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());
}
/// <summary>
/// Build the data graph from a sequence graph.
/// </summary>
private void BuildGraph()
{
var sequenceRev = _sequence.Reverse();
var sequence = sequenceRev.Aggregate(string.Empty, (current, aa) => current + aa);
sequence = "\0" + sequence;
vertices = new DataVertex[_maxSeqIndex][];
var mods = AminoAcidSet.GetModificationParams();
var id = 0;
var ntermIndex = 0;
var start = _maxSeqIndex - 2;
var end = 0;
var offset = 1;
if (nterminal != null)
{
start++;
sequence += nterminal.Residue;
}
if (cterminal != null)
{
end--;
offset = 0;
sequence = sequence.Insert(1, cterminal.Residue.ToString(CultureInfo.InvariantCulture));
}
// create vertices
for (var si = start; si > end; si--)
{
var graphSi = si - offset;
vertices[graphSi] = new DataVertex[_graph[si].Length];
for (var mi = 0; mi < _graph[si].Length; mi++)
{
var node = _graph[si][mi];
var mod = mods.GetModificationCombination(node.ModificationCombinationIndex);
SetSink(mi);
vertices[graphSi][mi] = new DataVertex
{
ID = id++,
NTermIndex = ntermIndex,
ModIndex = mi,
PrefixComposition = GetComplementaryComposition(si, mi),
SuffixComposition = GetComposition(si, mi),
ModificationCombination = mod,
Text = string.Empty
};
var vertex = vertices[graphSi][mi];
DataGraph.AddVertex(vertex);
}
ntermIndex++;
}
// connect vertices
for (var si = start; si > (end + 1); si--)
{
var graphSi = si - offset;
for (var mi = 0; mi < _graph[si].Length; mi++)
{
var node = _graph[si][mi];
var currVertex = vertices[graphSi][mi];
foreach (var nextModIndex in node.GetPrevNodeIndices())
{
var nextVertex = vertices[graphSi - 1][nextModIndex];
var currVertexMods = currVertex.ModificationCombination.Modifications;
var nextVertexMods = nextVertex.ModificationCombination.Modifications;
var result = new List <Modification>(currVertexMods);
foreach (var mod in nextVertexMods)
{
if (result.Contains(mod))
{
result.Remove(mod);
}
}
AminoAcid aminoAcid;
if (si == start && nterminal != null)
{
aminoAcid = nterminal;
}
else if (si == end + 2 && cterminal != null)
{
aminoAcid = cterminal;
}
else
{
aminoAcid = AminoAcidSet.GetAminoAcid(sequence[graphSi]);
}
var modAa = aminoAcid as ModifiedAminoAcid;
Modification aminoAcidMod = null;
if (modAa != null)
{
aminoAcidMod = modAa.Modification;
}
if (aminoAcidMod != null)
{
result.Add(aminoAcidMod);
}
var edgeModifications = new ModificationCombination(result);
var edge = new DataEdge(currVertex, nextVertex)
{
AminoAcid = aminoAcid,
SequenceIndex = graphSi,
Modifications = edgeModifications
};
DataGraph.AddEdge(edge);
}
}
}
}
