private Tuple<double, LinkedList<ModificationInstance>> GetFragmentScoreAndModifications(int seqIndex, int modIndex,
IScorer scorer, double?[][] nodeScore, Tuple<double, LinkedList<ModificationInstance>>[][] maxScoreAndMods)
{
var scoreAndMods = maxScoreAndMods[seqIndex][modIndex];
if (scoreAndMods != null) return scoreAndMods;
var node = _graph[seqIndex][modIndex];
var curNodeScore = nodeScore[seqIndex][modIndex] ??
(nodeScore[seqIndex][modIndex] = _isForward
? scorer.GetFragmentScore(GetComposition(seqIndex, modIndex),
GetComplementaryComposition(seqIndex, modIndex))
: scorer.GetFragmentScore(GetComplementaryComposition(seqIndex, modIndex),
GetComposition(seqIndex, modIndex))
);
var bestPrevNodeIndex = -1;
var bestPrevNodeScore = double.NegativeInfinity;
LinkedList<ModificationInstance> bestPrevMods = null;
foreach (var prevNodeIndex in node.GetPrevNodeIndices())
{
var prevNodeScoreAndSequence = GetFragmentScoreAndModifications(seqIndex - 1, prevNodeIndex, scorer,
nodeScore, maxScoreAndMods);
var prevNodeScore = prevNodeScoreAndSequence.Item1;
if (prevNodeScore > bestPrevNodeScore)
{
bestPrevNodeIndex = prevNodeIndex;
bestPrevNodeScore = prevNodeScore;
bestPrevMods = prevNodeScoreAndSequence.Item2;
}
}
if (bestPrevNodeIndex < 0) // source
{
return maxScoreAndMods[seqIndex][modIndex] = new Tuple<double, LinkedList<ModificationInstance>>((double)curNodeScore, new LinkedList<ModificationInstance>());
}
var modPos = _isForward ? seqIndex : _index - seqIndex;
if (modPos <= 1) --modPos;
var aminoAcid = _aminoAcidSequence[seqIndex];
var modAa = aminoAcid as ModifiedAminoAcid;
LinkedList<ModificationInstance> newMods = null;
if (modAa != null)
{
newMods = bestPrevMods == null ? new LinkedList<ModificationInstance>() : new LinkedList<ModificationInstance>(bestPrevMods);
var modIns = new ModificationInstance(modAa.Modification, modPos);
if (_isForward) newMods.AddLast(modIns);
else newMods.AddFirst(modIns);
}
var prevModCombIndex = _graph[seqIndex - 1][bestPrevNodeIndex].ModificationCombinationIndex;
var curModCombIndex = node.ModificationCombinationIndex;
if (prevModCombIndex != curModCombIndex) // modified
{
if (newMods == null)
{
newMods = bestPrevMods == null ? new LinkedList<ModificationInstance>() : new LinkedList<ModificationInstance>(bestPrevMods);
}
var modification = ModificationParams.GetModificationIndexBetween(prevModCombIndex, curModCombIndex);
var modIns = new ModificationInstance(modification, modPos);
if (_isForward) newMods.AddLast(modIns);
else newMods.AddFirst(modIns);
}
return maxScoreAndMods[seqIndex][modIndex] = new Tuple<double, LinkedList<ModificationInstance>>
((double)curNodeScore + bestPrevNodeScore, newMods ?? bestPrevMods);
}
/// <summary>
/// Get the fragment score and modifications
/// </summary>
/// <param name="seqIndex"></param>
/// <param name="modIndex"></param>
/// <param name="scorer"></param>
/// <param name="nodeScore"></param>
/// <param name="maxScoreAndMods"></param>
/// <returns></returns>
private Tuple <double, LinkedList <ModificationInstance> > GetFragmentScoreAndModifications(
int seqIndex,
int modIndex,
IScorer scorer,
IReadOnlyList <double?[]> nodeScore,
IReadOnlyList <Tuple <double, LinkedList <ModificationInstance> >[]> maxScoreAndMods)
{
var scoreAndMods = maxScoreAndMods[seqIndex][modIndex];
if (scoreAndMods != null)
{
return(scoreAndMods);
}
var node = _graph[seqIndex][modIndex];
var curNodeScore = nodeScore[seqIndex][modIndex] ??
(nodeScore[seqIndex][modIndex] = _isForward
? scorer.GetFragmentScore(GetComposition(seqIndex, modIndex),
GetComplementaryComposition(seqIndex, modIndex))
: scorer.GetFragmentScore(GetComplementaryComposition(seqIndex, modIndex),
GetComposition(seqIndex, modIndex))
);
var bestPrevNodeIndex = -1;
var bestPrevNodeScore = double.NegativeInfinity;
LinkedList <ModificationInstance> bestPrevMods = null;
foreach (var prevNodeIndex in node.GetPrevNodeIndices())
{
var prevNodeScoreAndSequence = GetFragmentScoreAndModifications(seqIndex - 1, prevNodeIndex, scorer,
nodeScore, maxScoreAndMods);
var prevNodeScore = prevNodeScoreAndSequence.Item1;
if (prevNodeScore > bestPrevNodeScore)
{
bestPrevNodeIndex = prevNodeIndex;
bestPrevNodeScore = prevNodeScore;
bestPrevMods = prevNodeScoreAndSequence.Item2;
}
}
if (bestPrevNodeIndex < 0) // source
{
return(maxScoreAndMods[seqIndex][modIndex] = new Tuple <double, LinkedList <ModificationInstance> >((double)curNodeScore, new LinkedList <ModificationInstance>()));
}
var modPos = _isForward ? seqIndex : _index - seqIndex;
if (modPos <= 1)
{
--modPos;
}
var aminoAcid = _aminoAcidSequence[seqIndex];
var modAa = aminoAcid as ModifiedAminoAcid;
LinkedList <ModificationInstance> newMods = null;
if (modAa != null)
{
newMods = bestPrevMods == null ? new LinkedList <ModificationInstance>() : new LinkedList <ModificationInstance>(bestPrevMods);
var modIns = new ModificationInstance(modAa.Modification, modPos);
if (_isForward)
{
newMods.AddLast(modIns);
}
else
{
newMods.AddFirst(modIns);
}
}
var prevModCombIndex = _graph[seqIndex - 1][bestPrevNodeIndex].ModificationCombinationIndex;
var curModCombIndex = node.ModificationCombinationIndex;
if (prevModCombIndex != curModCombIndex) // modified
{
if (newMods == null)
{
newMods = bestPrevMods == null ? new LinkedList <ModificationInstance>() : new LinkedList <ModificationInstance>(bestPrevMods);
}
var modification = ModificationParams.GetModificationIndexBetween(prevModCombIndex, curModCombIndex);
var modIns = new ModificationInstance(modification, modPos);
if (_isForward)
{
newMods.AddLast(modIns);
}
else
{
newMods.AddFirst(modIns);
}
}
return(maxScoreAndMods[seqIndex][modIndex] = new Tuple <double, LinkedList <ModificationInstance> >
((double)curNodeScore + bestPrevNodeScore, newMods ?? bestPrevMods));
}