// private constant string COL_TAG = "Mass_Correction_Tag";
// private constant string COL_COUNT = "Occurrence_Count";
/// <summary>
/// Look for the mod summary file for the given PSM results file
/// </summary>
/// <param name="datasetName"></param>
/// <param name="psmResultsFilePath"></param>
/// <param name="ascoreParams"></param>
/// <returns>True if a mod summary file is found and successfully processed, otherwise false</returns>
public bool ReadModSummary(
string datasetName,
string psmResultsFilePath,
ParameterFileManager ascoreParams)
{
var psmResultsFile = new FileInfo(psmResultsFilePath);
var workingDirectory = psmResultsFile.Directory;
if (workingDirectory == null)
{
return(false);
}
var modSummaryFileSpec = datasetName + "*ModSummary.txt";
var modSummaryFiles = workingDirectory.GetFiles(modSummaryFileSpec).ToList();
if (modSummaryFiles.Count == 0)
{
if (ascoreParams.DynamicMods.Count == 0)
{
OnWarningEvent(string.Format(
"ModSummary.txt file not found; PSMs may not be recognized properly;\nLooked for {0} in directory {1}",
modSummaryFileSpec, PathUtils.CompactPathString(workingDirectory.FullName, 100)));
}
return(false);
}
var modSummaryFile = modSummaryFiles.First();
var success = ReadModSummary(modSummaryFile, ascoreParams);
return(success);
}
/// <summary>
/// Read mod information from the specified mod summary file
/// </summary>
/// <param name="modSummaryFile"></param>
/// <param name="ascoreParams"></param>
/// <returns>True if the mod summary file exists, otherwise false</returns>
public bool ReadModSummary(FileInfo modSummaryFile, ParameterFileManager ascoreParams)
{
if (!modSummaryFile.Exists)
{
OnWarningEvent("File not found: " + modSummaryFile.FullName);
return(false);
}
ascoreParams.DynamicMods.Clear();
ascoreParams.StaticMods.Clear();
ascoreParams.TerminiMods.Clear();
var mods = Utilities.TextFileToDataTableAssignTypeString(modSummaryFile.FullName);
for (var i = 0; i < mods.Rows.Count; i++)
{
switch ((string)mods.Rows[i][COL_TYPE])
{
case "T":
ascoreParams.TerminiMods.Add(ParseMod(mods, i));
break;
case "S":
ascoreParams.StaticMods.Add(ParseMod(mods, i));
break;
case "D":
ascoreParams.DynamicMods.Add(ParseDynamicMod(mods, i));
break;
}
}
OnStatusEvent("Loaded modifications from: " + modSummaryFile.Name);
foreach (var mod in ascoreParams.StaticMods)
{
OnStatusEvent(Utilities.GetModDescription("Static, ", mod));
}
foreach (var mod in ascoreParams.DynamicMods)
{
OnStatusEvent(Utilities.GetModDescription("Dynamic, ", mod));
}
foreach (var mod in ascoreParams.TerminiMods)
{
OnStatusEvent(Utilities.GetModDescription("Terminus, ", mod));
}
return(true);
}
