/// <summary>
/// write out a subset of high quality spectra based on ScanRanker metrics file
/// using ProteoWizard library
/// </summary>
public void Write()
{
foreach (FileInfo file in inFileList)
{
string fileBaseName = Path.GetFileNameWithoutExtension(file.FullName);
string metricsFileName = fileBaseName + metricsFileSuffix + ".txt";
string outFileName = fileBaseName + outFileSuffix + "." + outFormat;
Workspace.SetText("\r\nStart writing high quality spectra for file: " + file.Name + " ...\r\n\r\n");
if (File.Exists(outFileName))
{
File.Delete(outFileName);
}
if (!File.Exists(metricsFileName))
{
Workspace.SetText("\r\nError: Cannot find quality metrics file: " + metricsFileName + " in output directory!");
Workspace.ChangeButtonTo("Close");
return;
}
//List<int> allIndices = new List<int>();
//List<int> highQualIndices = new List<int>();
List <string> allIndices = new List <string>();
List <string> highQualIndices = new List <string>();
// read metrics file, split and get high quality spectra indecies from the second column
try
{
Workspace.SetText("\r\nExtracting scan index from metrics file: " + metricsFileName);
using (TextReader tr = File.OpenText(metricsFileName))
{
tr.ReadLine(); // read the header line but do nothing, first three lines are header
tr.ReadLine(); // read the header line but do nothing
tr.ReadLine(); // read the header line but do nothing
string line = string.Empty;
while ((line = tr.ReadLine()) != null)
{
string[] items = line.Split('\t');
//int index = Convert.ToInt32(items[1]); //index
string index = Convert.ToString(items[1]); //nativeID
if (!allIndices.Exists(element => element == index)) // remove duplicate index
{
allIndices.Add(index);
}
}
}
}
catch (Exception exc)
{
//throw new Exception("Error in reading metrics file for spectra removal\r\n",exc);
Workspace.SetText("\r\nError in reading metrics file for spectra removal\r\n");
Workspace.ChangeButtonTo("Close");
throw new Exception(exc.Message);
}
// get indices for high quality spectra
Workspace.SetText("\r\nGenerating indices of high quality spectra");
int numOutputSpectra = Convert.ToInt32(allIndices.Count * cutoff);
highQualIndices = allIndices.GetRange(0, numOutputSpectra);
//highQualIndices.Sort();
//var predicate = new SpectrumList_FilterPredicate_IndexSet();
//foreach (int i in highQualIndices)
//{
// predicate.indexSet.Add(i);
//}
var predicate = new SpectrumList_FilterPredicate_NativeIDSet();
foreach (string i in highQualIndices)
{
predicate.nativeIDSet.Add(i);
}
//var sorterPredicate = new SpectrumList_SorterPredicate_IndexSet();
//foreach (int i in highQualIndices)
//{
// sorterPredicate.indexSet.Add(i);
//}
//MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(MSDataFile.Format.Format_mzXML);
MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig();
if (outFormat.Equals("mzXML") || outFormat.Equals("mzxml"))
{
writeConfig.format = MSDataFile.Format.Format_mzXML;
}
else if (outFormat.Equals("mzML") || outFormat.Equals("mzml"))
{
writeConfig.format = MSDataFile.Format.Format_mzML;
}
else if (outFormat.Equals("MGF") || outFormat.Equals("mgf"))
{
writeConfig.format = MSDataFile.Format.Format_MGF;
}
else if (outFormat.Equals("MS2") || outFormat.Equals("ms2"))
{
writeConfig.format = MSDataFile.Format.Format_MS2;
}
else
{
MessageBox.Show("Plese select output format");
}
writeConfig.precision = MSDataFile.Precision.Precision_32;
try
{
Workspace.SetText("\r\nWriting high quality spectra to file: " + outFileName);
using (var msFile = new MSDataFile(file.FullName))
{
var indexSet = new string[highQualIndices.Count];
var sl = msFile.run.spectrumList;
for (int i = 0; i < highQualIndices.Count; ++i)
{
string id = highQualIndices[i];
int index = sl.find(id);
if (index == sl.size())
{
throw new Exception("nativeID \"" + id + "\" not found in file");
}
indexSet[i] = index.ToString();
}
var indexSetString = String.Join(" ", indexSet);
var predicate2 = new SpectrumList_FilterPredicate_IndexSet(indexSetString);
var filter = new SpectrumList_Filter(msFile.run.spectrumList, predicate2);
msFile.run.spectrumList = filter;
//msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan( sorterPredicate.lessThan ));
//msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan(lessThan));
//Workspace.SetText("\r\nFinished msFile.run.spectrumList");
msFile.write(outFileName, writeConfig);
}
}
catch (Exception exc)
{
//throw new Exception("Error in writiing new spectra file", exc);
Workspace.SetText("\r\nError in writing new spectra file\r\n");
Workspace.ChangeButtonTo("Close");
throw new Exception(exc.Message);
}
Workspace.SetText("\r\nFinished writing high quality spectra for file: " + file.Name + " \r\n\r\n");
}// end of foreach file
Workspace.SetText("\r\nFinished writing high quality spectra!");
Workspace.ChangeButtonTo("Close");
} // end of write()
/// <summary>
/// write out a subset of high quality spectra based on ScanRanker metrics file
/// using ProteoWizard library
/// </summary>
public void Write()
{
foreach (FileInfo file in inFileList)
{
string fileBaseName = Path.GetFileNameWithoutExtension(file.FullName);
string metricsFileName = fileBaseName + metricsFileSuffix + ".txt";
string outFileName = fileBaseName + outFileSuffix + "." + outFormat;
Workspace.SetText("\r\nStart writing high quality spectra for file: " + file.Name + " ...\r\n\r\n");
if (File.Exists(outFileName))
{
File.Delete(outFileName);
}
if (!File.Exists(metricsFileName))
{
Workspace.SetText("\r\nError: Cannot find quality metrics file: " + metricsFileName + " in output directory!");
Workspace.ChangeButtonTo("Close");
return;
}
//List<int> allIndices = new List<int>();
//List<int> highQualIndices = new List<int>();
List<string> allIndices = new List<string>();
List<string> highQualIndices = new List<string>();
// read metrics file, split and get high quality spectra indecies from the second column
try
{
Workspace.SetText("\r\nExtracting scan index from metrics file: " + metricsFileName);
using (TextReader tr = File.OpenText(metricsFileName))
{
tr.ReadLine(); // read the header line but do nothing, first three lines are header
tr.ReadLine(); // read the header line but do nothing
tr.ReadLine(); // read the header line but do nothing
string line = string.Empty;
while ((line = tr.ReadLine()) != null)
{
string[] items = line.Split('\t');
//int index = Convert.ToInt32(items[1]); //index
string index = Convert.ToString(items[1]); //nativeID
if (!allIndices.Exists(element => element == index)) // remove duplicate index
{
allIndices.Add(index);
}
}
}
}
catch (Exception exc)
{
//throw new Exception("Error in reading metrics file for spectra removal\r\n",exc);
Workspace.SetText("\r\nError in reading metrics file for spectra removal\r\n");
Workspace.ChangeButtonTo("Close");
throw new Exception(exc.Message);
}
// get indices for high quality spectra
Workspace.SetText("\r\nGenerating indices of high quality spectra");
int numOutputSpectra = Convert.ToInt32(allIndices.Count * cutoff);
highQualIndices = allIndices.GetRange(0, numOutputSpectra);
//highQualIndices.Sort();
//var predicate = new SpectrumList_FilterPredicate_IndexSet();
//foreach (int i in highQualIndices)
//{
// predicate.indexSet.Add(i);
//}
var predicate = new SpectrumList_FilterPredicate_NativeIDSet();
foreach (string i in highQualIndices)
{
predicate.nativeIDSet.Add(i);
}
//var sorterPredicate = new SpectrumList_SorterPredicate_IndexSet();
//foreach (int i in highQualIndices)
//{
// sorterPredicate.indexSet.Add(i);
//}
//MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(MSDataFile.Format.Format_mzXML);
MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig();
if (outFormat.Equals("mzXML") || outFormat.Equals("mzxml"))
{
writeConfig.format = MSDataFile.Format.Format_mzXML;
}
else if (outFormat.Equals("mzML") || outFormat.Equals("mzml"))
{
writeConfig.format = MSDataFile.Format.Format_mzML;
}
else if (outFormat.Equals("MGF") || outFormat.Equals("mgf"))
{
writeConfig.format = MSDataFile.Format.Format_MGF;
}
else if (outFormat.Equals("MS2") || outFormat.Equals("ms2"))
{
writeConfig.format = MSDataFile.Format.Format_MS2;
}
else
{
MessageBox.Show("Plese select output format");
}
writeConfig.precision = MSDataFile.Precision.Precision_32;
try
{
Workspace.SetText("\r\nWriting high quality spectra to file: " + outFileName);
using (var msFile = new MSDataFile(file.FullName))
{
var indexSet = new string[highQualIndices.Count];
var sl = msFile.run.spectrumList;
for (int i=0; i < highQualIndices.Count; ++i)
{
string id = highQualIndices[i];
int index = sl.find(id);
if (index == sl.size())
throw new Exception("nativeID \"" + id + "\" not found in file");
indexSet[i] = index.ToString();
}
var indexSetString = String.Join(" ", indexSet);
var predicate2 = new SpectrumList_FilterPredicate_IndexSet(indexSetString);
var filter = new SpectrumList_Filter(msFile.run.spectrumList, predicate2);
msFile.run.spectrumList = filter;
//msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan( sorterPredicate.lessThan ));
//msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan(lessThan));
//Workspace.SetText("\r\nFinished msFile.run.spectrumList");
msFile.write(outFileName, writeConfig);
}
}
catch (Exception exc)
{
//throw new Exception("Error in writiing new spectra file", exc);
Workspace.SetText("\r\nError in writing new spectra file\r\n");
Workspace.ChangeButtonTo("Close");
throw new Exception(exc.Message);
}
Workspace.SetText("\r\nFinished writing high quality spectra for file: " + file.Name + " \r\n\r\n");
}// end of foreach file
Workspace.SetText("\r\nFinished writing high quality spectra!");
Workspace.ChangeButtonTo("Close");
} // end of write()
