public List <IsosResult> getIsosResults(string isosInputFile, Globals.MSFileType fileType)
{
var isoUtil = new IsosResultUtilities();
isoUtil.LoadResults(isosInputFile, fileType);
return(isoUtil.Results);
}
public List <IsosResult> getIsosResults(string isosInputFile, Globals.MSFileType fileType, int minScan, int maxScan)
{
var isoUtil = new IsosResultUtilities();
isoUtil.LoadResults(isosInputFile, fileType);
return(isoUtil.Results.Where(p => p.ScanSet.PrimaryScanNumber >= minScan && p.ScanSet.PrimaryScanNumber <= maxScan).ToList());
}
public PeakListTextExporter(Globals.MSFileType fileType, int triggerValue, string outputFileName)
{
FileName = outputFileName;
TriggerToWriteValue = triggerValue; //will write out peaks if trigger value is reached
m_delimiter = '\t';
m_FileType = fileType; // need to know filetype so that frame_num can be outputted for UIMF data
bool fileExists;
try
{
fileExists = File.Exists(outputFileName);
}
catch (Exception ex)
{
Logger.Instance.AddEntry("PeakExporter failed. Details: " + ex.Message, true);
throw new Exception("Peak exporter failed. Check to see if output file is already open.");
}
if (fileExists)
{
try
{
File.Delete(outputFileName);
}
catch (Exception ex)
{
Logger.Instance.AddEntry("PeakExporter failed. Details: " + ex.Message, true);
throw new Exception("Peak exporter failed. Check to see if output file is already open.");
}
}
initializeAndWriteHeader();
}
public MSFileTypeSelectorForm(string filename)
{
InitializeComponent();
this.listBox1.DataSource = System.Enum.GetValues(typeof(Globals.MSFileType));
Globals.MSFileType guessedFileType = guessFileTypeFromFileName(filename);
this.listBox1.SelectedItem = guessedFileType;
}
public IsosImporter(string importFilename, Globals.MSFileType msFileType)
{
delimiter = ',';
fileType = msFileType;
filepath = importFilename;
minVal = int.MinValue;
maxVal = int.MaxValue;
try
{
reader = new StreamReader(importFilename);
}
catch (Exception)
{
throw new IOException("There was a problem reading the _isos data file " + filepath);
}
}
public static ScanResultExporter CreateScansExporter(Globals.MSFileType fileType, Globals.ExporterType exporterType, string outputFileName)
{
ScanResultExporter scansExporter;
switch (fileType)
{
case Globals.MSFileType.PNNL_UIMF:
switch (exporterType)
{
case Globals.ExporterType.Text:
scansExporter = new UIMFScanResult_TextFileExporter(outputFileName);
break;
case Globals.ExporterType.Sqlite:
scansExporter = new UIMFScanResult_SqliteExporter(outputFileName);
break;
default:
scansExporter = new UIMFScanResult_TextFileExporter(outputFileName);
break;
}
break;
default:
switch (exporterType)
{
case Globals.ExporterType.Text:
scansExporter = new BasicScanResult_TextFileExporter(outputFileName);
break;
case Globals.ExporterType.Sqlite:
scansExporter = new BasicScanResult_SqliteExporter(outputFileName);
break;
default:
scansExporter = new BasicScanResult_TextFileExporter(outputFileName);
break;
}
break;
}
return(scansExporter);
}
public static ExporterBase <ScanResult> CreateMSScanInfoExporterFactory(Globals.ExporterType exporterType,
Globals.MSFileType msFileType, string outputFileName)
{
Check.Assert(!string.IsNullOrEmpty(outputFileName), "MSScanInfoExporterFactory cannot work. OutputFileName is empty - which is bad.");
ExporterBase <ScanResult> msFeatureExporter;
switch (exporterType)
{
case Globals.ExporterType.Text:
switch (msFileType)
{
case Globals.MSFileType.PNNL_UIMF:
msFeatureExporter = new MSScanInfoToTextFileExporterUIMF(outputFileName);
break;
default:
msFeatureExporter = new MSScanInfoToTextFileExporterBasic(outputFileName);
break;
}
break;
case Globals.ExporterType.Sqlite:
switch (msFileType)
{
case Globals.MSFileType.PNNL_UIMF:
msFeatureExporter = new MSScanInfoToSQLiteExporterUIMF(outputFileName);
break;
default:
msFeatureExporter = new MSScanInfoToSQLiteExporterBasic(outputFileName);
break;
}
break;
default:
throw new NotImplementedException();
}
return(msFeatureExporter);
}
public static IPeakListExporter Create(Globals.ExporterType exporterType, Globals.MSFileType fileType, int triggerValue, string outputFileName)
{
IPeakListExporter exporter;
switch (exporterType)
{
case Globals.ExporterType.Text:
exporter = new PeakListTextExporter(fileType, triggerValue, outputFileName);
break;
case Globals.ExporterType.Sqlite:
exporter = new PeakListSQLiteExporter(triggerValue, outputFileName);
break;
default:
exporter = new PeakListTextExporter(fileType, triggerValue, outputFileName);
break;
}
return(exporter);
}
public void LoadResults(string isosTextFile, Globals.MSFileType fileType, int minVal, int maxVal)
{
var fileExists = false;
try
{
fileExists = File.Exists(isosTextFile);
}
catch (Exception)
{
// Ignore exceptions
}
Check.Require(fileExists, "IsosResultUtilities cannot open input file");
var importer = new IsosImporter(isosTextFile, fileType, minVal, maxVal);
var isosResults = importer.Import();
Results = isosResults;
}
public void LoadResults(string isosTextFile, Globals.MSFileType fileType)
{
var fileExists = false;
try
{
fileExists = System.IO.File.Exists(isosTextFile);
}
catch (Exception)
{
}
Check.Require(fileExists, "IsosResultUtilities cannot open input file");
var isosResults = new List <IsosResult>();
var importer = new IsosImporter(isosTextFile, fileType);
isosResults = importer.Import();
this.results = isosResults;
}
public PeakListTextExporter(Globals.MSFileType fileType, string outputFileName)
: this(fileType, 100000, outputFileName) // default allowed MSLevels = 1
{
}
public static MSGenerator CreateMSGenerator(Globals.MSFileType fileType)
{
MSGenerator msGenerator;
switch (fileType)
{
case Globals.MSFileType.Undefined:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Agilent_WIFF:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Agilent_D:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Ascii:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Bruker:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Bruker_Ascii:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Thermo_Raw:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.ICR2LS_Rawdata:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.Micromass_Rawdata:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.MZXML_Rawdata:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.PNNL_IMS:
msGenerator = new GenericMSGenerator();
break;
case Globals.MSFileType.PNNL_UIMF:
msGenerator = new UIMF_MSGenerator();
break;
case Globals.MSFileType.SUNEXTREL:
msGenerator = new GenericMSGenerator();
break;
default:
msGenerator = new GenericMSGenerator();
break;
}
return(msGenerator);
}
public Run CreateRun(Globals.MSFileType filetype, string f)
{
Run run;
if (filetype == Globals.MSFileType.MZXML_Rawdata)
{
pwiz.ProteowizardWrapper.DependencyLoader.ValidateLoader();
}
var fileName = getFullPath(f);
switch (filetype)
{
case Globals.MSFileType.Undefined:
run = null;
break;
case Globals.MSFileType.Agilent_WIFF:
run = null;
break;
case Globals.MSFileType.Agilent_D:
run = new AgilentDRun(fileName);
break;
case Globals.MSFileType.Ascii:
run = new MSScanFromTextFileRun(fileName);
break;
case Globals.MSFileType.Bruker:
run = new BrukerV3Run(fileName);
break;
#if !Disable_DeconToolsV2
case Globals.MSFileType.Bruker_V2:
run = new BrukerV2Run(fileName);
break;
#endif
case Globals.MSFileType.Bruker_Ascii:
run = null;
break;
case Globals.MSFileType.Finnigan:
run = new XCaliburRun2(fileName);
break;
case Globals.MSFileType.ICR2LS_Rawdata:
run = null;
break;
case Globals.MSFileType.Micromass_Rawdata:
run = null;
break;
case Globals.MSFileType.MZXML_Rawdata:
run = new MzRun(fileName);
break;
#if !Disable_DeconToolsV2
case Globals.MSFileType.PNNL_IMS:
run = new IMFRun(fileName);
break;
#endif
case Globals.MSFileType.PNNL_UIMF:
run = new UIMFRun(fileName);
break;
case Globals.MSFileType.SUNEXTREL:
run = null;
break;
// Deprecated in February 2017
// case Globals.MSFileType.YAFMS:
// run = new YAFMSRun(fileName);
// break;
default:
run = null;
break;
}
return(run);
}
public IsosImporter(string importFilename, Globals.MSFileType msFileType, int minValue, int maxValue)
: this(importFilename, msFileType)
{
minVal = minValue;
maxVal = maxValue;
}
private Run GetRunFromIsosFilename(string p, Globals.MSFileType msFileType)
{
var runFilename = p.Replace("_isos", "");
var replacementExtension = "";
switch (msFileType)
{
case Globals.MSFileType.Undefined:
break;
case Globals.MSFileType.Agilent_WIFF:
replacementExtension = ".WIFF";
break;
case Globals.MSFileType.Agilent_D:
replacementExtension = ".D";
break;
case Globals.MSFileType.Ascii:
break;
case Globals.MSFileType.Bruker:
break;
case Globals.MSFileType.Bruker_Ascii:
break;
case Globals.MSFileType.Thermo_Raw:
replacementExtension = ".RAW";
break;
case Globals.MSFileType.ICR2LS_Rawdata:
break;
case Globals.MSFileType.Micromass_Rawdata:
break;
case Globals.MSFileType.MZXML_Rawdata:
break;
case Globals.MSFileType.PNNL_IMS:
replacementExtension = ".IMF";
break;
case Globals.MSFileType.PNNL_UIMF:
replacementExtension = ".UIMF";
break;
case Globals.MSFileType.SUNEXTREL:
break;
default:
replacementExtension = ".undefined";
break;
}
runFilename = runFilename.Replace(".csv", replacementExtension);
var factory = new RunFactory();
Run run;
try
{
run = factory.CreateRun(runFilename);
}
catch (Exception)
{
run = null;
}
return(run);
}
public static ExporterBase <IsosResult> CreateMSFeatureExporter(Globals.ExporterType exporterType, Globals.MSFileType msFileType, string outputFileName)
{
Check.Assert(!string.IsNullOrEmpty(outputFileName), "MSFeatureExporterFactory cannot work. OutputFileName is empty - which is bad.");
ExporterBase <IsosResult> msFeatureExporter;
switch (exporterType)
{
case Globals.ExporterType.Text:
//IMS and UIMF filetypes have their own special export formats. All others will use a standard format.
switch (msFileType)
{
case Globals.MSFileType.PNNL_IMS:
msFeatureExporter = new MSFeatureToTextFileExporterIMF(outputFileName);
break;
case Globals.MSFileType.PNNL_UIMF:
msFeatureExporter = new MSFeatureToTextFileExporterUIMF(outputFileName);
break;
default:
msFeatureExporter = new MSFeatureToTextFileExporterBasic(outputFileName);
break;
}
break;
case Globals.ExporterType.Sqlite:
switch (msFileType)
{
case Globals.MSFileType.PNNL_UIMF:
msFeatureExporter = new MSFeatureToSQLiteExporterUIMF(outputFileName);
break;
default:
msFeatureExporter = new MSFeatureToSQLiteExporterBasic(outputFileName);
break;
}
break;
default:
throw new NotImplementedException();
//break;
}
return(msFeatureExporter);
}
private void btnOK_Click(object sender, EventArgs e)
{
this.DialogResult = DialogResult.OK;
this.selectedFiletype = (Globals.MSFileType)listBox1.SelectedItem;
this.Close();
}
public void LoadResults(string uimfIsos1, Globals.MSFileType mSFileType, int frameNum)
{
Check.Require(mSFileType == Globals.MSFileType.PNNL_UIMF, "This option only works for UIMF files");
}
