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 ShiftedSequenceGraph(AminoAcidSet aminoAcidSet, double shiftedMass, bool isForward, int maxSequenceLength, double maxSequenceMass = 50000.0)
{
_aminoAcidSet = aminoAcidSet;
_modificationParams = aminoAcidSet.GetModificationParams();
_isForward = isForward;
_index = 0;
_maxSeqIndex = maxSequenceLength + 2; // shift + Term + length
_maxSequenceMass = maxSequenceMass;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
var shiftAa = new AminoAcid('\0', "Shift", new CompositionWithDeltaMass(shiftedMass));
_aminoAcidSequence[0] = shiftAa;
ShiftMass = shiftedMass;
_fragmentComposition = new Composition.Composition[_maxSeqIndex];
_fragmentComposition[0] = shiftAa.Composition;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
IsValid = true;
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="aminoAcidSet"></param>
/// <param name="shiftedMass"></param>
/// <param name="isForward"></param>
/// <param name="maxSequenceLength"></param>
/// <param name="maxSequenceMass"></param>
public ShiftedSequenceGraph(AminoAcidSet aminoAcidSet, double shiftedMass, bool isForward, int maxSequenceLength, double maxSequenceMass = 50000.0)
{
AminoAcidSet = aminoAcidSet;
_modificationParams = aminoAcidSet.GetModificationParams();
_isForward = isForward;
_index = 0;
_maxSeqIndex = maxSequenceLength + 2; // shift + Term + length
_maxSequenceMass = maxSequenceMass;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
var shiftAa = new AminoAcid('\0', "Shift", new CompositionWithDeltaMass(shiftedMass));
_aminoAcidSequence[0] = shiftAa;
ShiftMass = shiftedMass;
_fragmentComposition = new Composition.Composition[_maxSeqIndex];
_fragmentComposition[0] = shiftAa.Composition;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
IsValid = true;
}
/// <summary>
/// Generate a sequence graph for the provided data
/// </summary>
/// <param name="aminoAcidSet"></param>
/// <param name="nTerm"></param>
/// <param name="sequence"></param>
/// <param name="cTerm"></param>
protected SequenceGraph(AminoAcidSet aminoAcidSet, AminoAcid nTerm, string sequence, AminoAcid cTerm)
{
_aminoAcidSet = aminoAcidSet;
_sequence = sequence;
_nTerm = nTerm;
_modificationParams = aminoAcidSet.GetModificationParams();
_maxSeqIndex = sequence.Length + 3; // init + C-term + sequence length + N-term
_index = 0;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
_aminoAcidSequence[0] = AminoAcid.Empty;
_suffixComposition = new Composition.Composition[_maxSeqIndex];
_suffixComposition[0] = Composition.Composition.Zero;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
NumNTermCleavages = 0;
IsValid = true;
SetNTerminalAminoAcid(nTerm);
AddAminoAcid(cTerm.Residue);
for (var i = sequence.Length - 1; i >= 0; i--)
{
if (AddAminoAcid(sequence[i]) == false)
{
IsValid = false;
break;
}
}
if (IsValid)
{
AddAminoAcid(nTerm.Residue);
}
}
public static Modification[] GetTerminalModifications(AminoAcidSet aminoAcidSet)
{
var terminalModifications = new HashSet<Modification>();
var terminalLocations = new[] {SequenceLocation.ProteinNTerm, SequenceLocation.ProteinCTerm};
var terminalResidues = new char[] {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();
}
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();
}
protected SequenceGraph(AminoAcidSet aminoAcidSet, AminoAcid nTerm, string sequence, AminoAcid cTerm)
{
_aminoAcidSet = aminoAcidSet;
_sequence = sequence;
_nTerm = nTerm;
_modificationParams = aminoAcidSet.GetModificationParams();
_maxSeqIndex = sequence.Length + 3; // init + C-term + sequence length + N-term
_index = 0;
_aminoAcidSequence = new AminoAcid[_maxSeqIndex];
_aminoAcidSequence[0] = AminoAcid.Empty;
_suffixComposition = new Composition.Composition[_maxSeqIndex];
_suffixComposition[0] = Composition.Composition.Zero;
_graph = new Node[_maxSeqIndex][];
_graph[0] = new[] { new Node(0) };
_nodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
_compNodeComposition = new Composition.Composition[_maxSeqIndex][]; //, _modificationParams.NumModificationCombinations];
for (var i = 0; i < _maxSeqIndex; i++)
{
_compNodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
_nodeComposition[i] = new Composition.Composition[_modificationParams.NumModificationCombinations];
}
NumNTermCleavages = 0;
IsValid = true;
SetNTerminalAminoAcid(nTerm);
AddAminoAcid(cTerm.Residue);
for (var i = sequence.Length - 1; i >= 0; i--)
{
if (AddAminoAcid(sequence[i]) == false)
{
IsValid = false;
break;
}
}
if (IsValid) AddAminoAcid(nTerm.Residue);
}
