private void PrepareDeNovoRegistries()
{
deNovoRegistryList = new List <DeNovoRegistry>();
if (PeptideList == null || PeptideList.Equals(""))
{
if (Arguments.MPexResultPath.Length > 0)
{
Console.WriteLine("Loading " + Arguments.MPexResultPath);
ResultPckg2 pkg = ResultPckg2.DeserializeResultPackage(Arguments.MPexResultPath);
deNovoRegistryList = new List <DeNovoRegistry>();
foreach (KeyValuePair <string, List <DeNovoRegistry> > kvp in pkg.MyUnmappedRegistries)
{
deNovoRegistryList.AddRange(kvp.Value);
}
}
else
{
deNovoRegistryList = PreprareDeNovoRegistries();
}
//Eliminate denovo registries not having the minimum score
int removedForNotHavingMinDenovoScore = deNovoRegistryList.RemoveAll(a => a.DeNovoScore < Arguments.MinDeNovoScore);
Console.WriteLine("Removed elements for not attending the minimum denovo score: " + removedForNotHavingMinDenovoScore);
}
else
{
List <string> peptides = Regex.Split(PeptideList, "\n").ToList();
for (int i = 0; i < peptides.Count; i++)
{
string cleanSequence = PatternTools.pTools.CleanPeptide(peptides[i], true);
cleanSequence = Regex.Replace(cleanSequence, " ", "");
cleanSequence = Regex.Replace(cleanSequence, "\t", "");
deNovoRegistryList.Add(new DeNovoRegistry(0, i, 1, cleanSequence, 1, "Provided"));
}
}
//Lets make sure we are satisfying the top hit constraint
if (Arguments.DeNovoOption == DeNovoOption.PepNovoFull || Arguments.DeNovoOption == DeNovoOption.PepNovo)
{
deNovoRegistryList.RemoveAll(a => a.Rank + 1 > Arguments.TopHits);
}
else
{
deNovoRegistryList.RemoveAll(a => a.Rank > Arguments.TopHits);
}
//Finally, lets remove registries that do not satisfy the minimum left criterion
int removedForNotHavingMinimumLength = deNovoRegistryList.RemoveAll(a => a.CleanSequence.Length < Arguments.PeptideMinNumAA);
Console.WriteLine("Removed for not attending the minimum number of aa : " + removedForNotHavingMinimumLength);
}
private void FeedLocusFastaDictPex(DirectoryClassDescription myDir, FileInfo[] resultFilteredFiles)
{
foreach (FileInfo fi in resultFilteredFiles)
{
Console.WriteLine("Parsing " + fi.FullName);
ResultPckg2 thisPckg = ResultPckg2.DeserializeResultPackage(fi.FullName);
myResultPackages.Add(new FileInfoResultPackage(fi, thisPckg, myDir.ClassLabel));
foreach (FastaItem fastaItem in thisPckg.MyFasta)
{
if (!locusFastaDict.ContainsKey(fastaItem.SequenceIdentifier))
{
locusFastaDict.Add(fastaItem.SequenceIdentifier, fastaItem.Sequence);
}
}
}
}
public void ParseDirs(List <DirectoryClassDescription> dirs)
{
MyDirectoryDescriptionDictionary = dirs;
MyResultPackages = new List <ThePackage>();
foreach (DirectoryClassDescription dcd in dirs)
{
//Get all Sepro Files in this and in deeper directories
FileInfo[] fileInfo = new DirectoryInfo(dcd.MyDirectoryFullName).GetFiles("*.mpex", SearchOption.AllDirectories);
foreach (FileInfo file in fileInfo)
{
//First lets unserialize the object
Console.WriteLine("Loading .. " + file.FullName);
ResultPckg2 rp = ResultPckg2.DeserializeResultPackage(file.FullName);
MyResultPackages.Add(new ThePackage(rp, file, dcd.ClassLabel));
}
Console.WriteLine("Done loading.");
}
}
