public string Parse(Dictionary<string, string> parameters)
{
var message = CheckIsValid(parameters);
if (message != null) return message;
var specFilePath = parameters["-s"];
if (Directory.Exists(specFilePath)) // Directory
{
SpecFilePaths = Directory.GetFiles(specFilePath, "*.raw");
}
else
{
SpecFilePaths = new[] {specFilePath};
}
DatabaseFilePath = parameters["-d"];
var outputDir = parameters["-o"] ?? Environment.CurrentDirectory;
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
return "OutputDir " + outputDir + " is not a directory!";
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
var modFilePath = parameters["-mod"];
if (modFilePath != null)
{
var parser = new ModFileParser(modFilePath);
_searchModifications = parser.SearchModifications;
_maxNumDynModsPerSequence = parser.MaxNumDynModsPerSequence;
if (_searchModifications == null) return "Error while parsing " + modFilePath + "!";
AminoAcidSet = new AminoAcidSet(_searchModifications, _maxNumDynModsPerSequence);
}
else
{
AminoAcidSet = new AminoAcidSet();
_searchModifications = new SearchModification[0];
}
var enzymeId = Convert.ToInt32(parameters["-e"]);
Enzyme enzyme;
switch (enzymeId)
{
case 0:
enzyme = Enzyme.UnspecificCleavage;
break;
case 1:
enzyme = Enzyme.Trypsin;
break;
case 2:
enzyme = Enzyme.Chymotrypsin;
break;
case 3:
enzyme = Enzyme.LysC;
break;
case 4:
enzyme = Enzyme.LysN;
break;
case 5:
enzyme = Enzyme.GluC;
break;
case 6:
enzyme = Enzyme.ArgC;
break;
case 7:
enzyme = Enzyme.AspN;
break;
case 8:
enzyme = Enzyme.Alp;
break;
case 9:
enzyme = Enzyme.NoCleavage;
break;
default:
return "Invalid enzyme ID (" + enzymeId + ") for parameter -e";
}
Enzyme = enzyme;
NumTolerableTermini = Convert.ToInt32(parameters["-ntt"]);
if (NumTolerableTermini < 0 || NumTolerableTermini > 2)
{
return "Invalid value (" + NumTolerableTermini + ") for parameter -m";
}
PrecursorIonTolerancePpm = Convert.ToDouble(parameters["-t"]);
ProductIonTolerancePpm = Convert.ToDouble(parameters["-f"]);
var tdaVal = Convert.ToInt32(parameters["-tda"]);
if (tdaVal != 0 && tdaVal != 1)
{
return "Invalid value (" + tdaVal + ") for parameter -tda";
}
TdaBool = (tdaVal == 1);
MinSequenceLength = Convert.ToInt32(parameters["-minLength"]);
MaxSequenceLength = Convert.ToInt32(parameters["-maxLength"]);
if (MinSequenceLength > MaxSequenceLength)
{
return "MinSequenceLength (" + MinSequenceLength + ") is larger than MaxSequenceLength (" + MaxSequenceLength + ")!";
}
MinPrecursorIonCharge = Convert.ToInt32(parameters["-minCharge"]);
MaxPrecursorIonCharge = Convert.ToInt32(parameters["-maxCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return "MinPrecursorCharge (" + MinPrecursorIonCharge + ") is larger than MaxPrecursorCharge (" + MaxPrecursorIonCharge + ")!";
}
MinProductIonCharge = Convert.ToInt32(parameters["-minFragCharge"]);
MaxProductIonCharge = Convert.ToInt32(parameters["-maxFragCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return "MinFragmentCharge (" + MinProductIonCharge + ") is larger than MaxFragmentCharge (" + MaxProductIonCharge + ")!";
}
return null;
}
public void TestReadingModFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string modFilePath = @"..\..\..\TestFiles\Mods.txt";
if (!File.Exists(modFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modFilePath);
}
var modFileParser = new ModFileParser(modFilePath);
Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
foreach (var searhMod in modFileParser.SearchModifications)
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
}
var aaSet = new AminoAcidSet(modFilePath);
aaSet.Display();
}
private AminoAcidSet(ModFileParser modFileParser)
: this(modFileParser.SearchModifications, modFileParser.MaxNumDynModsPerSequence)
{
}
private AminoAcidSet(ModFileParser modFileParser)
: this(modFileParser.SearchModifications, modFileParser.MaxNumDynModsPerSequence)
{
}
public string Parse(Dictionary<string, string> parameters)
{
var message = CheckIsValid(parameters);
if (message != null)
return message;
try
{
var specFilePath = parameters["-s"];
SpecFilePaths = Directory.Exists(specFilePath) ? Directory.GetFiles(specFilePath, "*.raw") : new[] { specFilePath };
}
catch (Exception ex)
{
Console.WriteLine("Exception parsing the file path for parameter -s: " + ex.Message);
throw;
}
DatabaseFilePath = parameters["-d"];
try
{
var outputDir = parameters["-o"] ?? Environment.CurrentDirectory;
if (!Directory.Exists(outputDir))
{
if (File.Exists(outputDir) && !File.GetAttributes(outputDir).HasFlag(FileAttributes.Directory))
{
return "OutputDir is not a directory: " + outputDir;
}
Directory.CreateDirectory(outputDir);
}
OutputDir = outputDir;
}
catch (Exception ex)
{
Console.WriteLine("Exception validating the path for parameter -o: " + ex.Message);
throw;
}
try
{
var modFilePath = parameters["-mod"];
if (modFilePath != null)
{
var parser = new ModFileParser(modFilePath);
_searchModifications = parser.SearchModifications;
_maxNumDynModsPerSequence = parser.MaxNumDynModsPerSequence;
if (_searchModifications == null)
return "Error while parsing " + modFilePath;
AminoAcidSet = new AminoAcidSet(_searchModifications, _maxNumDynModsPerSequence);
}
else
{
AminoAcidSet = new AminoAcidSet();
_searchModifications = new SearchModification[0];
}
}
catch (Exception ex)
{
Console.WriteLine("Exception parsing the path for parameter -mod: " + ex.Message);
throw;
}
var currentParameter = string.Empty;
try
{
currentParameter = "-feature";
FeatureFilePath = parameters["-feature"];
currentParameter = "-m";
var searchMode = Convert.ToInt32(parameters["-m"]);
if (searchMode < 0 || searchMode > 2)
{
return "Invalid value (" + searchMode + ") for parameter -m";
}
SearchModeInt = searchMode;
currentParameter = "-t";
PrecursorIonTolerancePpm = Convert.ToDouble(parameters["-t"]);
currentParameter = "-f";
ProductIonTolerancePpm = Convert.ToDouble(parameters["-f"]);
currentParameter = "-tda";
var tdaVal = Convert.ToInt32(parameters["-tda"]);
if (tdaVal != 0 && tdaVal != 1 && tdaVal != -1)
{
return "Invalid value (" + tdaVal + ") for parameter -tda";
}
if (tdaVal == 1)
{
Tda = DatabaseSearchMode.Both;
}
else if (tdaVal == -1)
{
Tda = DatabaseSearchMode.Decoy;
}
else
{
Tda = DatabaseSearchMode.Target;
}
currentParameter = "-minLength";
MinSequenceLength = Convert.ToInt32(parameters["-minLength"]);
currentParameter = "-maxLength";
MaxSequenceLength = Convert.ToInt32(parameters["-maxLength"]);
if (MinSequenceLength > MaxSequenceLength)
{
return "MinSequenceLength (" + MinSequenceLength + ") is larger than MaxSequenceLength (" + MaxSequenceLength + ")!";
}
currentParameter = "-feature";
MinPrecursorIonCharge = Convert.ToInt32(parameters["-minCharge"]);
currentParameter = "-feature";
MaxPrecursorIonCharge = Convert.ToInt32(parameters["-maxCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return "MinPrecursorCharge (" + MinPrecursorIonCharge + ") is larger than MaxPrecursorCharge (" + MaxPrecursorIonCharge + ")!";
}
currentParameter = "-minFragCharge";
MinProductIonCharge = Convert.ToInt32(parameters["-minFragCharge"]);
currentParameter = "-maxFragCharge";
MaxProductIonCharge = Convert.ToInt32(parameters["-maxFragCharge"]);
if (MinSequenceLength > MaxSequenceLength)
{
return "MinFragmentCharge (" + MinProductIonCharge + ") is larger than MaxFragmentCharge (" + MaxProductIonCharge + ")!";
}
currentParameter = "-minMass";
MinSequenceMass = Convert.ToDouble(parameters["-minMass"]);
currentParameter = "-maxMass";
MaxSequenceMass = Convert.ToDouble(parameters["-maxMass"]);
if (MinSequenceMass > MaxSequenceMass)
{
return "MinSequenceMassInDa (" + MinSequenceMass + ") is larger than MaxSequenceMassInDa (" + MaxSequenceMass + ")!";
}
currentParameter = "-threads";
MaxNumThreads = Convert.ToInt32(parameters["-threads"]);
MaxNumThreads = GetOptimalMaxThreads(MaxNumThreads);
currentParameter = "-tagSearch";
TagBasedSearch = Convert.ToInt32(parameters["-tagSearch"]) == 1;
}
catch (Exception ex)
{
Console.WriteLine("Exception parsing parameter '" + currentParameter + "': " + ex.Message);
throw;
}
return null;
}
