/// <summary>
/// Constructor where the PeptideHit result type is explicitly set
/// </summary>
/// <param name="inputFilePath">Input file to read</param>
/// <param name="resultType">Source file PeptideHit result type</param>
/// <param name="startupOptions">Startup options</param>
public clsPHRPReader(string inputFilePath, PeptideHitResultTypes resultType, clsPHRPStartupOptions startupOptions)
{
ErrorMessages = new List <string>();
WarningMessages = new List <string>();
throw new Exception("Class clsPHRPReader is obsolete; replace with the ReaderFactory class");
}
/// <summary>
/// Constructor where the PeptideHit result type is explicitly set
/// </summary>
/// <param name="inputFilePath">Input file to read</param>
/// <param name="resultType">Source file PeptideHit result type</param>
/// <param name="loadModsAndSeqInfo">If True, looks for and auto-loads the modification definitions from the _ModSummary.txt file</param>
/// <param name="loadMSGFResults">If True, looks for and auto-loads the MSGF results from the _msg.txt file</param>
/// <param name="loadScanStats">If True, looks for and auto-loads the MASIC scan stats files (used to determine collision mode and to refine the precursor m/z values)</param>
public clsPHRPReader(string inputFilePath, PeptideHitResultTypes resultType, bool loadModsAndSeqInfo, bool loadMSGFResults,
bool loadScanStats)
{
ErrorMessages = new List <string>();
WarningMessages = new List <string>();
throw new Exception("Class clsPHRPReader is obsolete; replace with the ReaderFactory class");
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="datasetName">Dataset name</param>
/// <param name="inputDirectoryPath">Input file path</param>
/// <param name="peptideHitResultType">Peptide Hit result type</param>
/// <param name="phrpDataFileName">The base PHRP data file name; used when calling AutoSwitchToLegacyMSGFDBIfRequired and AutoSwitchToFHTIfRequired</param>
public PHRPSeqMapReader(string datasetName, string inputDirectoryPath, PeptideHitResultTypes peptideHitResultType, string phrpDataFileName)
{
DatasetName = datasetName;
if (string.IsNullOrEmpty(DatasetName))
{
ErrorMessage = "Dataset name cannot be empty";
throw new Exception(ErrorMessage);
}
InputDirectoryPath = inputDirectoryPath;
if (string.IsNullOrEmpty(InputDirectoryPath))
{
InputDirectoryPath = string.Empty;
}
PeptideHitResultType = peptideHitResultType;
ResultToSeqMapFilename = ReaderFactory.GetPHRPResultToSeqMapFileName(peptideHitResultType, DatasetName);
if (string.IsNullOrEmpty(ResultToSeqMapFilename))
{
ErrorMessage = "Unable to determine ResultToSeqMap filename for peptideHitResultType: " + peptideHitResultType.ToString();
throw new Exception(ErrorMessage);
}
ResultToSeqMapFilename = ReaderFactory.FindPHRPFile(InputDirectoryPath, phrpDataFileName, ResultToSeqMapFilename, out _);
SeqToProteinMapFilename = ReaderFactory.GetPHRPSeqToProteinMapFileName(peptideHitResultType, DatasetName);
if (string.IsNullOrEmpty(SeqToProteinMapFilename))
{
ErrorMessage = "Unable to determine SeqToProteinMap filename for peptideHitResultType: " + peptideHitResultType.ToString();
throw new Exception(ErrorMessage);
}
SeqToProteinMapFilename = ReaderFactory.FindPHRPFile(InputDirectoryPath, phrpDataFileName, SeqToProteinMapFilename, out _);
mSeqInfoFilename = ReaderFactory.GetPHRPSeqInfoFileName(peptideHitResultType, DatasetName);
if (string.IsNullOrEmpty(mSeqInfoFilename))
{
ErrorMessage = "Unable to determine SeqInfo filename for peptideHitResultType: " + peptideHitResultType.ToString();
throw new Exception(ErrorMessage);
}
mSeqInfoFilename = ReaderFactory.FindPHRPFile(InputDirectoryPath, phrpDataFileName, mSeqInfoFilename, out _);
PepToProteinMapFilename = ReaderFactory.GetPHRPPepToProteinMapFileName(peptideHitResultType, DatasetName);
if (string.IsNullOrEmpty(PepToProteinMapFilename))
{
ErrorMessage = "Unable to determine PepToProtMap filename for PeptideHitResultType: " + peptideHitResultType.ToString();
throw new Exception(ErrorMessage);
}
PepToProteinMapFilename = ReaderFactory.FindPHRPFile(InputDirectoryPath, phrpDataFileName, PepToProteinMapFilename, out _);
MaxProteinsPerSeqID = 0;
}
public static string FindModSummaryFile(
PeptideHitResultTypes peptideHitResultType,
string datasetName,
string inputDirectoryPath,
string inputFileName,
out string modSummaryFileNamePreferred)
{
modSummaryFileNamePreferred = string.Empty;
return(string.Empty);
}
public static string AutoDetermineBestInputFile(string inputDirectoryPath, string datasetName,
out PeptideHitResultTypes matchedResultType)
{
var datasetNames = new List <string>
{
datasetName
};
return(AutoDetermineBestInputFile(inputDirectoryPath, datasetNames, out matchedResultType));
}
public void TestLoadSearchEngineParameters(PeptideHitResultTypes resultType, string parameterFilePath)
{
var parameterFile = FindFile(parameterFilePath);
if (parameterFile.Directory == null)
{
throw new NullReferenceException("Unable to determine the parent directory of the parameter file");
}
var startupOptions = new StartupOptions
{
DisableOpeningInputFiles = true
};
var placeholderInputFilePath = Path.Combine(parameterFile.Directory.FullName, ReaderFactory.NON_EXISTENT_FILE_PLACEHOLDER_NAME);
var factory = new ReaderFactory(placeholderInputFilePath, resultType, startupOptions);
factory.SynFileReader.LoadSearchEngineParameters(parameterFile.Name, out var searchEngineParams);
Console.WriteLine();
Console.WriteLine("{0,-21} {1}", "Search Engine:", searchEngineParams.SearchEngineName);
Console.WriteLine("{0,-21} {1} {2}", "Precursor tolerance:", searchEngineParams.PrecursorMassTolerancePpm, "ppm");
Console.WriteLine("{0,-21} {1} {2}", "Precursor tolerance:", searchEngineParams.PrecursorMassToleranceDa, "Da");
Console.WriteLine("{0,-21} {1}", "Min number termini:", searchEngineParams.MinNumberTermini);
Console.WriteLine("{0,-21} {1}", "Enzyme:", searchEngineParams.Enzyme);
if (!string.IsNullOrWhiteSpace(searchEngineParams.FastaFilePath))
{
Console.WriteLine("{0,-21} {1}", "FASTA File:", searchEngineParams.FastaFilePath);
}
foreach (var modInfo in searchEngineParams.ModList)
{
Console.WriteLine(modInfo.ToString());
}
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="datasetName">Dataset name</param>
/// <param name="inputDirectoryPath">Input file path</param>
/// <param name="peptideHitResultType">Peptide Hit result type</param>
public PHRPSeqMapReader(string datasetName, string inputDirectoryPath, PeptideHitResultTypes peptideHitResultType)
: this(datasetName, inputDirectoryPath, peptideHitResultType, ReaderFactory.GetPHRPSynopsisFileName(peptideHitResultType, datasetName))
{
}
public static string GetToolVersionInfoFilename(PeptideHitResultTypes resultType)
{
return(ReaderFactory.GetToolVersionInfoFilename(resultType));
}
public static string GetPHRPSeqToProteinMapFileName(PeptideHitResultTypes resultType, string datasetName)
{
return(ReaderFactory.GetPHRPSeqToProteinMapFileName(resultType, datasetName));
}
public static string GetPHRPSynopsisFileName(PeptideHitResultTypes resultType, string datasetName)
{
return(ReaderFactory.GetPHRPSynopsisFileName(resultType, datasetName));
}
public static string AutoDetermineDatasetName(string filePath, PeptideHitResultTypes resultType)
{
return(ReaderFactory.AutoDetermineDatasetName(filePath, resultType));
}
public static string AutoDetermineBestInputFile(string inputDirectoryPath, List <string> datasetNames,
out PeptideHitResultTypes matchedResultType)
{
return(ReaderFactory.AutoDetermineBestInputFile(inputDirectoryPath, datasetNames, out matchedResultType));
}
/// <summary>
/// Constructor where the PeptideHit result type is explicitly set
/// </summary>
/// <param name="inputFilePath">Input file to read</param>
/// <param name="resultType">Source file PeptideHit result type</param>
/// <param name="loadModsAndSeqInfo">If True, looks for and auto-loads the modification definitions from the _ModSummary.txt file</param>
/// <param name="loadMSGFResults">If True, looks for and auto-loads the MSGF results from the _msg.txt file</param>
public clsPHRPReader(string inputFilePath, PeptideHitResultTypes resultType, bool loadModsAndSeqInfo, bool loadMSGFResults)
: this(inputFilePath, resultType, loadModsAndSeqInfo, loadMSGFResults, loadScanStats : false)
{
}
