/// <summary>
/// Constructor
/// </summary>
/// <param name="mod"></param>
/// <param name="targetResidue"></param>
/// <param name="loc"></param>
/// <param name="isFixedModification"></param>
public SearchModification(Modification mod, char targetResidue, SequenceLocation loc, bool isFixedModification)
{
Modification = mod;
TargetResidue = targetResidue;
Location = loc;
IsFixedModification = isFixedModification;
}
public SearchModification(Modification mod, char targetResidue, SequenceLocation loc, bool isFixedModification)
{
Modification = mod;
TargetResidue = targetResidue;
Location = loc;
IsFixedModification = isFixedModification;
}
/// <summary>
/// Get the indices of modifications that apply to residue <paramref name="residue"/> at location <paramref name="location"/>
/// </summary>
/// <param name="residue"></param>
/// <param name="location"></param>
/// <returns></returns>
public int[] GetModificationIndices(char residue, SequenceLocation location)
{
var residueModMap = _locationSpecificResidueModMap[location];
if (residueModMap.TryGetValue(residue, out var modIndexArr))
{
return(modIndexArr);
}
return(new int[0]);
}
/// <summary>
/// Get the amino acid specified by character <paramref name="residue"/> that occurs at location <paramref name="location"/>, with any static modifications
/// </summary>
/// <param name="residue"></param>
/// <param name="location"></param>
/// <returns></returns>
public AminoAcid GetAminoAcid(char residue, SequenceLocation location)
{
var residueMap = _locationSpecificResidueMap[location];
if (residueMap.TryGetValue(residue, out var aminoAcid))
{
return(aminoAcid);
}
return(null);
}
public bool AddAminoAcid(char residue, SequenceLocation location = SequenceLocation.Everywhere)
{
return PutAminoAcid(_index, residue, location);
}
/// <summary>
/// Add an amino acid residue to this generator.
/// </summary>
/// <param name="index">index to add the amino acid. 0 is C-term. 1 is the C-term amino acid.</param>
/// <param name="residue">amino acid residue to add.</param>
/// <param name="loc">location of the residue</param>
/// <returns>true if residue is a valid amino acid; false otherwise.</returns>
private bool PutAminoAcid(int index, char residue, SequenceLocation loc)
{
_index = index + 1;
var aminoAcid = AminoAcidSet.GetAminoAcid(residue, loc);
if (aminoAcid == null) // residue is not valid
{
return false;
}
var fragmentComposition = _fragmentComposition[_index - 1] + aminoAcid.Composition;
if (fragmentComposition.Mass > _maxSequenceMass) return false;
_aminoAcidSequence[_index] = aminoAcid;
_fragmentComposition[_index] = fragmentComposition;
var modIndices = AminoAcidSet.GetModificationIndices(residue, loc);
if (!modIndices.Any()) // No modification
{
_graph[_index] = new Node[_graph[_index - 1].Length];
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
_graph[_index][i] = new Node(_graph[_index - 1][i].ModificationCombinationIndex, i);
}
}
else
{
var modCombIndexToNodeMap = new Dictionary<int, Node>();
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
var prevNodeIndex = i;
var prevNode = _graph[_index - 1][i];
var prevModCombIndex = prevNode.ModificationCombinationIndex;
Node newNode;
// unmodified edge
if (modCombIndexToNodeMap.TryGetValue(prevModCombIndex, out newNode))
{
newNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(prevModCombIndex, new Node(prevModCombIndex, prevNodeIndex));
}
// modified edge
foreach (var modIndex in modIndices)
{
var modCombIndex = ModificationParams.GetModificationCombinationIndex(
prevNode.ModificationCombinationIndex, modIndex);
if (modCombIndex < 0) // too many modifications
continue;
if (modCombIndexToNodeMap.TryGetValue(modCombIndex, out newNode))
{
newNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(modCombIndex, new Node(modCombIndex, prevNodeIndex));
}
}
_graph[_index] = modCombIndexToNodeMap.Values.ToArray();
}
}
return true;
}
public int[] GetModificationIndices(char residue, SequenceLocation location)
{
var residueModMap = _locationSpecificResidueModMap[location];
int[] modIndexArr;
if (residueModMap.TryGetValue(residue, out modIndexArr))
{
return modIndexArr;
}
return new int[0];
}
public AminoAcid GetAminoAcid(char residue, SequenceLocation location)
{
var residueMap = _locationSpecificResidueMap[location];
AminoAcid aminoAcid;
if (residueMap.TryGetValue(residue, out aminoAcid))
{
return aminoAcid;
}
return null;
}
/// <summary>
/// Add an amino acid to this shifted sequence graph
/// </summary>
/// <param name="residue"></param>
/// <param name="location"></param>
/// <returns></returns>
public bool AddAminoAcid(char residue, SequenceLocation location = SequenceLocation.Everywhere)
{
return(PutAminoAcid(_index, residue, location));
}
/// <summary>
/// Add an amino acid residue to this generator.
/// </summary>
/// <param name="index">index to add the amino acid. 0 is C-term. 1 is the C-term amino acid.</param>
/// <param name="residue">amino acid residue to add.</param>
/// <param name="loc">location of the residue</param>
/// <returns>true if residue is a valid amino acid; false otherwise.</returns>
private bool PutAminoAcid(int index, char residue, SequenceLocation loc)
{
_index = index + 1;
var aminoAcid = AminoAcidSet.GetAminoAcid(residue, loc);
if (aminoAcid == null) // residue is not valid
{
return(false);
}
var fragmentComposition = _fragmentComposition[_index - 1] + aminoAcid.Composition;
if (fragmentComposition.Mass > _maxSequenceMass)
{
return(false);
}
_aminoAcidSequence[_index] = aminoAcid;
_fragmentComposition[_index] = fragmentComposition;
var modIndices = AminoAcidSet.GetModificationIndices(residue, loc);
if (!modIndices.Any()) // No modification
{
_graph[_index] = new Node[_graph[_index - 1].Length];
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
_graph[_index][i] = new Node(_graph[_index - 1][i].ModificationCombinationIndex, i);
}
}
else
{
var modCombIndexToNodeMap = new Dictionary <int, Node>();
for (var i = 0; i < _graph[_index - 1].Length; i++)
{
var prevNodeIndex = i;
var prevNode = _graph[_index - 1][i];
var prevModCombIndex = prevNode.ModificationCombinationIndex;
// unmodified edge
if (modCombIndexToNodeMap.TryGetValue(prevModCombIndex, out var unmodifiedEdgeNode))
{
unmodifiedEdgeNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(prevModCombIndex, new Node(prevModCombIndex, prevNodeIndex));
}
// modified edge
foreach (var modIndex in modIndices)
{
var modCombIndex = ModificationParams.GetModificationCombinationIndex(
prevNode.ModificationCombinationIndex, modIndex);
if (modCombIndex < 0) // too many modifications
{
continue;
}
if (modCombIndexToNodeMap.TryGetValue(modCombIndex, out var modifiedEdgeNode))
{
modifiedEdgeNode.AddPrevNodeIndex(prevNodeIndex);
}
else
{
modCombIndexToNodeMap.Add(modCombIndex, new Node(modCombIndex, prevNodeIndex));
}
}
_graph[_index] = modCombIndexToNodeMap.Values.ToArray();
}
}
return(true);
}