/// <summary>
/// Search for containing and overlapping paths.
/// </summary>
/// <param name="scaffoldPath">Current Path</param>
/// <param name="isConsumed">Path status</param>
/// <returns>Update list or not</returns>
private bool SearchContainingAndOverlappingPaths(
ScaffoldPath scaffoldPath,
bool[] isConsumed)
{
bool isUpdated = false;
for (int index = 0; index < _scaffoldPaths.Count; index++)
{
if (!isConsumed[index] && scaffoldPath != _scaffoldPaths[index])
{
if (RemoveContainingPaths(scaffoldPath, _scaffoldPaths[index]))
{
isConsumed[index] = true;
isUpdated = true;
}
else
{
if (RemoveOverlappingPaths(scaffoldPath, _scaffoldPaths[index]))
{
isConsumed[index] = true;
isUpdated = true;
}
}
}
}
return(isUpdated);
}
/// <summary>
/// Remove containing paths.
/// </summary>
/// <param name="scaffoldPath">Current path</param>
/// <param name="path">Path to be compared with</param>
/// <returns>containing paths or not</returns>
private static bool RemoveContainingPaths(
ScaffoldPath scaffoldPath,
ScaffoldPath path)
{
if (scaffoldPath.Count >= path.Count)
{
if (path.All(t => scaffoldPath.Where(k => k.Key == t.Key).ToList().Count > 0))
{
return(true);
}
else
{
return(false);
}
}
else
{
if (scaffoldPath.All(t => path.Where(k => k.Key == t.Key).ToList().Count > 0))
{
scaffoldPath.Clear();
((List <KeyValuePair <DeBruijnNode, DeBruijnEdge> >)scaffoldPath).AddRange(path);
return(true);
}
else
{
return(false);
}
}
}
/// <summary>
/// Removes Overlapping paths by generating pairwise overlaps between paths.
/// </summary>
/// <param name="scaffoldPath">Current path</param>
/// <param name="path">Path to be compared with</param>
/// <returns>Overlapping paths or not</returns>
private static bool RemoveOverlappingPaths(
ScaffoldPath scaffoldPath,
ScaffoldPath path)
{
// Generate Overlap Matrix [Similar To Pairwise Overlap aligner]
bool[,] matrix = new bool[scaffoldPath.Count, path.Count];
for (int index = 0; index < scaffoldPath.Count; index++)
{
for (int index1 = 0; index1 < path.Count; index1++)
{
if (scaffoldPath[index].Key == path[index1].Key)
{
matrix.SetValue(true, index, index1);
}
else
{
matrix.SetValue(false, index, index1);
}
}
}
//Search in last row for a match.
int startPosOfRow = -1;
for (int index = scaffoldPath.Count - 1; index >= 0; index--)
{
if ((bool)matrix.GetValue(index, path.Count - 1))
{
int index1 = 1;
while (path.Count - 1 - index1 >= 0 && index - index1 >= 0)
{
if ((bool)matrix.GetValue(index - index1, path.Count - 1 - index1))
{
index1++;
}
else
{
break;
}
}
if (path.Count - 1 - index1 <= 0 || index - index1 <= 0)
{
startPosOfRow = index;
break;
}
}
}
//Search in last column for match.
int startPosOfCol = -1;
for (int index = path.Count - 2; index >= 0; index--)
{
if ((bool)matrix.GetValue(scaffoldPath.Count - 1, index))
{
int index1 = 1;
while (scaffoldPath.Count - 1 - index1 > 0 && index - index1 > 0)
{
if ((bool)matrix.GetValue(scaffoldPath.Count - 1 - index1, index - index1))
{
index1++;
}
else
{
break;
}
}
if (scaffoldPath.Count - 1 - index1 <= 0 || index - index1 <= 0)
{
startPosOfCol = index;
break;
}
}
}
if (startPosOfCol != -1 || startPosOfRow != -1)
{
if (startPosOfRow >= startPosOfCol)
{
StitchPath(scaffoldPath, path, startPosOfRow, path.Count - 1);
return(true);
}
else
{
StitchPath(scaffoldPath, path, scaffoldPath.Count - 1, startPosOfCol);
return(true);
}
}
return(false);
}
/// <summary>
/// Add right extension of the nodes to queue.
/// </summary>
/// <param name="node">Current node.</param>
/// <param name="search">Queue for BFS.</param>
/// <param name="paths">List of paths</param>
/// <param name="familyTree">nodes visited for construction of paths.</param>
/// <param name="contigPairedReadMap">contig and valid mate pair map.</param>
private void RightExtension(
KeyValuePair <DeBruijnNode, DeBruijnEdge> node,
Queue <Paths> search,
List <Paths> paths,
ScaffoldPath familyTree,
Dictionary <ISequence, IList <ValidMatePair> > contigPairedReadMap)
{
Paths childPath;
if (node.Key.RightExtensionNodes.Count > 0)
{
foreach (KeyValuePair <DeBruijnNode, DeBruijnEdge> child in node.Key.RightExtensionNodes)
{
childPath = new Paths();
childPath.CurrentNode = child;
if (familyTree == null)
{
childPath.FamilyTree.Add(node);
}
else
{
childPath.FamilyTree.AddRange(familyTree);
childPath.FamilyTree.Add(node);
}
childPath.NodeOrientation = true;
if (DistanceConstraint(childPath, contigPairedReadMap) &&
childPath.FamilyTree.Count < _depth &&
!contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == _graph.GetNodeSequence(k.Key))))
{
search.Enqueue(childPath);
}
else
{
if (contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == _graph.GetNodeSequence(k.Key))))
{
paths.Add(childPath);
}
}
}
}
else
{
childPath = new Paths();
if (familyTree == null)
{
childPath.FamilyTree.Add(node);
}
else
{
childPath.FamilyTree.AddRange(familyTree);
childPath.FamilyTree.Add(node);
}
if (contigPairedReadMap.All(
t => childPath.FamilyTree.Any(k => t.Key == _graph.GetNodeSequence(k.Key))))
{
paths.Add(childPath);
}
}
}
