bool SaveTask(string path, _Task _task)
{
try
{
if (!Directory.Exists(path))
{
Directory.CreateDirectory(path);
}
if (!Directory.Exists(path + "\\param"))
{
Directory.CreateDirectory(path + "\\param");
}
//Directory.CreateDirectory(path + "\\result");
CreateTaskFile(path, _task);
//generate pParse.cfg
Factory.Create_pParse_Instance().pParse_write(_task);
Factory.Create_pTop_Instance().pTop_write(_task);
if (_task.T_Quantify.Quantitation_type != (int)Quant_Type.Label_None)
{
Factory.Create_pQuant_Instance().pQuant_write(_task);
}
return(true);
}
catch (Exception exe)
{
MessageBox.Show(exe.Message + "\nSave Failed!");
return(false);
}
}
public void SaveChangeTask(TaskBLL task, string assigneeName)
{
_Task taskForEdit = db.Tasks.Get(task.Id);
if (taskForEdit != null)
{
if (!taskForEdit.ParentId.HasValue)
{
if ((assigneeName == null) && (task.ParentId != null))
{
//We cannot change assignee for subtask - only for main task
throw new ArgumentNullException("assigneeName", "Cannot be null");
}
if (taskForEdit.Assignee.Name != assigneeName)
{
Person assignee;
assignee = db.People.Find(p => (p.Name == assigneeName)).Single();
taskForEdit.Assignee = assignee;
if (taskForEdit.ParentId == null)
{
subtaskService.ChangeAssigneeOfSubtasks(taskForEdit.ParentId.Value, assignee.Id);
}
}
}
taskForEdit.Name = task.Name;
taskForEdit.ETA = task.ETA;
taskForEdit.DueDate = task.DueDate;
taskForEdit.Comment = task.Comment;
db.Tasks.Update(taskForEdit);
db.Save();
}
}
bool SaveTask(string path, _Task _task)
{
try
{
if (!Directory.Exists(path))
{
Directory.CreateDirectory(path);
}
if (!Directory.Exists(path + "\\param"))
{
Directory.CreateDirectory(path + "\\param");
}
//Directory.CreateDirectory(path + "\\result");
//CreateTaskFile(path,_task); // comment by luolan @20150610
//generate pParse.cfg
Factory.Create_pParse_Instance().pParse_write(_task);
Factory.Create_pTop_Instance().pTop_write(_task);
return(true);
}
catch (Exception exe)
{
MessageBox.Show(exe.Message + "\nSave Failed!");
return(false);
}
}
public ActionResult DeleteConfirmed(int id)
{
_Task _Task = db.Tasks.Find(id);
db.Tasks.Remove(_Task);
db.SaveChanges();
return RedirectToAction("Index");
}
public void DeleteTask(int taskId, string currentUserName)
{
TaskBLL task = mapper.Map <_Task, TaskBLL>(db.Tasks.Get(taskId));
if (task == null)
{
throw new ArgumentException("Task with this id not found", "taskId");
}
if (task.Author.Name == currentUserName)
{
if (!task.ParentId.HasValue)
{
IEnumerable <TaskBLL> subtasksForDelete = subtaskService.GetSubtasksOfTask(task.Id);
foreach (var subtask in subtasksForDelete)
{
db.Tasks.Delete(subtask.Id);
}
}
else
{
//then need to calculate new progress for parent task
_Task parrentTask = db.Tasks.Get(task.ParentId.Value);
parrentTask.Progress = subtaskService.CalculateProgressOfSubtask(task.ParentId.Value, task.Id, deleting: true);
db.Tasks.Update(parrentTask);
}
db.Tasks.Delete(task.Id);
db.Save();
}
else
{
throw new InvalidOperationException("Access error. You cannot delete this task");
}
}
public void ProcessAvailableTasks()
{
Console.WriteLine("Выберите задачу для выполнения:");
for (int i = 1; i < _tasks.Count + 1; ++i)
{
_Task task = _tasks[i - 1];
Console.WriteLine("{0}. {1}".f(i.ToString(), task.Name));
}
Console.WriteLine("{0}. {1}.".f((_tasks.Count + 1).ToString(), "Все"));
Console.WriteLine("{0}.".f("Для выхода наберите x"));
string inc;
do
{
Console.Write("Номер задачи: ");
int value;
inc = Console.ReadLine();
if (int.TryParse(inc, out value) && value != default(int))
{
value--;
if (value == _tasks.Count)
{
ExecuteTasks();
}
else
{
ExecuteTask(value);
}
}
}while (inc != null && inc.ToLower() != "x");
}
public void AddSubtask(TaskBLL subtask, int taskId, bool forceToSave = true)
{
var task = mapper.Map <_Task, TaskBLL>(db.Tasks.Get(taskId));
if (task == null)
{
throw new ArgumentException("Parent task wasn't found", "taskId");
}
var status = mapper.Map <Status, StatusBLL>(db.Statuses.Find(s => (s.Name == "New")).Single());
var newSubtask = new TaskBLL
{
ParentId = task.Id,
Author = task.Author,
Name = subtask.Name,
Assignee = task.Assignee,
Status = status,
Progress = 0,
DateStart = null,
ETA = subtask.ETA,
DueDate = subtask.DueDate,
Comment = subtask.Comment
};
db.Tasks.Create(mapper.Map <TaskBLL, _Task>(newSubtask));
if (forceToSave)
{
_Task parentTask = db.Tasks.Get(taskId);
parentTask.Progress = CalculateProgressOfSubtask(taskId, 1);
db.Tasks.Update(parentTask);
db.Save();
}
}
bool SaveTask(string path, _Task _task)
{
try
{
if (Directory.Exists(path))
{
//迟浩：感觉现在对话框提示有点多了，只提示有修改的话需要保存即可，至于是否覆盖则不提示。尝试一下，如果有不妥，再修改
//String tmp = "The Directory Already Contains An Item Named '" + _task.Task_name + "' .\n Do you want to overwrite it ?";
//MessageBoxResult result = System.Windows.MessageBox.Show(tmp, "pFind", MessageBoxButton.OKCancel, MessageBoxImage.Question);
//if (result == MessageBoxResult.Cancel) //No
//{
// return false; //cancel, or rename the task and then save
//}
}
else
{
Directory.CreateDirectory(path);
Directory.CreateDirectory(path + "\\param");
Directory.CreateDirectory(path + "\\result");
}
//wrm 2014/10/20:
CreateTaskFile(path, _task);
//System.IO.File.Create(path + "\\pFind.pFind");
//generate pParse.para
Factory.Create_pParse_Instance().pParse_write(_task);
//generate pFind.pfd
Factory.Create_pFind_Instance().pFind_write(_task);
if (_task.T_File.File_format.Equals("raw"))
{
Factory.Create_pQuant_Instance().pQuant_write(_task);
}
else
{
if (System.IO.File.Exists(path + "\\param\\pQuant.cfg"))
{
System.IO.File.Delete(path + "\\param\\pQuant.cfg");
}
}
if (_task.T_MS2Quant.Enable_ms2quant)
{
Factory.Create_pQuant_Instance().pIsobariQ_write(_task);
}
if (path[path.Length - 1] == '\\')
{
path = path.Substring(0, path.Length - 1);
}
ConfigHelper.update_recent_task(Advanced.recent_tasks_file_path, path);
return(true);
}
catch (Exception exe)
{
MessageBox.Show(exe.Message + "\nSave Failed!");
return(false);
}
}
public Rename(ref _Task _task)
{
InitializeComponent();
this.TaskReName.Text = _task.Task_name;
this.TaskReName.Focus();
this.TaskReName.SelectAll();
tsk = _task;
}
void pParse_Inter.pParse_write(_Task _task)
{
/**产生pParse.cfg**/
try
{
pTop.classes.File _file = _task.T_File;
string filepath = _task.Path + "param\\pParseTD.cfg";
FileStream pPfst = new FileStream(filepath, FileMode.Create, FileAccess.Write);
StreamWriter pPsw = new StreamWriter(pPfst, Encoding.Default);
pPsw.WriteLine("# This is a standard pParseTD configuration file");
pPsw.WriteLine("# For help: mail to [email protected]");
pPsw.WriteLine("# Time: " + DateTime.Now.ToString());
pPsw.WriteLine();
pPsw.WriteLine("[Basic Options]");
pPsw.WriteLine("datanum=" + _file.Data_file_list.Count.ToString());
if (_file.Data_file_list.Count == 0)
{
_task.Check_ok = false;
}
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
pPsw.WriteLine("datapath" + (i + 1).ToString() + "=" + _file.Data_file_list[i].FilePath);
}
pPsw.WriteLine("input_format=" + (_file.File_format_index == (int)FormatOptions.RAW ? "raw":"mgf"));
pPsw.WriteLine();
pPsw.WriteLine("[Advanced Options]");
pPsw.WriteLine("max_charge=" + _file.Pparse_advanced.Max_charge);
pPsw.WriteLine("max_mass=" + _file.Pparse_advanced.Max_mass);
pPsw.WriteLine("SN_threshold=" + _file.Pparse_advanced.Sn_ratio);
pPsw.WriteLine("mz_error_tolerance=" + _file.Pparse_advanced.Mz_tolerance);
pPsw.WriteLine();
string co = _file.Pparse_advanced.Mix_spectra == true ? "1" : "0";
pPsw.WriteLine("co-elute=" + co);
//pPsw.WriteLine("# 0, output single precursor for single scan;");
//pPsw.WriteLine("# 1, output all co-eluted precursors.");
pPsw.WriteLine("isolation_width=" + _file.Pparse_advanced.Isolation_width.ToString());
pPsw.WriteLine();
//pPsw.WriteLine("model_type=" +( _file.Pparse_advanced.Model == (int)ModelOptions.SVM ? "svm" : "mars"));
//pPsw.WriteLine("mars_threshold=" + _file.Pparse_advanced.Threshold);
pPsw.WriteLine();
if (_file.Pparse_advanced.Threshold.ToString() == "" || _file.Pparse_advanced.Mz_decimal.ToString() == "" || _file.Pparse_advanced.Intensity_decimal.ToString() == "")
{
_task.Check_ok = false;
}
pPsw.WriteLine("[About pXtract]");
pPsw.WriteLine("m/z=" + _file.Pparse_advanced.Mz_decimal.ToString());
pPsw.WriteLine("Intensity=" + _file.Pparse_advanced.Intensity_decimal.ToString());
pPsw.Close();
pPfst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
//创建任务文件
void CreateTaskFile(string path, _Task _task)
{
FileStream tskst = new FileStream(path + "\\" + _task.Task_name + ".tsk", FileMode.Create, FileAccess.Write);
StreamWriter tsksw = new StreamWriter(tskst, Encoding.Default);
tsksw.WriteLine("pTop Task File, Format Version " + ConfigHelper.ptop_version);
tsksw.WriteLine("# pTop " + ConfigHelper.ptop_version);
tsksw.Close();
tskst.Close();
}
//创建任务文件
//wrm 2014/10/20:
void CreateTaskFile(string path, _Task _task)
{
FileStream tskst = new FileStream(path + "\\" + _task.Task_name + ".tsk", FileMode.Create, FileAccess.Write);
StreamWriter tsksw = new StreamWriter(tskst, Encoding.Default);
tsksw.WriteLine("pFind Studio Task File, Format Version 3.0");
tsksw.WriteLine("# pFind 3.0");
tsksw.Close();
tskst.Close();
}
public ActionResult Edit([Bind(Include = "Id,Description,IsDone")] _Task _Task)
{
if (ModelState.IsValid)
{
db.Entry(_Task).State = EntityState.Modified;
db.SaveChanges();
return RedirectToAction("Index");
}
return View(_Task);
}
//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);
}
bool Run_Inter.SaveAsParams(string path, _Task _task)
{
try
{
return(SaveTask(path, _task));
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
//save params
bool Run_Inter.SaveParams(_Task _task)
{
try
{
string pathName = _task.Path.Trim();
return(SaveTask(pathName, _task));
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
// GET: _Tasks/Details/5
public ActionResult Details(int? id)
{
if (id == null)
{
return new HttpStatusCodeResult(HttpStatusCode.BadRequest);
}
_Task _Task = db.Tasks.Find(id);
if (_Task == null)
{
return HttpNotFound();
}
return View(_Task);
}
public ActionResult Create([Bind(Include = "Id,Description,IsDone")] _Task _Task)
{
if (ModelState.IsValid)
{
string currentUserId = User.Identity.GetUserId();
ApplicationUser currentUser = db.Users.FirstOrDefault(
x => x.Id == currentUserId);
_Task.User = currentUser;
db.Tasks.Add(_Task);
db.SaveChanges();
return RedirectToAction("Index");
}
return View(_Task);
}
public ActionResult AJAXCreate([Bind(Include = "Id,Description")] _Task _Task)
{
if (ModelState.IsValid)
{
string currentUserId = User.Identity.GetUserId();
ApplicationUser currentUser = db.Users.FirstOrDefault(
x => x.Id == currentUserId);
_Task.User = currentUser;
_Task.IsDone = false;
db.Tasks.Add(_Task);
db.SaveChanges();
}
return PartialView("_TaskTable", Get_Tasks());
}
private void AddBtn_Click(object sender, EventArgs e)
{
try
{
_Task task = new _Task(content, deadline);
_Tasks.Add(task);
TaskSerializer(_Tasks, path);
Logger.Log($"Задание:{task.Content}, дедлайн {task.DeadLine}");
}catch (Exception ex)
{
MessageBox.Show($"Возникла ошибка: {ex.Message}");
}
}
//写入鉴定结果文件路径
void pQuant_Inter.pQuant_writeResultFile(_Task _task)
{
try
{
FileStream fst = new FileStream(_task.Path + "\\param\\pQuant.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
string strLine = sr.ReadLine();
List <string> text = new List <string>();
while (strLine != null)
{
if (strLine.Trim() == "")
{
text.Add("");
}
else if (strLine.Trim().Length > 0 && strLine.Contains("=") && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PATH_IDENTIFICATION_FILE"))
{
string resultfile = ConfigHelper.getFileBySuffix(_task.Path + "result\\", "spectra");
text.Add("PATH_IDENTIFICATION_FILE=" + resultfile + "|;");
}
else
{
text.Add(strLine);
}
strLine = sr.ReadLine();
}
sr.Close();
fst.Close();
fst = new FileStream(_task.Path + "\\param\\pQuant.cfg", FileMode.Open, FileAccess.Write);
StreamWriter sw = new StreamWriter(fst, Encoding.Default);
foreach (string str in text)
{
sw.WriteLine(str);
}
sw.Flush();
sw.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
private static TResult DoRun(object taskData)
{
_Task <TResult, TState> task = ((Data <TResult, TState>)taskData).Task;
if (task._prev != null)
{
try
{
task._prev.Wait();
}
catch (AggregateException ex)
{
if (!(ex.InnerException is TaskCanceledException))
{
throw ex.InnerException;
}
}
}
return(task._config.RunFunction(task));
}
public ActionResult AJAXEdit(int? id, bool value)
{
if (id == null)
{
return new HttpStatusCodeResult(HttpStatusCode.BadRequest);
}
_Task _Task = db.Tasks.Find(id);
if (_Task == null)
{
return HttpNotFound();
}
else
{
_Task.IsDone = value;
db.Entry(_Task).State = EntityState.Modified;
db.SaveChanges();
return PartialView("_TaskTable", Get_Tasks());
}
}
public void AddSubtasksFromTemplate(int taskId, int templateId, string authorName)
{
IEnumerable <TaskTemplateBLL> subtaskNames = GetSubtasksOfTemplate(templateId);
if (!subtaskNames.Any())
{
throw new ArgumentException("subtasks from template with this Id wasn't found", "templateId");
}
if (string.IsNullOrWhiteSpace(authorName))
{
throw new ArgumentNullException("Name of author is null or empty", "authorName");
}
PersonBLL author = mapper.Map <Person, PersonBLL>(db.People.Find(p => (p.Name == authorName)).SingleOrDefault());
if (author == null)
{
throw new ArgumentException("Author with tis name wasn't found", "authorName");
}
foreach (var subtaskName in subtaskNames)
{
var subtask = new TaskBLL
{
Name = subtaskName.Name,
ParentId = taskId,
ETA = null,
DueDate = null,
Comment = null,
Author = author
};
subtaskService.AddSubtask(subtask, taskId, false);
}
_Task parentTask = db.Tasks.Get(taskId);
parentTask.Progress = subtaskService.CalculateProgressOfSubtask(taskId, subtaskNames.Count());
db.Tasks.Update(parentTask);
db.Save();
}
void Run_Inter.JustSaveParams(_Task _task)
{
string pathName = _task.Path;
Directory.CreateDirectory(pathName);
CreateTaskFile(pathName, _task);
Directory.CreateDirectory(pathName + "\\param");
Directory.CreateDirectory(pathName + "\\result");
if (_task.T_File.File_format.Equals("raw"))
{
//generate pParse.para,pQuant.qnt
Factory.Create_pParse_Instance().pParse_write(_task);
Factory.Create_pQuant_Instance().pQuant_write(_task);
}
//generate pFind.pfd
Factory.Create_pFind_Instance().pFind_write(_task);
if (_task.T_MS2Quant.Enable_ms2quant)
{
Factory.Create_pQuant_Instance().pIsobariQ_write(_task);
}
}
//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);
}
}
private static void DoContinue(Task <TResult> baseTask)
{
_Task <TResult, TState> task = (_Task <TResult, TState>)baseTask;
task._config.ContinueAction(task);
}
//read from pParse.para
void pParse_Inter.pParse_read(string task_path, ref _Task _task)
{
string strLine = "";
try
{
pTop.classes.File _file = _task.T_File;
FileStream fst = new FileStream(task_path + "\\param\\pParseTD.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
strLine = sr.ReadLine();
string subtitle = "";
ObservableCollection <_FileInfo> dfl = new ObservableCollection <_FileInfo>();
#region
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine.StartsWith("#"))
{
}
else if (strLine.Length > 0 && strLine[0] == '[' && strLine[strLine.Length - 1] == ']')
{
subtitle = strLine;
}
else if (strLine.Length > 0 && strLine.LastIndexOf("=") > -1)
{
if (subtitle.Equals("[Basic Options]"))
{
if (strLine.Length > 7 && strLine.Substring(0, 7).Equals("datanum"))
{
//if new a task, then dtnum=0
int dtnum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
for (int i = 0; i < dtnum; i++)
{
strLine = sr.ReadLine();
strLine = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (System.IO.File.Exists(@strLine))
{
_FileInfo _fi = new _FileInfo(strLine);
dfl.Add(_fi);
}
else
{
System.Windows.MessageBox.Show("\"" + strLine + "\" does not exist.");
}
}
}
else if (strLine.Length > 12 && strLine.Substring(0, 12).Equals("input_format"))
{
_file.File_format = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (_file.File_format.Equals("raw")) //raw
{
_file.File_format_index = (int)FormatOptions.RAW; //format改变会引起Data_file_list的清空
}
else if (_file.File_format.Equals("mgf"))
{
_file.File_format_index = (int)FormatOptions.MGF;
}
_file.Data_file_list.Clear();
for (int i = 0; i < dfl.Count; i++)
{
_file.Data_file_list.Add(dfl[i]);
}
}
}
#region
else if (subtitle.Equals("[Advanced Options]"))
{
if (strLine.Length > ("max_charge").Length && strLine.Substring(0, ("max_charge").Length).Equals("max_charge"))
{
_file.Pparse_advanced.Max_charge = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > ("max_mass").Length && strLine.Substring(0, ("max_mass").Length).Equals("max_mass"))
{
_file.Pparse_advanced.Max_mass = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > ("SN_threshold").Length && strLine.Substring(0, ("SN_threshold").Length).Equals("SN_threshold"))
{
_file.Pparse_advanced.Sn_ratio = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > ("mz_error_tolerance").Length && strLine.Substring(0, ("mz_error_tolerance").Length).Equals("mz_error_tolerance"))
{
_file.Pparse_advanced.Mz_tolerance = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > 8 && strLine.Substring(0, 8).Equals("co-elute"))
{
if (strLine.Substring(strLine.LastIndexOf("=") + 1).Equals("1"))
{
_file.Pparse_advanced.Mix_spectra = true;
}
else
{
_file.Pparse_advanced.Mix_spectra = false;
}
}
else if (strLine.Length > 15 && strLine.Substring(0, 15).Equals("isolation_width"))
{
_file.Pparse_advanced.Isolation_width = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > ("model_type").Length && strLine.Substring(0, ("model_type").Length).Equals("model_type"))
{
_file.Pparse_advanced.Model = strLine.Substring(strLine.LastIndexOf("=") + 1).Trim().ToLower().Equals("svm") ? (int)ModelOptions.SVM : (int)ModelOptions.MARS;
}
else if (strLine.Length > 14 && strLine.Substring(0, 14).Equals("mars_threshold"))
{
_file.Pparse_advanced.Threshold = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
}
#endregion
else if (subtitle.Equals("[About pXtract]"))
{
if (strLine.Length > 3 && strLine.Substring(0, 3).Equals("m/z"))
{
_file.Pparse_advanced.Mz_decimal = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_file.Pparse_advanced.Mz_decimal_index = _file.Pparse_advanced.Mz_decimal - 1;
}
else if (strLine.Length > 9 && (strLine.Substring(0, 9).Equals("intensity") || strLine.Substring(0, 9).Equals("Intensity")))
{
_file.Pparse_advanced.Intensity_decimal = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_file.Pparse_advanced.Intensity_decimal_index = _file.Pparse_advanced.Intensity_decimal - 1;
}
}
}
strLine = sr.ReadLine();
}
sr.Close();
fst.Close();
#endregion
}
catch (Exception exe)
{
throw new Exception("[pParseTD_read] line: " + strLine + "\n" + exe.Message);
}
}
//read from pParse.para
void pParse_Inter.readpParse_para(string task_path, ref _Task _task)
{
try
{
File _file = _task.T_File;
FileStream fst = new FileStream(task_path + "\\param\\pParse.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
string strLine = sr.ReadLine();
string subtitle = "";
ObservableCollection <_FileInfo> dfl = new ObservableCollection <_FileInfo>();
#region
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine.StartsWith("#"))
{
}
else if (strLine.Length > 0 && strLine[0] == '[' && strLine[strLine.Length - 1] == ']')
{
subtitle = strLine;
}
else
{
if (subtitle.Equals("[Basic Options]"))
{
if (strLine.Length > 7 && strLine.Substring(0, 7).Equals("datanum"))
{
//if new a task, then dtnum=0
int dtnum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
for (int i = 0; i < dtnum; i++)
{
strLine = sr.ReadLine();
strLine = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (System.IO.File.Exists(@strLine))
{
_FileInfo _fi = new _FileInfo(strLine);
dfl.Add(_fi);
}
else
{
System.Windows.MessageBox.Show("\"" + strLine + "\" does not exist.");
}
}
}
}
#region
else if (subtitle.Equals("[Advanced Options]"))
{
if (strLine.Length > 8 && strLine.Substring(0, 8).Equals("co-elute"))
{
if (strLine.Substring(strLine.LastIndexOf("=") + 1).Equals("1"))
{
_file.Mix_spectra = true;
}
else
{
_file.Mix_spectra = false;
}
}
else if (strLine.Length > 12 && strLine.Substring(0, 12).Equals("input_format"))
{
_file.File_format = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (_file.File_format.Equals("raw")) //raw
{
_file.File_format_index = (int)FormatOptions.RAW; //format改变会引起Data_file_list的清空
}
else if (_file.File_format.Equals("mgf"))
{
_file.File_format_index = (int)FormatOptions.MGF;
}
else if (_file.File_format.Equals("wiff"))
{
_file.File_format_index = (int)FormatOptions.WIFF;
}
_file.Data_file_list.Clear();
for (int i = 0; i < dfl.Count; i++)
{
_file.Data_file_list.Add(dfl[i]);
}
}
else if (strLine.Length > 15 && strLine.Substring(0, 15).Equals("isolation_width"))
{
_file.Pparse_advanced.Isolation_width = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > 14 && strLine.Substring(0, 14).Equals("mars_threshold"))
{
_file.Threshold = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1).Trim());
}
else if (strLine.Length > 8 && strLine.Substring(0, 8).Equals("ipv_file"))
{
_file.Pparse_advanced.Ipv_file = strLine.Substring(strLine.LastIndexOf("=") + 1).Trim();
}
else if (strLine.Length > 11 && strLine.Substring(0, 11).Equals("trainingset"))
{
_file.Pparse_advanced.Trainingset = strLine.Substring(strLine.LastIndexOf("=") + 1).Trim();
}
}
#endregion
#region
else if (subtitle.Equals("[Internal Switches]"))
{
if (strLine.Length > 13 && strLine.Substring(0, 13).Equals("output_mars_y"))
{
_file.Pparse_advanced.Output_mars_y = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("delete_msn"))
{
_file.Pparse_advanced.Output_msn = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) == 0 ? 1 : 0;
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("output_mgf"))
{
_file.Pparse_advanced.Output_mgf = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 9 && strLine.Substring(0, 9).Equals("output_pf"))
{
_file.Pparse_advanced.Output_pf = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("debug_mode"))
{
_file.Pparse_advanced.Debug_mode = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("check_activationcenter").Length && strLine.Substring(0, ("check_activationcenter").Length).Equals("check_activationcenter"))
{
_file.Pparse_advanced.Check_activationcenter = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("output_all_mars_y").Length && strLine.Substring(0, ("output_all_mars_y").Length).Equals("output_all_mars_y"))
{
_file.Pparse_advanced.Output_all_mars_y = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 13 && strLine.Substring(0, 13).Equals("rewrite_files"))
{
_file.Pparse_advanced.Rewrite_files = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("export_unchecked_mono").Length && strLine.Substring(0, ("export_unchecked_mono").Length).Equals("export_unchecked_mono"))
{
_file.Pparse_advanced.Export_unchecked_mono = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("cut_similiar_mono").Length && strLine.Substring(0, ("cut_similiar_mono").Length).Equals("cut_similiar_mono"))
{
_file.Pparse_advanced.Cut_similiar_mono = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > 10 && strLine.Substring(0, 10).Equals("mars_model"))
{
_file.Model = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_file.ModelIndex = ConfigHelper.mars_model.IndexOf(_file.Model);
//if the value is invalid
if (_file.ModelIndex == -1)
{
_file.ModelIndex = 0;
_file.Model = ConfigHelper.mars_model[_file.ModelIndex];
}
}
else if (strLine.Length > ("output_trainingdata").Length && strLine.Substring(0, ("output_trainingdata").Length).Equals("output_trainingdata"))
{
_file.Pparse_advanced.Output_trainingdata = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
}
#endregion
else if (subtitle.Equals("[About pXtract]"))
{
if (strLine.Length > 3 && strLine.Substring(0, 3).Equals("m/z"))
{
_file.Mz_decimal = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_file.Mz_decimal_index = _file.Mz_decimal - 1;
}
else if (strLine.Length > 9 && (strLine.Substring(0, 9).Equals("intensity") || strLine.Substring(0, 9).Equals("Intensity")))
{
_file.Intensity_decimal = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_file.Intensity_decimal_index = _file.Intensity_decimal - 1;
}
}
}
strLine = sr.ReadLine();
}
sr.Close();
fst.Close();
#endregion
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
