public void FindPathTree(IVertex root)
{
if (root == null)
{
return;
}
// reset path tree
foreach (IVertex node in fVerticesList)
{
node.Dist = int.MaxValue;
node.Visited = false;
node.EdgeIn = null;
}
// init root
root.Dist = 0;
root.Visited = true;
root.EdgeIn = null;
PathCandidate topCandidate = new PathCandidate(root, null);
// processing
while (topCandidate != null)
{
IVertex topNode = topCandidate.Node;
topCandidate = topCandidate.Next;
int nodeDist = topNode.Dist;
topNode.Visited = false;
foreach (IEdge link in topNode.EdgesOut)
{
IVertex target = link.Target;
int newDist = nodeDist + link.Cost;
if (newDist < target.Dist)
{
target.Dist = newDist;
target.EdgeIn = link;
if (!target.Visited)
{
target.Visited = true;
topCandidate = new PathCandidate(target, topCandidate);
}
}
}
}
}
public IMovementPath GetPath(ICharacter user, IWorldObject targetObject)
{
Tile playerTile = user.Tile;
Vector2Ushort targetTilePos = targetObject.TilePosition;
if (playerTile.Position == targetTilePos) // User activated the script while already standing near to the target
{
return(new StraightMovementPath(user.Position, GeometryHelper.TileCenter(playerTile), targetObject));
}
SortedSet <PathCandidate> candidates = new SortedSet <PathCandidate>();
HashSet <Tile> visited = new HashSet <Tile>();
candidates.Add(PathCandidate.Init(playerTile, targetTilePos));
// Api.Logger.Dev($"Automaton: finding path from {playerTile.Position} to {targetTilePos}");
while (candidates.Count != 0)
{
PathCandidate withLeastWeight = candidates.Min();
candidates.Remove(withLeastWeight);
var undiscovered = new HashSet <Tile>(withLeastWeight.Neighbours).Except(visited);
visited.Add(withLeastWeight.Head);
foreach (Tile next in undiscovered)
{
if (next.Position == targetTilePos)
{
return(new WaypointMovementPath(withLeastWeight.Fork(next).AsTilesCenters(), targetObject));
}
if (CanTravel(user, withLeastWeight.Head, next) && withLeastWeight.Length < MAX_PATH_TILES)
{
candidates.Add(withLeastWeight.Fork(next));
}
}
}
// Api.Logger.Error($"Automaton: failed to find proper path from {playerTile.Position} to {targetTilePos}.");
return(new NoPathPath(user));
}
/// <summary>
///
/// </summary>
/// <param name="precursorMass">If you dont wish to use precursor information, set the value to -1</param>
/// <param name="precursorTolerance"></param>
/// <param name="theRegexes"></param>
/// <param name="scanNumber"></param>
/// <param name="measuredPrecursorMZ"></param>
/// <param name="estimatedPrecursorCharge"></param>
/// <returns></returns>
///
public SearchResult Search(double searchLowerBound, double searchUpperBound, List <PathCandidate> pathCandidates, int maxRegexes, int scanNumber, double measuredPrecursorMZ, double estimatedPrecursorCharge)
{
if (fastaParser.MyItems.Count == 0)
{
throw (new Exception("Please load a FASTA DB prior to search"));
}
//Now lets score the sequences
//First lets set all the counters to zero
foreach (FastaItem seq in fastaParser.MyItems)
{
seq.ExtraDouble = 0;
//We will use this to store the matching regexes
seq.Objects.Clear();
}
//Prepare the regexes
if (pathCandidates.Count > maxRegexes)
{
pathCandidates.RemoveRange(maxRegexes - 1, pathCandidates.Count - maxRegexes);
}
//The search is done in 2 steps, we first rank a regex for specificity, then we do the search with the score.
Parallel.ForEach(pathCandidates, p =>
//foreach (PathCandidate p in pathCandidates)
{
Regex r = new Regex(@p.StringRegexForwardReverse, RegexOptions.Compiled);
List <FastaItem> theMatches = new List <FastaItem>();
foreach (FastaItem seq in fastaParser.MyItems)
{
if (seq.MonoisotopicMass >= searchLowerBound)
{
if (seq.MonoisotopicMass <= searchUpperBound || searchUpperBound == -1)
{
if (r.IsMatch(seq.Sequence))
{
theMatches.Add(seq);
seq.Objects.Add(p);
}
}
}
}
if (theMatches.Count > 0)
{
theMatches.Sort((a, b) => a.ExtraDouble.CompareTo(b.ExtraDouble));
double points = 1 / (double)theMatches.Count;
for (int i = 0; i < theMatches.Count; i++)
{
double rankingCorrectionFactor = (double)(i + 1) / (double)theMatches.Count;
if (rankingCorrectionFactor < 0.2)
{
rankingCorrectionFactor = 0.2;
}
double sequenceCorrectionFactor = 1 / (double)theMatches[i].Sequence.Length;
theMatches[i].ExtraDouble += points * sequenceCorrectionFactor * rankingCorrectionFactor;
}
}
});
//}
SearchResult result = new SearchResult(scanNumber, measuredPrecursorMZ, estimatedPrecursorCharge);
//System.Threading.Parallel.ForEach(fastaParser.MyItems, fi =>
foreach (FastaItem fi in fastaParser.MyItems)
{
if (fi.ExtraDouble > 0)
{
SearchResult.SearchResultCandidate sr = new SearchResult.SearchResultCandidate();
sr.Name = fi.SequenceIdentifier;
sr.Sequence = fi.Sequence;
sr.Score = fi.ExtraDouble;
sr.TheoreticalMass = fi.MonoisotopicMass;
foreach (object o in fi.Objects)
{
PathCandidate pc = (PathCandidate)o;
PatternTools.T_ReXS.RegexGenerationTools.SearchResult.RegexAndPath rp = new PatternTools.T_ReXS.RegexGenerationTools.SearchResult.RegexAndPath(pc.NodePath, pc.StringRegexForwardReverse);
sr.RegexAndPaths.Add(rp);
}
result.TheResults.Add(sr);
}
}
//);
return(result);
}
public PathCandidate(IVertex node, PathCandidate next)
{
Node = node;
Next = next;
}
