//read from pTop.pfd
void pTop_Inter.pTop_read(string task_path, bool pParse, ref _Task _task)
{
string strLine = "";
try
{
pTop.classes.File _file = _task.T_File;
Identification _search = _task.T_Identify;
Quantitation _quantitation = _task.T_Quantify;
FileStream fst = new FileStream(task_path + "\\param\\pTop.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
strLine = sr.ReadLine();
string subtitle = "";
#region
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine[0] == '[' && strLine[strLine.Length - 1] == ']')
{
subtitle = strLine;
}
else if (strLine.Length > 0 && strLine.IndexOf("=") > -1)
{
if (subtitle.Equals("[spectrum]"))
{
// msmspath and input_format were read from pParseTD.cfg
if (strLine.Length > ("Activation").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Activation"))
{
_file.Instrument = strLine.Substring(strLine.LastIndexOf("=") + 1);
_file.setInstrument_index();
}
else if (strLine.Length > ("Precursor_Tolerance").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Precursor_Tolerance"))
{
_search.Ptl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Fragment_Tolerance").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Fragment_Tolerance"))
{
_search.Ftl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
}
else if (subtitle.Equals("[param]"))
{
if (strLine.Length > ("workflow").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("workflow"))
{
_search.SearchModeIndex = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("output_top_k").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("output_top_k"))
{
_search.OutputTopK = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("max_truncated_mass").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("max_truncated_mass"))
{
_search.MaxTruncatedMass = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("second_search").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("second_search"))
{
if (strLine.Substring(strLine.LastIndexOf("=") + 1).Equals("1"))
{
_search.SecondSearch = true;
}
else
{
_search.SecondSearch = false;
}
}
}
else if (subtitle.Equals("[fixmodify]"))
{
if (strLine.Length > ("fixedModify_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("fixedModify_num"))
{
int fix_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_search.Fix_mods.Clear();
for (int i = 0; i < fix_num; i++)
{
strLine = sr.ReadLine();
string fixmod = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Fix_mods.Add(fixmod);
}
}
}
else if (subtitle.Equals("[modify]"))
{
if (strLine.Length > ("Max_mod_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Max_mod_num"))
{
_search.Max_mod = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("unexpected_mod").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("unexpected_mod"))
{
_search.UnexpectedModNum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Max_mod_mass").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Max_mod_mass"))
{
_search.MaxModMass = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Modify_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Modify_num"))
{
int var_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_search.Var_mods.Clear();
for (int i = 0; i < var_num; i++)
{
strLine = sr.ReadLine();
string varmod = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Var_mods.Add(varmod);
}
}
}
else if (subtitle.Equals("[filter]"))
{
if (strLine.Length > ("threshold").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("threshold"))
{
_search.Filter.Fdr_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) * 100;
}
else if (strLine.Length > ("separate_filtering").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("separate_filtering"))
{
if (strLine.Substring(strLine.LastIndexOf("=") + 1).Equals("1"))
{
_search.Filter.SeparateFiltering = true;
}
else
{
_search.Filter.SeparateFiltering = false;
}
}
}
#region [file]
if (subtitle.Equals("[file]"))
{
if (strLine.Length > ("Database").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Database"))
{
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 > ("pParseTD_cfg").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pParseTD_cfg"))
{
}
else if (strLine.Length > ("pQuant_cfg").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pQuant_cfg"))
{
}
else if (strLine.Length > ("outputpath").Length && strLine.Substring(0, strLine.LastIndexOf("=")).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);
}
}
}
#endregion
else if (subtitle.Equals("[quantify]"))
{
if (strLine.Length > 5 && strLine.Substring(0, strLine.LastIndexOf("=")).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.Label_None;
}
else
{
_quantitation.Quantitation_type = (int)Quant_Type.Labeling; //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)
{
_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]);
}
}
}
}
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception("[pTop_read] line: " + strLine + "\n" + exe.Message);
}
}
//read from pTop.pfd
void pTop_Inter.pTop_read(string task_path, bool pParse, ref _Task _task)
{
//try
{
pTop.classes.File _file = _task.T_File;
Identification _search = _task.T_Identify;
FileStream fst = new FileStream(task_path + "\\param\\pTop.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[strLine.Length - 1] == ']')
{
subtitle = strLine;
}
else
{
#region [database]
if (subtitle.Equals("[database]"))
{
if (strLine.Length > 9 && strLine.Substring(0, ("Database").Length).Equals("Database"))
{
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
}
}
#endregion
#region [spectrum]
if (subtitle.Equals("[spectrum]"))
{
if (strLine.Length > ("Activation").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Activation"))
{
_file.Instrument = strLine.Substring(strLine.LastIndexOf("=") + 1);
_file.setInstrument_index();
}
else if (strLine.Length > ("Precursor_Tolerance").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Precursor_Tolerance"))
{
_search.Ptl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Fragment_Tolerance").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Fragment_Tolerance"))
{
_search.Ftl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
}
#endregion
else if (subtitle.Equals("[fixmodify]"))
{
if (strLine.Length > ("fixedModify_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("fixedModify_num"))
{
int fix_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_search.Fix_mods.Clear();
for (int i = 0; i < fix_num; i++)
{
strLine = sr.ReadLine();
string fixmod = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Fix_mods.Add(fixmod);
}
}
}
else if (subtitle.Equals("[modify]"))
{
if (strLine.Length > ("Max_mod").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Max_mod"))
{
_search.Max_mod = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Modify_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Modify_num"))
{
int var_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_search.Var_mods.Clear();
for (int i = 0; i < var_num; i++)
{
strLine = sr.ReadLine();
string varmod = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Var_mods.Add(varmod);
}
}
}
else if (subtitle.Equals("[filter]"))
{
if (strLine.Length > ("threshold").Length && strLine.Substring(0, ("threshold").Length).Equals("threshold"))
{
_search.Filter.Fdr_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) * 100;
}
}
else if (subtitle.Equals("[output]"))
{
if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("outputpath"))
{
string tpath = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (tpath.Trim().Length > 0)
{
_task.Path = task_path + "\\";
_task.Task_name = sr.ReadLine().Trim().Substring(strLine.LastIndexOf("=") + 1);
}
}
}
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
//catch(Exception exe)
//{
// throw new Exception(exe.Message);
//}
}
