFind.cfg";
FileStream pFfst = new FileStream(filepath, FileMode.Create, FileAccess.Write);
StreamWriter pFsw = new StreamWriter(pFfst, Encoding.Default);
pFsw.WriteLine("# This is a standard pFind configure file");
pFsw.WriteLine("# For help: mail to [email protected]");
pFsw.WriteLine("# Time: " + DateTime.Now.ToString());
pFsw.WriteLine();
pFsw.WriteLine("[Version]");
pFsw.WriteLine("pFind_Version=EVA.3.0.11");
pFsw.WriteLine();
pFsw.WriteLine("[param]");
pFsw.WriteLine("thread=" + thread);
pFsw.WriteLine("activation_type=" + _file.Instrument);
pFsw.WriteLine("mstol=" + _search.Ptl.Tl_value.ToString());
pFsw.WriteLine("mstolppm=" + _search.Ptl.Isppm.ToString());
pFsw.WriteLine("msmstol=" + _search.Ftl.Tl_value.ToString());
pFsw.WriteLine("msmstolppm=" + _search.Ftl.Isppm.ToString());
pFsw.WriteLine("temppepnum=" + _search.Search_advanced.Temppepnum.ToString()); //中间结果数目，Hidden parameters
pFsw.WriteLine("pepnum=" + _search.Search_advanced.Pepnum.ToString()); //number of output_peptides
pFsw.WriteLine("selectpeak=" + _search.Search_advanced.Selectpeak.ToString()); //预处理保存谱峰数目,Hidden parameters
pFsw.WriteLine("maxprolen=" + _search.Search_advanced.Maxprolen.ToString()); //切分数据库长度限制,Hidden parameters or advanced
pFsw.WriteLine("maxspec=" + _search.Search_advanced.Maxspec.ToString()); //切分谱图规模限制,Hidden parameters or advanced
pFsw.WriteLine("IeqL=" + (_search.Search_advanced.IeqL?"1":"0"));
pFsw.WriteLine("npep=" + _search.Search_advanced.NPeP.ToString());
pFsw.WriteLine("maxdelta=" + _search.Search_advanced.MAXDelta.ToString()); //
string varmods = "selectmod=";
string fixmods = "fixmod=";
//if (!_search.Open_search) //开放和限定都要写修饰信息
{
for (int i = 0; i < _search.Var_mods.Count; i++)
{
if (_search.Var_mods[i].Trim().Length > 0)
{
varmods += _search.Var_mods[i] + ";";
}
}
for (int i = 0; i < _search.Fix_mods.Count; i++)
{
if (_search.Fix_mods[i].Trim().Length > 0)
{
fixmods += _search.Fix_mods[i] + ";";
}
}
}
pFsw.WriteLine(varmods);
pFsw.WriteLine(fixmods);
pFsw.WriteLine("maxmod=" + _search.Search_advanced.Maxmod); //when beam search, advanced
pFsw.WriteLine("enzyme=" + _search.Enzyme);
int digest = 3;
if (_search.Enzyme_Spec_index == 1)
{
digest = 1;
}
else if (_search.Enzyme_Spec_index == 2)
{
digest = 0;
}
pFsw.WriteLine("digest=" + digest);
pFsw.WriteLine("max_clv_sites=" + _search.Cleavages.ToString());
pFsw.WriteLine();
pFsw.WriteLine("[filter]");
pFsw.WriteLine("psm_fdr=" + (_filter.Fdr.Fdr_value / 100).ToString());
pFsw.WriteLine("psm_fdr_type=" + _filter.Fdr.IsPeptides.ToString()); //1是peptide，0是spectra
pFsw.WriteLine("mass_lower=" + _filter.Pep_mass_range.Left_value.ToString());
pFsw.WriteLine("mass_upper=" + _filter.Pep_mass_range.Right_value.ToString());
pFsw.WriteLine("len_lower=" + _filter.Pep_length_range.Left_value.ToString());
pFsw.WriteLine("len_upper=" + _filter.Pep_length_range.Right_value.ToString());
pFsw.WriteLine("pep_per_pro=" + _filter.Min_pep_num.ToString());
pFsw.WriteLine("pro_fdr=" + (_filter.Protein_Fdr / 100).ToString());
pFsw.WriteLine();
pFsw.WriteLine("[engine]");
pFsw.WriteLine("open=" + (_search.Open_search ? "1" : "0")); //open search default param
pFsw.WriteLine("open_tag_len=" + _search.Search_advanced.Open_tag_len.ToString()); //open search default param
pFsw.WriteLine();
pFsw.WriteLine("rest_tag_iteration=" + _search.Search_advanced.Rest_tag_iteration.ToString());
pFsw.WriteLine("rest_tag_len=" + _search.Search_advanced.Rest_tag_len.ToString());
pFsw.WriteLine("rest_mod_num=" + _search.Search_advanced.Rest_mod_num.ToString());
pFsw.WriteLine();
pFsw.WriteLine("salvo_iteration=" + _search.Search_advanced.Salvo_iteration.ToString());
pFsw.WriteLine("salvo_mod_num=" + _search.Search_advanced.Salvo_mod_num.ToString()); //
pFsw.WriteLine();
pFsw.WriteLine("[file]");
string modpath = "modpath=";
//获取modification.ini路径
//获取启动了应用程序的可执行文件的路径，不包括可执行文件的名称
modpath += ConfigHelper.startup_path;
modpath += "\\modification.ini"; //relative path
pFsw.WriteLine(modpath);
pFsw.WriteLine("fastapath=" + _search.Db.Db_path);
pFsw.WriteLine("outputpath=" + _task.Path + "result\\");
pFsw.WriteLine("outputname=" + _task.Task_name);
pFsw.WriteLine();
pFsw.WriteLine("[datalist]");
pFsw.WriteLine("msmsnum=" + _file.Data_file_list.Count.ToString());
string format = "PF2";
string instr = "_";
if (_file.File_format.Equals("raw") || _file.File_format.Equals("wiff"))
{
switch (_file.Instrument_index) // TODO: 冗余！ 可直接调用 setInstrument()
{
case (int)InstrumentOptions.CID_FTMS: instr += "CIDFT"; break;
case (int)InstrumentOptions.HCD_ITMS: instr += "HCDIT"; break;
case (int)InstrumentOptions.HCD_FTMS: instr += "HCDFT"; break;
case (int)InstrumentOptions.CID_ITMS: instr += "CIDIT"; break;
}
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
string pfpath = _file.Data_file_list[i].FilePath;
pfpath = pfpath.Substring(0, pfpath.LastIndexOf(".")) + instr + ".pf2"; //原raw的路径
pFsw.WriteLine("msmspath" + (i + 1).ToString() + "=" + pfpath);
}
}
else if (_file.File_format.Equals("mgf"))
{
format = "MGF";
instr = "";
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
string mgfpath = _file.Data_file_list[i].FilePath;
pFsw.WriteLine("msmspath" + (i + 1).ToString() + "=" + mgfpath);
}
}
//else
//{
// format = _file.File_format.ToUpper();
// for (int i = 0; i < _file.Data_file_list.Count; i++)
// {
// string pfpath = _file.Data_file_list[i].FilePath;
// pFsw.WriteLine("msmspath" + (i + 1).ToString() + "=" + pfpath);
// }
//}
pFsw.WriteLine("msmstype=" + format);
pFsw.WriteLine();
#region Quant
pFsw.WriteLine("[quant]");
if (_quantitation.Quantitation_type == (int)Quant_Type.Labeling_None)
{
pFsw.WriteLine("quant=1|None");
}
else if (_quantitation.Quantitation_type == (int)Quant_Type.Labeling_15N || _quantitation.Quantitation_type == (int)Quant_Type.Labeling_SILAC)
{
string labels = "quant=" + _quantitation.Labeling.Multiplicity.ToString(); //Multiplicity
if (_quantitation.Labeling.Multiplicity == 1)
{
if (_quantitation.Labeling.Medium_label.Count == 0)
{
labels += "|None";
}
else
{
labels += "|" + _quantitation.Labeling.Medium_label[0];
}
}
else if (_quantitation.Labeling.Multiplicity == 2)
{
if (_quantitation.Labeling.Light_label.Count == 0) //light label
{
labels += "|None";
}
else
{
labels += "|" + _quantitation.Labeling.Light_label[0];
}
if (_quantitation.Labeling.Heavy_label.Count == 0) //heavy label
{
labels += "|None";
}
else
{
labels += "|" + _quantitation.Labeling.Heavy_label[0];
}
}
else if (_quantitation.Labeling.Multiplicity == 3)
{
if (_quantitation.Labeling.Light_label.Count == 0) //light label
{
labels += "|None";
}
else
{
labels += "|" + _quantitation.Labeling.Light_label[0];
}
/*
* for (int i = 1; i < _quantitation.Labeling.Light_label.Count; i++)
* {
* labels += "," + _quantitation.Labeling.Light_label[i];
* }*/
if (_quantitation.Labeling.Medium_label.Count == 0) //medium label
{
labels += "|None";
}
else
{
labels += "|" + _quantitation.Labeling.Medium_label[0];
}
if (_quantitation.Labeling.Heavy_label.Count == 0) //heavy label
{
labels += "|None";
}
else
{
labels += "|" + _quantitation.Labeling.Heavy_label[0];
}
}
pFsw.WriteLine(labels);
}
else if (_quantitation.Quantitation_type == (int)Quant_Type.Label_free)
{
}
pFsw.WriteLine();
#endregion
pFsw.WriteLine("[system]");
pFsw.WriteLine("log=LOG_INFO");
pFsw.Close();
pFfst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
//read from pQuant.qnt
//wrm20150821:将来代码重构时可考虑在读参数文件时，先获取‘=’前和‘=’后的部分，再给参数赋值
void pQuant_Inter.readpQuant_qnt(string task_path, ref _Task _task)
{
QuantitationParam _quantitation = _task.T_Quantitation;
try
{
FileStream fst = new FileStream(task_path + "\\param\\pQuant.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
string strLine = sr.ReadLine();
#region
QuantitationParam _quant = _task.T_Quantitation;
int lb = 0;
string[] labels = { "" };;
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine.Contains("="))
{
if (strLine.Length > ("NUMBER_MAX_PSM_PER_BLOCK").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("NUMBER_MAX_PSM_PER_BLOCK"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Number_max_psm_per_block = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_START").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_START"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Type_start = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("EXTENSION_TEXT_MS1").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("EXTENSION_TEXT_MS1"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Extension_text_ms1 = strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1);
}
//else if (strLine.Length > ("LL_INFO_LABEL").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("LL_INFO_LABEL"))
//{
// int tmp=strLine.LastIndexOf("=");
// string qt = strLine.Substring(tmp + 1,strLine.LastIndexOf(";")-tmp-1);
// labels = qt.Split('|');
// lb = int.Parse(labels[0]);
//}
else if (strLine.Length > ("LL_ELEMENT_ENRICHMENT_CALIBRATION").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("LL_ELEMENT_ENRICHMENT_CALIBRATION"))
{
int tmp = strLine.LastIndexOf("=");
string lfec = strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1);
_quant.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.None;
if (lfec.ToLower() == "15n")
{
_quant.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.N15;
}
else if (lfec.ToLower() == "13c")
{
_quant.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.C13;
}
//bool is15N = false;
//if (lb == 2 && labels.Length == 3 && (labels[1].Equals(ConfigHelper.N15_label) || labels[2].Equals(ConfigHelper.N15_label)))
//{
// is15N = true;
//}
//if (is15N && (flag == 1 || flag == 2))
//{
// _quant.Quantitation_type = (int)Quant_Type.Labeling_15N;
//}
}
#region Todo LabelFree
else if (strLine.Length > ("LF_INFO_SAMPLE").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("LF_INFO_SAMPLE"))
{
}
#endregion
else if (strLine.Length > ("NUMBER_SCANS_HALF_CMTG").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("NUMBER_SCANS_HALF_CMTG"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Number_scans_half_cmtg = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("PPM_FOR_CALIBRATION").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PPM_FOR_CALIBRATION"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Ppm_for_calibration = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("PPM_HALF_WIN_ACCURACY_PEAK").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PPM_HALF_WIN_ACCURACY_PEAK"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Ppm_half_win_accuracy_peak = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("NUMBER_HOLE_IN_CMTG").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("NUMBER_HOLE_IN_CMTG"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Number_hole_in_cmtg = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1)) - 1;
}
else if (strLine.Length > ("TYPE_SAME_START_END_BETWEEN_EVIDENCE").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_SAME_START_END_BETWEEN_EVIDENCE"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Type_same_start_end_between_evidence = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_PEPTIDE_RATIO").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_PEPTIDE_RATIO"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_peptide_ratio = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_PROTEIN_RATIO_CALCULATION").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_PROTEIN_RATIO_CALCULATION"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_protein_ratio_calculation = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_UNIQUE_PEPTIDE_ONLY").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_UNIQUE_PEPTIDE_ONLY"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_unique_peptide_only = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("THRESHOLD_SCORE_INTERFERENCE").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("THRESHOLD_SCORE_INTERFERENCE"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Threshold_score_interference = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("THRESHOLD_SCORE_INTENSITY").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("THRESHOLD_SCORE_INTENSITY"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Threshold_score_intensity = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_GET_GROUP").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_GET_GROUP"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_get_group = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
//generate pQuant.qnt
void pQuant_Inter.pQuant_write(_Task _task)
{
try
{
QuantitationParam _quant = _task.T_Quantitation;
File _file = _task.T_File;
string filepath = _task.Path + "param\\pQuant.cfg";
FileStream qfst = new FileStream(filepath, FileMode.Create, FileAccess.Write);
StreamWriter qsw = new StreamWriter(qfst, Encoding.Default);
qsw.WriteLine("# This is a standard pQuant configure file.");
qsw.WriteLine("# Dear user,After '=' and before ';' is the content you can modify.");
qsw.WriteLine("# Please keep serious when configuring. For some of the options,you can use the default value.");
qsw.WriteLine("# For help: mail to [email protected]");
qsw.WriteLine("# Time: " + DateTime.Now.ToString());
qsw.WriteLine();
qsw.WriteLine("[INI]");
qsw.WriteLine("PATH_INI_ELEMENT=" + ConfigHelper.startup_path + "\\element.ini;");
qsw.WriteLine("PATH_INI_MODIFICATION=" + ConfigHelper.startup_path + "\\modification.ini;");
qsw.WriteLine("PATH_INI_RESIDUE=" + ConfigHelper.startup_path + "\\aa.ini;");
qsw.WriteLine();
qsw.WriteLine("[Performance]");
qsw.WriteLine("PATH_BIN=" + ConfigHelper.startup_path + ";");
qsw.WriteLine("NUMBER_MAX_PSM_PER_BLOCK=" + _quant.Quant_advanced.Number_max_psm_per_block + ";");
qsw.WriteLine("TYPE_START=" + _quant.Quant_advanced.Type_start + ";");
qsw.WriteLine();
qsw.WriteLine("[MS1]");
string ms1path = "";
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
string tmp = _file.Data_file_list[i].FilePath;
ms1path += tmp.Substring(0, tmp.LastIndexOf(".")) + ".pf1|";
}
qsw.WriteLine("PATH_MS1=" + ms1path + ";");
qsw.WriteLine("EXTENSION_TEXT_MS1=" + _quant.Quant_advanced.Extension_text_ms1 + ";");
qsw.WriteLine();
qsw.WriteLine("[Identification]");
#region TODO是否有多个spectra
#endregion
string resultfile = ConfigHelper.getFileBySuffix(_task.Path + "result\\", "spectra");
qsw.WriteLine("PATH_IDENTIFICATION_FILE=" + resultfile + "|;");
qsw.WriteLine("TYPE_IDENTIFICATION_FILE=2;"); //0是老pBuild;1是prolucid;2是pFind3.0
//2014.10.29 chihao：pQuant过滤阈值修改，保持与过滤时一致
qsw.WriteLine("THRESHOLD_FDR=" + (_task.T_Filter.Fdr.Fdr_value / 100.0).ToString() + ";");
qsw.WriteLine();
qsw.WriteLine("[Quantitation]");
//迟浩：定量初始值设置为0，表示标记定量。在搜非标记数据时，也是跑标记流程（画三维图）
string type_label = "0";
if (_quant.Quantitation_type == (int)Quant_Type.Labeling_None || _quant.Quantitation_type == (int)Quant_Type.Labeling_15N || _quant.Quantitation_type == (int)Quant_Type.Labeling_SILAC)
{
type_label = "0";
}
else if (_quant.Quantitation_type == (int)Quant_Type.Label_free)
{
type_label = "1";
}
qsw.WriteLine("TYPE_LABEL=" + type_label + ";");
string labelInfo = "";
#region 代码冗余
//迟浩：这一段代码写得不好，建议一起过一遍功能然后优化实现
if (_quant.Quantitation_type == (int)Quant_Type.Labeling_None)
{
labelInfo = "1|none";
}
else if (_quant.Quantitation_type == (int)Quant_Type.Labeling_15N) //multiplicity=2
{
if (_quant.Labeling.Light_label.Count == 0 && _quant.Labeling.Heavy_label.Count == 0)
{
labelInfo = "1|none";
}
else
{
labelInfo = "2|";
if (_quant.Labeling.Light_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Light_label[0]];
}
labelInfo += "|";
if (_quant.Labeling.Heavy_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Heavy_label[0]];
}
}
}
else if (_quant.Quantitation_type == (int)Quant_Type.Labeling_SILAC)
{
int label_num = _quant.Labeling.Multiplicity;
labelInfo = label_num.ToString();
if (label_num == 1)
{
labelInfo += "|";
if (_quant.Labeling.Medium_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Medium_label[0]];
}
}
else if (label_num == 2)
{
if (_quant.Labeling.Light_label.Count == 0 && _quant.Labeling.Heavy_label.Count == 0)
{
labelInfo = "1|none";
}
else
{
labelInfo += "|";
if (_quant.Labeling.Light_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Light_label[0]];
}
labelInfo += "|";
if (_quant.Labeling.Heavy_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Heavy_label[0]];
}
}
}
else if (label_num == 3)
{
labelInfo += "|";
if (_quant.Labeling.Light_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Light_label[0]];
}
labelInfo += "|";
if (_quant.Labeling.Medium_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Medium_label[0]];
}
labelInfo += "|";
if (_quant.Labeling.Heavy_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += ConfigHelper.Labelmap[_quant.Labeling.Heavy_label[0]];
}
}
}
qsw.WriteLine("LL_INFO_LABEL=" + labelInfo + ";");
#endregion
string lfec = "none";
if (_quant.Quant_advanced.Ll_element_enrichment_calibration == (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.N15)
{
lfec = "15N";
}
else if (_quant.Quant_advanced.Ll_element_enrichment_calibration == (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.C13)
{
lfec = "13C";
}
qsw.WriteLine("LL_ELEMENT_ENRICHMENT_CALIBRATION=" + lfec + ";");
#region Todo LabelFree
//Label Free
#endregion
qsw.WriteLine("LF_INFO_SAMPLE=; //Label Free暂不考虑");
qsw.WriteLine();
qsw.WriteLine("[Evidence]");
qsw.WriteLine("NUMBER_SCANS_HALF_CMTG=" + _quant.Quant_advanced.Number_scans_half_cmtg + ";");
qsw.WriteLine("PPM_FOR_CALIBRATION=" + _quant.Quant_advanced.Ppm_for_calibration + ";");
qsw.WriteLine("PPM_HALF_WIN_ACCURACY_PEAK=" + _quant.Quant_advanced.Ppm_half_win_accuracy_peak + ";");
qsw.WriteLine("NUMBER_HOLE_IN_CMTG=" + (_quant.Quant_advanced.Number_hole_in_cmtg + 1).ToString() + ";");
qsw.WriteLine("TYPE_SAME_START_END_BETWEEN_EVIDENCE=" + _quant.Quant_advanced.Type_same_start_end_between_evidence + ";");
qsw.WriteLine();
qsw.WriteLine("[Inference]");
qsw.WriteLine("TYPE_PEPTIDE_RATIO=" + _quant.Quant_inference.Type_peptide_ratio + ";");
qsw.WriteLine("TYPE_PROTEIN_RATIO_CALCULATION=" + _quant.Quant_inference.Type_protein_ratio_calculation + ";");
qsw.WriteLine("TYPE_UNIQUE_PEPTIDE_ONLY=" + _quant.Quant_inference.Type_unique_peptide_only + ";");
qsw.WriteLine("THRESHOLD_SCORE_INTERFERENCE=" + _quant.Quant_inference.Threshold_score_interference + ";");
qsw.WriteLine("THRESHOLD_SCORE_INTENSITY=" + _quant.Quant_inference.Threshold_score_intensity + ";");
qsw.WriteLine("TYPE_GET_GROUP=" + _quant.Quant_inference.Type_get_group + ";");
qsw.WriteLine("PATH_FASTA=" + _task.T_Search.Db.Db_path + ";");
qsw.WriteLine();
qsw.WriteLine("[Export]");
qsw.WriteLine("DIR_EXPORT=" + _task.Path + "result\\;");
qsw.WriteLine("FLAG_CREATE_NEW_FOLDER=0;"); //0表示直接使用dir_export的导出目录
qsw.Close();
qfst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
