internal Node(LongTextAligner aligner, Alignment alignment, int row, int column)
{
_longTextAligner = aligner;
_alignment = alignment;
DatabaseIndex = column;
QueryIndex = row;
//Trace.WriteLine(this + " : " + i);
//i++; //Todo: Remove
}
public Alignment(LongTextAligner longTextAligner, List <string> query, Range range)
{
_aligner = longTextAligner;
Query = query;
Indices = new List <Integer>();
var shiftSet = new SortedSet <Integer>();
for (var i = 0; i < query.Count; i++)
{
if (_aligner.TupleIndex.ContainsKey(query[i]))
{
Indices.Add(i);
foreach (var shift in _aligner.TupleIndex.Get(query[i]))
{
if (range.contains(shift))
{
shiftSet.Add(shift);
}
}
}
}
Shifts = new List <Integer>(shiftSet);
var cost = new HashMap <Node, Integer>();
var openSet = new PriorityQueue <Node>(1, new NodeComparer(cost));
var closedSet = new HashSet <Node>();
var parents = new HashMap <Node, Node>();
var startNode = new Node(_aligner, this, 0, 0);
cost.Put(startNode, 0);
openSet.Add(startNode);
while (openSet.Count != 0)
{
Node q = openSet.Dequeue();
if (closedSet.Contains(q))
{
continue;
}
if (q.IsTarget)
{
var backtrace = new List <Node>();
while (parents.ContainsKey(q))
{
if (!q.IsBoundary && q.HasMatch)
{
backtrace.Add(q);
}
q = parents.Get(q);
}
_alignment = new List <Node>(backtrace);
_alignment.Reverse();
//Collections.reverse(alignment);
return;
}
closedSet.Add(q);
foreach (Node nb in q.Adjacent())
{
if (closedSet.Contains(nb))
{
continue;
}
// FIXME: move to appropriate location
int l = Math.Abs(Indices.Count - Shifts.Count - q.QueryIndex +
q.DatabaseIndex) -
Math.Abs(Indices.Count - Shifts.Count -
nb.QueryIndex +
nb.DatabaseIndex);
Integer oldScore = cost.Get(nb);
Integer qScore = cost.Get(q);
if (oldScore == null)
{
oldScore = Integer.MAX_VALUE;
}
if (qScore == null)
{
qScore = Integer.MAX_VALUE;
}
int newScore = qScore + nb.GetValue() - l;
if (newScore < oldScore)
{
cost.Put(nb, newScore);
openSet.Add(nb);
parents.Put(nb, q);
}
}
}
_alignment = new List <Node>();
}