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PeptideHitResultsProcRunner.cs
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PeptideHitResultsProcRunner.cs
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// -------------------------------------------------------------------------------
// Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
// Program started January 6, 2006
//
// E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
// Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics
// -------------------------------------------------------------------------------
//
// Licensed under the 2-Clause BSD License; you may not use this file except
// in compliance with the License. You may obtain a copy of the License at
// https://opensource.org/licenses/BSD-2-Clause
//
// Copyright 2018 Battelle Memorial Institute
using System;
using System.Collections.Generic;
using System.IO;
using PeptideHitResultsProcessor;
using PeptideHitResultsProcessor.Processor;
using PHRPReader;
using PRISM;
namespace PeptideHitResultsProcRunner
{
/// <summary>
/// This class calls SequestSynopsisFileProcessor or XTandemResultsConverter
/// to process the files to determine the modifications present for each peptide,
/// along with other information
/// </summary>
public class PeptideHitResultsProcRunner : PRISM.FileProcessor.ProcessFilesBase
{
// ReSharper disable once CommentTypo
// Ignore Spelling: Battelle, enums, Hyperscore, MaxQuant, MODa, parm, proc
/// <summary>
/// Constructor
/// </summary>
public PeptideHitResultsProcRunner(PHRPOptions options)
{
mFileDate = PHRPBaseClass.PROGRAM_DATE;
Options = options;
UpdateLogFileOptions();
mPeptideHitResultsFileFormat = ResultsFileFormat.AutoDetermine;
mUseExistingMTSPepToProteinMapFile = false;
mLocalErrorCode = ResultsProcessorErrorCodes.NoError;
}
/// <summary>
/// Error codes specialized for this class
/// </summary>
public enum ResultsProcessorErrorCodes
{
NoError = 0,
UnspecifiedError = -1
}
private bool mFilePathsShown;
private bool mLogFileOptionsUpdated;
protected ResultsFileFormat mPeptideHitResultsFileFormat;
private PHRPBaseClass mPeptideHitResultsProcessor;
protected ResultsProcessorErrorCodes mLocalErrorCode;
private bool mOptionsDisplayed;
protected bool mUseExistingMTSPepToProteinMapFile;
/// <summary>
/// Processing options
/// </summary>
public PHRPOptions Options { get; }
// ReSharper disable once UnusedMember.Global
public ResultsProcessorErrorCodes LocalErrorCode => mLocalErrorCode;
/// <summary>
/// If filePath is an empty string, return textIfEmptyPath
/// Otherwise, return the file path, truncated if over the specified maximum length
/// </summary>
/// <param name="filePath">File path</param>
/// <param name="textIfEmptyPath">Text to return if filePath is an empty string</param>
/// <param name="maxPathLength">Maximum path length</param>
private string FilePathOrText(string filePath, string textIfEmptyPath, int maxPathLength = 110)
{
if (string.IsNullOrWhiteSpace(filePath))
return textIfEmptyPath;
return PathUtils.CompactPathString(filePath, maxPathLength);
}
/// <summary>
/// Get the default file extensions to parse
/// </summary>
public override IList<string> GetDefaultExtensionsToParse()
{
return new List<string>
{
".txt",
".xml",
".tsv"
};
}
/// <summary>
/// Get the error message, or an empty string if no error
/// </summary>
public override string GetErrorMessage()
{
if (ErrorCode is ProcessFilesErrorCodes.LocalizedError or ProcessFilesErrorCodes.NoError)
{
return mLocalErrorCode switch
{
ResultsProcessorErrorCodes.NoError => string.Empty,
ResultsProcessorErrorCodes.UnspecifiedError => "Unspecified localized error",
_ => "Unknown error state" // This shouldn't happen
};
}
return GetBaseClassErrorMessage();
}
private void InitializePeptideHitResultsProcessor(string inputFilePath)
{
var sourceFile = new FileInfo(PathUtils.GetCleanPath(inputFilePath));
mPeptideHitResultsProcessor.Options.MassCorrectionTagsFilePath = PHRPBaseClass.ResolveFilePath(sourceFile.DirectoryName, Options.MassCorrectionTagsFilePath);
mPeptideHitResultsProcessor.Options.ModificationDefinitionsFilePath = PHRPBaseClass.ResolveFilePath(sourceFile.DirectoryName, Options.ModificationDefinitionsFilePath);
mPeptideHitResultsProcessor.Options.SearchToolParameterFilePath = PHRPBaseClass.ResolveFilePath(sourceFile.DirectoryName, Options.SearchToolParameterFilePath);
}
/// <summary>
/// Log an additional message to the log file
/// </summary>
/// <param name="message">Message</param>
public void LogAdditionalMessage(string message)
{
LogMessage(message);
}
/// <summary>
/// Main processing routine
/// </summary>
/// <param name="inputFilePath">PSM tool results file</param>
/// <param name="outputDirectoryPath">Output directory path</param>
/// <param name="parameterFilePath">Parameter file path</param>
/// <param name="resetErrorCode">When true, reset the error code</param>
/// <returns>True if successful, False if failure</returns>
public override bool ProcessFile(string inputFilePath, string outputDirectoryPath, string parameterFilePath, bool resetErrorCode)
{
if (!mLogFileOptionsUpdated)
{
UpdateLogFileOptions();
}
if (resetErrorCode)
{
SetLocalErrorCode(ResultsProcessorErrorCodes.NoError);
}
try
{
if (string.IsNullOrWhiteSpace(inputFilePath))
{
ShowErrorMessage("Input file name is empty");
SetBaseClassErrorCode(ProcessFilesErrorCodes.InvalidInputFilePath);
return false;
}
if (PHRPBaseClass.FindInputFile(inputFilePath, Options.AlternateBasePath, out var inputFileToUse))
{
inputFilePath = inputFileToUse.FullName;
}
// Note that CleanupFilePaths() will update mOutputDirectoryPath, which is used by LogMessage()
if (!CleanupFilePaths(ref inputFilePath, ref outputDirectoryPath))
{
SetBaseClassErrorCode(ProcessFilesErrorCodes.FilePathError);
if (inputFilePath?.Contains("..") == true)
{
var inputFile = new FileInfo(inputFilePath);
OnStatusEvent("Absolute path: " + inputFile.DirectoryName);
}
return false;
}
UpdateProgress("Parsing " + Path.GetFileName(inputFilePath));
ResetProgress();
// ReSharper disable once ConvertIfStatementToReturnStatement
if (Options.CreateProteinModsUsingPHRPDataFile)
{
return StartCreateProteinModsViaPHRPData(inputFilePath, outputDirectoryPath);
}
return StartPHRP(inputFilePath, outputDirectoryPath, parameterFilePath);
}
catch (Exception ex)
{
HandleException("Error in ProcessFile", ex);
OnDebugEvent(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
return false;
}
}
private void RegisterResultsProcessEvents(PHRPBaseClass resultsProcessor)
{
resultsProcessor.ErrorEvent += PeptideHitResultsProcessor_ErrorOccurred;
resultsProcessor.StatusEvent += PeptideHitResultsProcessor_MessageEvent;
resultsProcessor.ProgressUpdate += PeptideHitResultsProcessor_ProgressChanged;
resultsProcessor.WarningEvent += PeptideHitResultsProcessor_WarningMessageEvent;
resultsProcessor.ProgressReset += PeptideHitResultsProcessor_ProgressReset;
}
private void SetLocalErrorCode(ResultsProcessorErrorCodes newErrorCode, bool leaveExistingErrorCodeUnchanged = false)
{
if (leaveExistingErrorCodeUnchanged && mLocalErrorCode != ResultsProcessorErrorCodes.NoError)
{
// An error code is already defined; do not change it
}
else
{
mLocalErrorCode = newErrorCode;
if (newErrorCode == ResultsProcessorErrorCodes.NoError)
{
if (ErrorCode == ProcessFilesErrorCodes.LocalizedError)
{
SetBaseClassErrorCode(ProcessFilesErrorCodes.NoError);
}
}
else
{
SetBaseClassErrorCode(ProcessFilesErrorCodes.LocalizedError);
}
}
}
private void ShowCurrentFilePaths(string inputFilePath, string outputDirectoryPath, string parameterFilePath)
{
Console.WriteLine();
LogMessage(string.Format("{0,-45} {1}",
"Input file:", PathUtils.CompactPathString(inputFilePath, 110)));
if (string.IsNullOrWhiteSpace(outputDirectoryPath))
{
LogMessage(string.Format("{0,-45} {1}",
"Output directory:", "Same directory as the input file"));
}
else
{
LogMessage(string.Format("{0,-45} {1}",
"Output directory:", PathUtils.CompactPathString(outputDirectoryPath, 110)));
}
if (!string.IsNullOrWhiteSpace(Options.OutputFileBaseName))
{
LogMessage(string.Format("{0,-45} {1}",
"Output file base name:", Options.OutputFileBaseName));
}
if (!string.IsNullOrWhiteSpace(parameterFilePath))
{
LogMessage(string.Format("{0,-45} {1}",
"Parameter file:", PathUtils.CompactPathString(parameterFilePath, 110)));
}
}
private void ShowProcessingOptions(PHRPBaseClass resultsProcessor)
{
Console.WriteLine();
// Processing options for MSGFPlus results processor
LogMessage("Processing options for " + resultsProcessor);
if (!string.IsNullOrWhiteSpace(resultsProcessor.Options.XmlParameterFile))
{
LogMessage(string.Format("{0,-45} {1}",
"Legacy XML parameter file:", PathUtils.CompactPathString(resultsProcessor.Options.XmlParameterFile, 110)));
}
LogMessage(string.Format("{0,-45} {1}",
"Search Tool Parameter File:", FilePathOrText(resultsProcessor.Options.SearchToolParameterFilePath, "Not defined")));
LogMessage(string.Format("{0,-45} {1}",
"Modification Definitions File:", FilePathOrText(resultsProcessor.Options.ModificationDefinitionsFilePath, "Not defined")));
LogMessage(string.Format("{0,-45} {1}",
"Mass Correction Tags File:", FilePathOrText(resultsProcessor.Options.MassCorrectionTagsFilePath, "Use internally defined tags")));
LogMessage(string.Format("{0,-45} {1}",
"FASTA File:", FilePathOrText(resultsProcessor.Options.FastaFilePath, "Not defined")));
Console.WriteLine();
LogMessage(string.Format("{0,-45} {1}",
"Create Protein Mods File:", resultsProcessor.Options.CreateProteinModsFile));
LogMessage(string.Format("{0,-45} {1}",
"Ignore Peptide to Protein Mapper Errors:", resultsProcessor.Options.IgnorePeptideToProteinMapperErrors));
LogMessage(string.Format("{0,-45} {1}",
"Protein Mods File Includes Reversed Proteins:", resultsProcessor.Options.ProteinModsFileIncludesReversedProteins));
LogMessage(string.Format("{0,-45} {1}",
"Use Existing MTS PepToProtein Map File:", resultsProcessor.Options.UseExistingMTSPepToProteinMapFile));
Console.WriteLine();
LogMessage(string.Format("{0,-45} {1}",
"Create First Hits File:", resultsProcessor.Options.CreateFirstHitsFile));
LogMessage(string.Format("{0,-45} {1}",
"Create Synopsis File:", resultsProcessor.Options.CreateSynopsisFile));
if (resultsProcessor is InSpecTResultsProcessor)
{
LogMessage(string.Format("{0,-45} {1:E2}",
"InSpecT Synopsis File PValue Threshold:", resultsProcessor.Options.InspectSynopsisFilePValueThreshold));
}
Console.WriteLine();
if (resultsProcessor is MODaResultsProcessor or MODPlusResultsProcessor)
{
LogMessage(string.Format("{0,-49} {1:F2}",
"MODa/MODPlus Synopsis File Probability Threshold:", resultsProcessor.Options.MODaMODPlusSynopsisFileProbabilityThreshold));
}
if (resultsProcessor is MSGFPlusResultsProcessor)
{
LogMessage(string.Format("{0,-45} {1:F2}",
"MSGFPlus Synopsis File EValue Threshold:", resultsProcessor.Options.MSGFPlusSynopsisFileEValueThreshold));
}
if (resultsProcessor is MSGFPlusResultsProcessor or MSPathFinderResultsProcessor)
{
LogMessage(string.Format("{0,-45} {1:E2}",
"MSGFPlus Synopsis File SpecEValue Threshold:", resultsProcessor.Options.MSGFPlusSynopsisFileSpecEValueThreshold));
}
if (resultsProcessor is DiaNNResultsProcessor)
{
LogMessage(string.Format("{0,-49} {1:F3}",
"DIA-NN Synopsis File Q-Value Threshold:", resultsProcessor.Options.DiaNNQValueThreshold));
LogMessage(string.Format("{0,-49} {1:F3}",
"DIA-NN Synopsis File Confidence Score Threshold:", resultsProcessor.Options.DiaNNConfidenceScoreThreshold));
}
if (resultsProcessor is MaxQuantResultsProcessor)
{
LogMessage(string.Format("{0,-49} {1:N0}",
"MaxQuant Synopsis File Andromeda Score Threshold:", resultsProcessor.Options.MaxQuantAndromedaScoreThreshold));
LogMessage(string.Format("{0,-49} {1:F3}",
"MaxQuant Synopsis File PEP Threshold:", resultsProcessor.Options.MaxQuantPosteriorErrorProbabilityThreshold));
}
if (resultsProcessor is MSFraggerResultsProcessor)
{
LogMessage(string.Format("{0,-45} {1:F3}",
"MSFragger Synopsis File E-Value Threshold:", resultsProcessor.Options.MSGFPlusSynopsisFileEValueThreshold));
LogMessage(string.Format("{0,-45} {1:N0}",
"MaxQuant Synopsis File Hyperscore Threshold:", resultsProcessor.Options.MSFraggerHyperscoreThreshold));
}
Console.WriteLine();
}
private bool StartCreateProteinModsViaPHRPData(string inputFilePath, string outputDirectoryPath)
{
try
{
if (!mFilePathsShown)
{
ShowCurrentFilePaths(inputFilePath, outputDirectoryPath, string.Empty);
mFilePathsShown = true;
}
PeptideHitResultTypes PeptideHitResultType;
switch (mPeptideHitResultsFileFormat)
{
case ResultsFileFormat.SequestFirstHitsFile:
PeptideHitResultType = PeptideHitResultTypes.Sequest;
LogMessage("Detected SEQUEST First Hits file");
break;
case ResultsFileFormat.SequestSynopsisFile:
PeptideHitResultType = PeptideHitResultTypes.Sequest;
LogMessage("Detected SEQUEST Synopsis file");
break;
case ResultsFileFormat.XTandemXMLFile:
PeptideHitResultType = PeptideHitResultTypes.XTandem;
LogMessage("Detected X!Tandem XML file");
break;
case ResultsFileFormat.InspectTXTFile:
PeptideHitResultType = PeptideHitResultTypes.Inspect;
LogMessage("Detected InSpecT results file");
break;
case ResultsFileFormat.MSGFPlusTXTFile:
PeptideHitResultType = PeptideHitResultTypes.MSGFPlus;
LogMessage("Detected MS-GF+ results file");
break;
case ResultsFileFormat.MSAlignTXTFile:
PeptideHitResultType = PeptideHitResultTypes.MSAlign;
LogMessage("Detected MSAlign results file");
break;
case ResultsFileFormat.MODPlusTXTFile:
PeptideHitResultType = PeptideHitResultTypes.MODPlus;
LogMessage("Detected MODPlus results file");
break;
case ResultsFileFormat.MSPathFinderTSVFile:
PeptideHitResultType = PeptideHitResultTypes.MSPathFinder;
LogMessage("Detected MSPathfinder results file");
break;
case ResultsFileFormat.TopPICTXTFile:
PeptideHitResultType = PeptideHitResultTypes.TopPIC;
LogMessage("Detected TopPIC results file");
break;
case ResultsFileFormat.MaxQuantTXTFile:
PeptideHitResultType = PeptideHitResultTypes.MaxQuant;
LogMessage("Detected MaxQuant results file");
break;
default:
// Includes PeptideHitResultsFileFormatConstants.AutoDetermine
PeptideHitResultType = ReaderFactory.AutoDetermineResultType(inputFilePath);
break;
}
if (PeptideHitResultType == PeptideHitResultTypes.Unknown)
{
ShowErrorMessage("Error: Could not determine the format of the PHRP data file: " + inputFilePath);
return false;
}
switch (PeptideHitResultType)
{
case PeptideHitResultTypes.Sequest:
mPeptideHitResultsProcessor = new SequestResultsProcessor(Options);
break;
case PeptideHitResultTypes.XTandem:
mPeptideHitResultsProcessor = new XTandemResultsProcessor(Options);
break;
case PeptideHitResultTypes.Inspect:
mPeptideHitResultsProcessor = new InSpecTResultsProcessor(Options);
break;
case PeptideHitResultTypes.MSGFPlus:
mPeptideHitResultsProcessor = new MSGFPlusResultsProcessor(Options);
break;
case PeptideHitResultTypes.MSAlign:
mPeptideHitResultsProcessor = new MSAlignResultsProcessor(Options);
break;
case PeptideHitResultTypes.MODa:
mPeptideHitResultsProcessor = new MODaResultsProcessor(Options);
break;
default:
// Unknown format
ShowErrorMessage("Error: Unrecognized value for PeptideHitResultType: " + PeptideHitResultType);
return false;
}
if (mPeptideHitResultsProcessor == null)
{
return false;
}
// Do not call RegisterEvents
// Instead use local event handlers that optionally log to a file
RegisterResultsProcessEvents(mPeptideHitResultsProcessor);
InitializePeptideHitResultsProcessor(inputFilePath);
if (!mOptionsDisplayed)
{
ShowProcessingOptions(mPeptideHitResultsProcessor);
mOptionsDisplayed = true;
}
var success = mPeptideHitResultsProcessor.CreateProteinModDetailsFile(inputFilePath, outputDirectoryPath);
if (!success)
{
ShowErrorMessage(mPeptideHitResultsProcessor.ErrorMessage);
return false;
}
LogMessage("Processing Complete");
OperationComplete();
return true;
}
catch (Exception ex)
{
HandleException("Error calling CreateProteinModDetailsFile in StartCreateProteinModsViaPHRPData", ex);
return false;
}
}
private bool StartPHRP(string inputFilePath, string outputDirectoryPath, string parameterFilePath)
{
try
{
if (!mFilePathsShown)
{
ShowCurrentFilePaths(inputFilePath, outputDirectoryPath, string.Empty);
mFilePathsShown = true;
}
ResultsFileFormat peptideHitResultsFormat;
bool inputFileIsSynOrFht;
if (mPeptideHitResultsFileFormat == ResultsFileFormat.AutoDetermine)
{
inputFileIsSynOrFht = ReaderFactory.IsSynopsisOrFirstHitsFile(inputFilePath);
if (inputFileIsSynOrFht)
{
var fileType = inputFilePath.EndsWith("fht.txt", StringComparison.OrdinalIgnoreCase)
? "first hits"
: "synopsis";
ShowWarning(string.Format(
"Invalid file format for PHRP; the input file is already a {0} file: {1}",
fileType, inputFilePath));
peptideHitResultsFormat = ResultsFileFormat.AutoDetermine;
}
else
{
peptideHitResultsFormat = PHRPBaseClass.DetermineResultsFileFormat(inputFilePath);
}
}
else
{
peptideHitResultsFormat = mPeptideHitResultsFileFormat;
inputFileIsSynOrFht = false;
}
if (inputFileIsSynOrFht || peptideHitResultsFormat == ResultsFileFormat.AutoDetermine)
{
// If peptideHitResultsFormat is still AutoDetermine that means we couldn't figure out the format
if (!inputFileIsSynOrFht)
{
ShowErrorMessage("Could not determine the format of the input file.");
}
Console.WriteLine();
ShowMessage(
"The filename must end in:\n" +
" " + MSGFPlusResultsProcessor.FILENAME_SUFFIX_MSGFPLUS_FILE + ".tsv or " +
MSGFPlusResultsProcessor.FILENAME_SUFFIX_MSGFDB_FILE + ".tsv (for MS-GF+),\n" +
" " + MSAlignResultsProcessor.FILENAME_SUFFIX_MSALIGN_FILE + ".txt (for MSAlign),\n" +
" " + MODaResultsProcessor.FILENAME_SUFFIX_MODA_FILE + ".txt (for MODA),\n" +
" " + MODPlusResultsProcessor.FILENAME_SUFFIX_MODPlus_FILE + ".txt (for MODPlus),\n" +
" " + MSPathFinderResultsProcessor.FILENAME_SUFFIX_MSPathFinder_FILE + ".tsv (for MSPathFinder),\n" +
" " + SequestResultsProcessor.FILENAME_SUFFIX_FIRST_HITS_FILE + ".txt or " +
SequestResultsProcessor.FILENAME_SUFFIX_SYNOPSIS_FILE + ".txt (for SEQUEST),\n" +
" " + TopPICResultsProcessor.FILENAME_SUFFIX_TopPIC_PRSMs_FILE + ".txt (for TopPIC), or\n" +
" .xml (for X!Tandem).");
Console.WriteLine();
ShowMessage(ConsoleMsgUtils.WrapParagraph(
"If the file ends in .tsv but does not match the other known .tsv suffixes shown above, " +
"this program will assume the results come from MS-GF+"));
return false;
}
switch (peptideHitResultsFormat)
{
case ResultsFileFormat.DiannTSVFile:
mPeptideHitResultsProcessor = new DiaNNResultsProcessor(Options);
LogMessage("Detected DIA-NN results file");
break;
case ResultsFileFormat.InspectTXTFile:
mPeptideHitResultsProcessor = new InSpecTResultsProcessor(Options);
LogMessage("Detected InSpecT results file");
break;
case ResultsFileFormat.MaxQuantTXTFile:
mPeptideHitResultsProcessor = new MaxQuantResultsProcessor(Options);
LogMessage("Detected MaxQuant results file");
break;
case ResultsFileFormat.MODaTXTFile:
mPeptideHitResultsProcessor = new MODaResultsProcessor(Options);
LogMessage("Detected MODa results file");
break;
case ResultsFileFormat.MODPlusTXTFile:
mPeptideHitResultsProcessor = new MODPlusResultsProcessor(Options);
LogMessage("Detected MODPlus results file");
break;
case ResultsFileFormat.MSAlignTXTFile:
mPeptideHitResultsProcessor = new MSAlignResultsProcessor(Options);
LogMessage("Detected MSAlign results file");
break;
case ResultsFileFormat.MSFraggerTSVFile:
mPeptideHitResultsProcessor = new MSFraggerResultsProcessor(Options);
LogMessage("Detected MSFragger results file");
break;
case ResultsFileFormat.MSGFPlusTXTFile:
mPeptideHitResultsProcessor = new MSGFPlusResultsProcessor(Options);
LogMessage("Detected MS-GF+ results file");
break;
case ResultsFileFormat.MSPathFinderTSVFile:
mPeptideHitResultsProcessor = new MSPathFinderResultsProcessor(Options);
LogMessage("Detected MSPathFinder results file");
break;
case ResultsFileFormat.SequestFirstHitsFile:
mPeptideHitResultsProcessor = new SequestResultsProcessor(Options);
LogMessage("Detected SEQUEST First Hits file");
break;
case ResultsFileFormat.SequestSynopsisFile:
mPeptideHitResultsProcessor = new SequestResultsProcessor(Options);
LogMessage("Detected SEQUEST Synopsis file");
break;
case ResultsFileFormat.TopPICTXTFile:
mPeptideHitResultsProcessor = new TopPICResultsProcessor(Options);
LogMessage("Detected TopPIC results file");
break;
case ResultsFileFormat.XTandemXMLFile:
mPeptideHitResultsProcessor = new XTandemResultsProcessor(Options);
LogMessage("Detected X!Tandem XML file");
break;
case ResultsFileFormat.AutoDetermine:
throw new Exception("This code should not be reached; logic error in AutoDetermine: branch of switch (peptideHitResultsFormat)");
default:
// Unknown format
throw new Exception("This code should not be reached; logic error in default: branch of switch (peptideHitResultsFormat)");
}
if (mPeptideHitResultsProcessor == null)
{
return false;
}
// Do not call RegisterEvents
// Instead use local event handlers that optionally log to a file
RegisterResultsProcessEvents(mPeptideHitResultsProcessor);
InitializePeptideHitResultsProcessor(inputFilePath);
if (!mOptionsDisplayed)
{
ShowProcessingOptions(mPeptideHitResultsProcessor);
mOptionsDisplayed = true;
}
var success = mPeptideHitResultsProcessor.ProcessFile(inputFilePath, outputDirectoryPath, parameterFilePath);
if (!success)
{
ShowErrorMessage(mPeptideHitResultsProcessor.ErrorMessage);
return false;
}
LogMessage("Processing Complete");
OperationComplete();
return true;
}
catch (Exception ex)
{
HandleException("Error calling ProcessFile in StartPHRP", ex);
return false;
}
}
private void UpdateLogFileOptions()
{
if (Options.LogFilePath != null && Options.LogFilePath.Equals("False", StringComparison.OrdinalIgnoreCase))
{
Options.LogMessagesToFile = false;
Options.LogFilePath = string.Empty;
}
LogMessagesToFile = Options.LogMessagesToFile;
if (Options.LogMessagesToFile)
{
LogFilePath = Options.LogFilePath == null ||
Options.LogFilePath.Equals("True", StringComparison.OrdinalIgnoreCase) ||
Options.LogFilePath.Equals(".")
? string.Empty
: Options.LogFilePath;
LogDirectoryPath = Options.LogDirectoryPath;
}
mLogFileOptionsUpdated = true;
}
private void PeptideHitResultsProcessor_ErrorOccurred(string message, Exception ex)
{
if (ex != null && !message.Contains(ex.Message))
{
LogMessage(message + ": " + ex.Message, MessageTypeConstants.ErrorMsg);
}
else
{
LogMessage(message, MessageTypeConstants.ErrorMsg);
}
if (ex != null)
{
Console.WriteLine(StackTraceFormatter.GetExceptionStackTraceMultiLine(ex));
}
}
private void PeptideHitResultsProcessor_MessageEvent(string message)
{
LogMessage(message);
}
private void PeptideHitResultsProcessor_ProgressChanged(string taskDescription, float percentComplete)
{
UpdateProgress(taskDescription, percentComplete);
}
private void PeptideHitResultsProcessor_ProgressReset()
{
ResetProgress();
}
private void PeptideHitResultsProcessor_WarningMessageEvent(string warningMessage)
{
LogMessage(warningMessage, MessageTypeConstants.Warning);
}
}
}