/// <summary>
/// Load the mapping between ResultID and Protein Name
/// </summary>
/// <param name="resultToSeqMap">Output: ResultToSeqMap list; keys are ResultID, Values as SeqID</param>
/// <param name="seqToProteinMap">Output: SeqToProteinMap list; keys are SeqID, Values are list of ProteinInfo objects</param>
/// <param name="seqInfo">Output: SeqInfo list; keys are SeqID, Values are seq details stored in SeqInfo objects</param>
/// <param name="pepToProteinMap">Output: PepToProteinMap list; keys are clean peptide sequences (no mods), Values are Protein name and residue start/end locations for the peptide</param>
/// <returns>True if successful, false if an error</returns>
public bool GetProteinMapping(
SortedList <int, int> resultToSeqMap,
SortedList <int, List <ProteinInfo> > seqToProteinMap,
SortedList <int, SequenceInfo> seqInfo,
Dictionary <string, PepToProteinMapInfo> pepToProteinMap)
{
bool success;
string filePath;
resultToSeqMap.Clear();
seqToProteinMap.Clear();
seqInfo.Clear();
pepToProteinMap.Clear();
// Note: do not put a Try/Catch handler in this method
// Instead, allow LoadResultToSeqMapping or LoadSeqToProteinMapping to raise exceptions
if (string.IsNullOrEmpty(ResultToSeqMapFilename))
{
success = false;
}
else
{
filePath = Path.Combine(InputDirectoryPath, ResultToSeqMapFilename);
if (!File.Exists(filePath))
{
ErrorMessage = "SeqInfo file not found: " + filePath;
success = false;
}
else
{
success = LoadResultToSeqMapping(filePath, resultToSeqMap);
}
}
if (!success)
{
return(false);
}
if (!string.IsNullOrEmpty(mSeqInfoFilename))
{
filePath = Path.Combine(InputDirectoryPath, mSeqInfoFilename);
if (File.Exists(filePath))
{
LoadSeqInfo(filePath, seqInfo);
}
}
if (!string.IsNullOrEmpty(SeqToProteinMapFilename))
{
filePath = Path.Combine(InputDirectoryPath, SeqToProteinMapFilename);
if (!File.Exists(filePath))
{
ErrorMessage = "SeqInfo file not found: " + filePath;
success = false;
}
else
{
success = LoadSeqToProteinMapping(filePath, seqToProteinMap);
}
}
else
{
success = false;
}
if (!success || string.IsNullOrEmpty(PepToProteinMapFilename))
{
return(success);
}
filePath = Path.Combine(InputDirectoryPath, PepToProteinMapFilename);
if (!File.Exists(filePath))
{
var filePathAlternate = ReaderFactory.AutoSwitchToLegacyMSGFDBIfRequired(filePath, "Dataset_msgfdb.txt");
if (File.Exists(filePathAlternate))
{
filePath = filePathAlternate;
}
}
if (!File.Exists(filePath))
{
Console.WriteLine("Warning: PepToProtMap file not found; protein residue start/end values will be zero");
Console.WriteLine(" " + filePath);
}
else
{
success = LoadPepToProtMapData(filePath, pepToProteinMap);
}
return(success);
}
public static string AutoSwitchToLegacyMSGFDBIfRequired(string filePath, string basePHRPFileName)
{
return(ReaderFactory.AutoSwitchToLegacyMSGFDBIfRequired(filePath, basePHRPFileName));
}