public void TestParsingManyMods(string modDefsFile)
{
var methodName = MethodBase.GetCurrentMethod().Name;
var modFile = Utils.GetTestFile(methodName, modDefsFile.Replace("TEST_FOLDER", Utils.DEFAULT_TEST_FILE_FOLDER));
if (!modFile.Exists)
{
Assert.Ignore("Ignoring test TestParsingManyMods since file not found: " + modFile.FullName);
}
var aaSet = new AminoAcidSet(modFile.FullName);
//aaSet.Display();
//SequenceLocation.ProteinNTerm
var residue = AminoAcid.ProteinNTerm.Residue;
var location = SequenceLocation.ProteinNTerm;
var aa = aaSet.GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
{
var modification = aaSet.GetModificationParams().GetModification(modIndex);
Console.WriteLine(modification.Mass);
//Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
Console.WriteLine();
residue = AminoAcid.ProteinCTerm.Residue;
location = SequenceLocation.ProteinCTerm;
aa = aaSet.GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
{
var modification = aaSet.GetModificationParams().GetModification(modIndex);
Console.WriteLine(modification.Mass);
//Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
//foreach (var aa in AminoAcid.StandardAminoAcidArr)
//{
/*
* var keys = _locationSpecificResidueMap[location].Keys.ToArray();
* Array.Sort(keys);
* foreach (var residue in keys)
* {
* var aa = GetAminoAcid(residue, location);
* Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
* foreach (var modIndex in GetModificationIndices(residue, location))
* {
* Console.Write("\t" + _modificationParams.GetModification(modIndex));
* }
* Console.WriteLine();
* }*/
//}
}
public void TestParsingManyMods()
{
const string modFilePath = @"\\protoapps\UserData\Jungkap\Lewy\db\Mods.txt";
var aaSet = new AminoAcidSet(modFilePath);
//aaSet.Display();
//SequenceLocation.ProteinNTerm
var residue = AminoAcid.ProteinNTerm.Residue;
var location = SequenceLocation.ProteinNTerm;
var aa = aaSet.GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
{
var modification = aaSet.GetModificationParams().GetModification(modIndex);
Console.WriteLine(modification.Mass);
//Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
Console.WriteLine();
residue = AminoAcid.ProteinCTerm.Residue;
location = SequenceLocation.ProteinCTerm;
aa = aaSet.GetAminoAcid(residue, location);
Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
foreach (var modIndex in aaSet.GetModificationIndices(residue, location))
{
var modification = aaSet.GetModificationParams().GetModification(modIndex);
Console.WriteLine(modification.Mass);
//Console.Write("\t" + _modificationParams.GetModification(modIndex));
}
//foreach (var aa in AminoAcid.StandardAminoAcidArr)
/*
* var keys = _locationSpecificResidueMap[location].Keys.ToArray();
* Array.Sort(keys);
* foreach (var residue in keys)
* {
* var aa = GetAminoAcid(residue, location);
* Console.Write("{0}\t{1}\t{2}", residue, aa.Mass, aa.Composition);
* foreach (var modIndex in GetModificationIndices(residue, location))
* {
* Console.Write("\t" + _modificationParams.GetModification(modIndex));
* }
* Console.WriteLine();
* }
* } */
}
public static AminoAcid[] GetExtendedAminoAcidArray(AminoAcidSet aaSet)
{
var ret = new List <AminoAcid>();
var modParam = aaSet.GetModificationParams();
var aminoAcidArray = AminoAcid.StandardAminoAcidArr;
foreach (var aa in aminoAcidArray)
{
ret.Add(aa);
foreach (var modIndex in aaSet.GetModificationIndices(aa.Residue, SequenceLocation.Everywhere))
{
var aa2 = new ModifiedAminoAcid(aa, modParam.GetModification(modIndex));
ret.Add(aa2);
}
}
return(ret.ToArray());
}
public static Modification[] GetTerminalModifications(AminoAcidSet aminoAcidSet)
{
var terminalModifications = new HashSet <Modification>();
var terminalLocations = new[] { SequenceLocation.ProteinNTerm, SequenceLocation.ProteinCTerm };
var terminalResidues = new[] { AminoAcid.ProteinNTerm.Residue, AminoAcid.ProteinCTerm.Residue };
var modParam = aminoAcidSet.GetModificationParams();
for (var i = 0; i < terminalLocations.Length; i++)
{
var location = terminalLocations[i];
var residue = terminalResidues[i];
foreach (var modIndex in aminoAcidSet.GetModificationIndices(residue, location))
{
var modification = modParam.GetModification(modIndex);
terminalModifications.Add(modification);
}
}
return(terminalModifications.ToArray());
}
