+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
-import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.CigarArray;
import jalview.datamodel.SeqCigar;
double maxDistValue;
- double maxheight;
+ double maxHeight;
int ycount;
Vector<SequenceNode> node;
+ protected ScoreModelI scoreModel;
+
+ protected SimilarityParamsI scoreParams;
+
+ private AlignmentViewport avport;
+
+ private AlignmentView seqStrings; // redundant? (see seqData)
+
/**
* Constructor
*
SimilarityParamsI scoreParameters)
{
int start, end;
+ avport = av;
boolean selview = av.getSelectionGroup() != null
&& av.getSelectionGroup().getSize() > 1;
- AlignmentView seqStrings = av.getAlignmentView(selview);
+ seqStrings = av.getAlignmentView(selview);
if (!selview)
{
start = 0;
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
- this.sequences = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
+ this.sequences = av.getSelectionGroup()
+ .getSequencesInOrder(av.getAlignment());
}
init(seqStrings, start, end);
{
if (nd == null)
{
- return maxheight;
+ return maxHeight;
}
-
+
if ((nd.left() == null) && (nd.right() == null))
{
nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
-
- if (nd.height > maxheight)
+
+ if (nd.height > maxHeight)
{
return nd.height;
}
else
{
- return maxheight;
+ return maxHeight;
}
}
else
}
else
{
- maxheight = 0;
+ maxHeight = 0;
nd.height = (float) 0.0;
}
-
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
+
+ maxHeight = findHeight((SequenceNode) (nd.left()));
+ maxHeight = findHeight((SequenceNode) (nd.right()));
}
-
- return maxheight;
+
+ return maxHeight;
}
/**
{
// if (_lycount<_lylimit)
// {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // System.err.println("Warning: depth of _recount greater than number of
+ // nodes.");
// }
if (nd == null)
{
return;
}
// _lycount++;
-
+
if ((nd.left() != null) && (nd.right() != null))
{
-
+
_reCount((SequenceNode) nd.left());
_reCount((SequenceNode) nd.right());
-
+
SequenceNode l = (SequenceNode) nd.left();
SequenceNode r = (SequenceNode) nd.right();
-
+
nd.count = l.count + r.count;
nd.ycount = (l.ycount + r.ycount) / 2;
}
while (noClus > 2)
{
findMinDistance();
-
+
joinClusters(mini, minj);
-
+
noClus--;
}
-
+
int rightChild = done.nextClearBit(0);
int leftChild = done.nextClearBit(rightChild + 1);
-
+
joinClusters(leftChild, rightChild);
top = (node.elementAt(leftChild));
-
+
reCount(top);
findHeight(top);
findMaxDist(top);
}
+ /**
+ * Returns the minimum distance between two clusters, and also sets the
+ * indices of the clusters in fields mini and minj
+ *
+ * @return
+ */
protected abstract double findMinDistance();
/**
*/
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
- if (sm instanceof DistanceScoreModelI)
- {
- distances = ((DistanceScoreModelI) sm).findDistances(seqData,
- scoreOptions);
- }
- else if (sm instanceof SimilarityScoreModelI)
- {
- /*
- * compute similarity and invert it to give a distance measure
- * reverseRange(true) converts maximum similarity to zero distance
- */
- MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
- seqData, scoreOptions);
- result.reverseRange(true);
- distances = result;
- }
-
+
+ this.scoreModel = sm;
+ this.scoreParams = scoreOptions;
+
+ distances = scoreModel.findDistances(seqData, scoreParams);
+
makeLeaves();
-
+
noClus = clusters.size();
-
+
cluster();
}
/**
- * DOCUMENT ME!
+ * Finds the node, at or below the given node, with the maximum distance, and
+ * saves the node and the distance value
*
* @param nd
- * DOCUMENT ME!
*/
void findMaxDist(SequenceNode nd)
{
{
return;
}
-
+
if ((nd.left() == null) && (nd.right() == null))
{
double dist = nd.dist;
-
+
if (dist > maxDistValue)
{
maxdist = nd;
}
/**
- * DOCUMENT ME!
+ * Calculates and returns r, whatever that is
*
* @param i
- * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
protected double findr(int i, int j)
{
double tmp = 1;
-
+
for (int k = 0; k < noseqs; k++)
{
if ((k != i) && (k != j) && (!done.get(k)))
tmp = tmp + distances.getValue(i, k);
}
}
-
+
if (noClus > 2)
{
tmp = tmp / (noClus - 2);
}
-
+
return tmp;
}
protected void init(AlignmentView seqView, int start, int end)
{
- this.node = new Vector<SequenceNode>();
+ this.node = new Vector<>();
if (seqView != null)
{
this.seqData = seqView;
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
-
+
/*
* count the non-null sequences
*/
noseqs = 0;
-
+
done = new BitSet();
-
+
for (SequenceI seq : sequences)
{
if (seq != null)
void joinClusters(final int i, final int j)
{
double dist = distances.getValue(i, j);
-
+
ri = findr(i, j);
rj = findr(j, i);
-
+
findClusterDistance(i, j);
-
+
SequenceNode sn = new SequenceNode();
-
+
sn.setLeft((node.elementAt(i)));
sn.setRight((node.elementAt(j)));
-
+
SequenceNode tmpi = (node.elementAt(i));
SequenceNode tmpj = (node.elementAt(j));
-
+
findNewDistances(tmpi, tmpj, dist);
-
+
tmpi.setParent(sn);
tmpj.setParent(sn);
-
+
node.setElementAt(sn, i);
-
+
/*
* move the members of cluster(j) to cluster(i)
* and mark cluster j as out of the game
done.set(j);
}
- protected abstract void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- double dist);
+ /*
+ * Computes and stores new distances for nodei and nodej, given the previous
+ * distance between them
+ */
+ protected abstract void findNewDistances(SequenceNode nodei,
+ SequenceNode nodej, double previousDistance);
/**
* Calculates and saves the distance between the combination of cluster(i) and
*/
void makeLeaves()
{
- clusters = new Vector<BitSet>();
-
+ clusters = new Vector<>();
+
for (int i = 0; i < noseqs; i++)
{
SequenceNode sn = new SequenceNode();
-
+
sn.setElement(sequences[i]);
sn.setName(sequences[i].getName());
node.addElement(sn);
+
BitSet bs = new BitSet();
bs.set(i);
clusters.addElement(bs);
}
}
+ public AlignmentView getOriginalData()
+ {
+ return seqStrings;
+ }
+
+ public MatrixI getDistances()
+ {
+ return distances;
+ }
+
+ public ScoreModelI getScoreModel()
+ {
+ return scoreModel;
+ }
+
+ public SimilarityParamsI getScoreParams()
+ {
+ return scoreParams;
+ }
+
+ public AlignmentViewport getAvport()
+ {
+ return avport;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff