package jalview.analysis;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.CigarArray;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.io.NewickFile;
+import jalview.math.MatrixI;
import java.util.Enumeration;
import java.util.List;
int noClus;
- float[][] distance;
+ MatrixI distance;
int mini;
int minj;
- float ri;
+ double ri;
- float rj;
+ double rj;
Vector<SequenceNode> groups = new Vector<SequenceNode>();
SequenceNode top;
- float maxDistValue;
+ double maxDistValue;
- float maxheight;
+ double maxheight;
int ycount;
*
* @param sequence
* DOCUMENT ME!
- * @param type
+ * @param treeType
* DOCUMENT ME!
- * @param pwtype
+ * @param modelType
* DOCUMENT ME!
* @param start
* DOCUMENT ME!
* @param end
* DOCUMENT ME!
*/
- public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
- String pwtype, ScoreModelI sm, int start, int end)
+ public NJTree(SequenceI[] sqs, AlignmentView seqView, String treeType,
+ String modelType, ScoreModelI sm, int start, int end)
{
- this.sequence = sequence;
+ this.sequence = sqs;
this.node = new Vector<SequenceNode>();
- this.type = type;
- this.pwtype = pwtype;
- if (seqData != null)
+ if (!(treeType.equals(NEIGHBOUR_JOINING)))
{
- this.seqData = seqData;
+ treeType = AVERAGE_DISTANCE;
+ }
+ this.type = treeType;
+ this.pwtype = modelType;
+ if (seqView != null)
+ {
+ this.seqData = seqView;
}
else
{
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
- // System.err.println("Made seqData");// dbg
- if (!(type.equals(NEIGHBOUR_JOINING)))
- {
- type = AVERAGE_DISTANCE;
- }
- if (sm == null && !(pwtype.equals("PID")))
+ if (sm == null && !(modelType.equals("PID")))
{
- if (ScoreModels.getInstance().forName(pwtype) == null)
+ if (ScoreModels.getInstance().forName(modelType) == null)
{
- pwtype = "BLOSUM62";
+ modelType = "BLOSUM62";
}
}
noseqs = i++;
- distance = findDistances(sm);
- // System.err.println("Made distances");// dbg
+ // TODO pass choice of params from GUI in constructo
+ if (sm instanceof DistanceScoreModelI)
+ {
+ distance = ((DistanceScoreModelI) sm).findDistances(seqData,
+ SimilarityParams.Jalview);
+ }
+ else if (sm instanceof SimilarityScoreModelI)
+ {
+ /*
+ * compute similarity and invert it to give a distance measure
+ */
+ MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
+ seqData, SimilarityParams.Jalview);
+ result.reverseRange(true);
+ distance = result;
+ }
+
makeLeaves();
- // System.err.println("Made leaves");// dbg
noClus = cluster.size();
cluster();
- // System.err.println("Made clusters");// dbg
-
}
/**
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
- return fout.print(isHasBootstrap(), isHasDistances(),
- isHasRootDistance()); // output all data available for tree
+ return fout.print(hasBootstrap(), hasDistances(),
+ hasRootDistance()); // output all data available for tree
}
/**
* @param list
* Sequence set to be associated with tree nodes
*/
- public void UpdatePlaceHolders(List<SequenceI> list)
+ public void updatePlaceHolders(List<SequenceI> list)
{
Vector<SequenceNode> leaves = findLeaves(top);
/**
* DOCUMENT ME!
*/
- public void cluster()
+ void cluster()
{
while (noClus > 2)
{
*
* @return DOCUMENT ME!
*/
- public Cluster joinClusters(int i, int j)
+ Cluster joinClusters(int i, int j)
{
- float dist = distance[i][j];
+ double dist = distance.getValue(i, j);
int noi = cluster.elementAt(i).value.length;
int noj = cluster.elementAt(j).value.length;
* @param dist
* DOCUMENT ME!
*/
- public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
+ void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+ double dist)
{
tmpi.dist = ((dist + ri) - rj) / 2;
* @param dist
* DOCUMENT ME!
*/
- public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
+ void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+ double dist)
{
- float ih = 0;
- float jh = 0;
+ double ih = 0;
+ double jh = 0;
SequenceNode sni = tmpi;
SequenceNode snj = tmpj;
* @param j
* DOCUMENT ME!
*/
- public void findClusterDistance(int i, int j)
+ void findClusterDistance(int i, int j)
{
int noi = cluster.elementAt(i).value.length;
int noj = cluster.elementAt(j).value.length;
// New distances from cluster to others
- float[] newdist = new float[noseqs];
+ double[] newdist = new double[noseqs];
for (int l = 0; l < noseqs; l++)
{
if ((l != i) && (l != j))
{
- newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj))
+ // newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj))
+ // / (noi + noj);
+ newdist[l] = ((distance.getValue(i, l) * noi) + (distance.getValue(
+ j, l) * noj))
/ (noi + noj);
}
else
for (int ii = 0; ii < noseqs; ii++)
{
- distance[i][ii] = newdist[ii];
- distance[ii][i] = newdist[ii];
+ // distance[i][ii] = newdist[ii];
+ // distance[ii][i] = newdist[ii];
+ distance.setValue(i, ii, newdist[ii]);
+ distance.setValue(ii, i, newdist[ii]);
}
}
* @param j
* DOCUMENT ME!
*/
- public void findClusterNJDistance(int i, int j)
+ void findClusterNJDistance(int i, int j)
{
// New distances from cluster to others
- float[] newdist = new float[noseqs];
+ double[] newdist = new double[noseqs];
for (int l = 0; l < noseqs; l++)
{
if ((l != i) && (l != j))
{
- newdist[l] = ((distance[i][l] + distance[j][l]) - distance[i][j]) / 2;
+ // newdist[l] = ((distance[i][l] + distance[j][l]) - distance[i][j]) /
+ // 2;
+ newdist[l] = (distance.getValue(i, l) + distance.getValue(j, l) - distance
+ .getValue(i, j)) / 2;
}
else
{
for (int ii = 0; ii < noseqs; ii++)
{
- distance[i][ii] = newdist[ii];
- distance[ii][i] = newdist[ii];
+ // distance[i][ii] = newdist[ii];
+ // distance[ii][i] = newdist[ii];
+ distance.setValue(i, ii, newdist[ii]);
+ distance.setValue(ii, i, newdist[ii]);
}
}
*
* @return DOCUMENT ME!
*/
- public float findr(int i, int j)
+ double findr(int i, int j)
{
- float tmp = 1;
+ double tmp = 1;
for (int k = 0; k < noseqs; k++)
{
if ((k != i) && (k != j) && (done[k] != 1))
{
- tmp = tmp + distance[i][k];
+ // tmp = tmp + distance[i][k];
+ tmp = tmp + distance.getValue(i, k);
}
}
*
* @return DOCUMENT ME!
*/
- public float findMinNJDistance()
+ double findMinNJDistance()
{
- float min = 100000;
+ double min = Double.MAX_VALUE;
for (int i = 0; i < (noseqs - 1); i++)
{
{
if ((done[i] != 1) && (done[j] != 1))
{
- float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
+ // float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
+ double tmp = distance.getValue(i, j)
+ - (findr(i, j) + findr(j, i));
if (tmp < min)
{
*
* @return DOCUMENT ME!
*/
- public float findMinDistance()
+ double findMinDistance()
{
- float min = 100000;
+ double min = Double.MAX_VALUE;
for (int i = 0; i < (noseqs - 1); i++)
{
{
if ((done[i] != 1) && (done[j] != 1))
{
- if (distance[i][j] < min)
+ // if (distance[i][j] < min)
+ if (distance.getValue(i, j) < min)
{
mini = i;
minj = j;
- min = distance[i][j];
+ // min = distance[i][j];
+ min = distance.getValue(i, j);
}
}
}
}
/**
- * Calculate a distance matrix given the sequence input data and score model
- *
- * @return similarity matrix used to compute tree
- */
- public float[][] findDistances(ScoreModelI _pwmatrix)
- {
-
- float[][] dist = new float[noseqs][noseqs];
- if (_pwmatrix == null)
- {
- // Resolve substitution model
- _pwmatrix = ScoreModels.getInstance().forName(pwtype);
- if (_pwmatrix == null)
- {
- _pwmatrix = ScoreModels.getInstance().forName("BLOSUM62");
- }
- }
- dist = _pwmatrix.findDistances(seqData);
- return dist;
-
- }
-
- /**
* DOCUMENT ME!
*/
- public void makeLeaves()
+ void makeLeaves()
{
cluster = new Vector<Cluster>();
}
/**
- * Find the leaf node with a particular ycount
- *
- * @param nd
- * initial point on tree to search from
- * @param count
- * value to search for
- *
- * @return null or the node with ycound=count
- */
- public Object findLeaf(SequenceNode nd, int count)
- {
- found = _findLeaf(nd, count);
-
- return found;
- }
-
- /*
- * #see findLeaf(SequenceNode node, count)
- */
- public Object _findLeaf(SequenceNode nd, int count)
- {
- if (nd == null)
- {
- return null;
- }
-
- if (nd.ycount == count)
- {
- found = nd.element();
-
- return found;
- }
- else
- {
- _findLeaf((SequenceNode) nd.left(), count);
- _findLeaf((SequenceNode) nd.right(), count);
- }
-
- return found;
- }
-
- /**
* printNode is mainly for debugging purposes.
*
* @param nd
* SequenceNode
*/
- public void printNode(SequenceNode nd)
+ void printNode(SequenceNode nd)
{
if (nd == null)
{
* @param nd
* DOCUMENT ME!
*/
- public void findMaxDist(SequenceNode nd)
+ void findMaxDist(SequenceNode nd)
{
if (nd == null)
{
if ((nd.left() == null) && (nd.right() == null))
{
- float dist = nd.dist;
+ double dist = nd.dist;
if (dist > maxDistValue)
{
*
* @return DOCUMENT ME!
*/
- public float getMaxHeight()
+ public double getMaxHeight()
{
return maxheight;
}
*
* @return DOCUMENT ME!
*/
- public float findHeight(SequenceNode nd)
+ public double findHeight(SequenceNode nd)
{
if (nd == null)
{
*
* @return DOCUMENT ME!
*/
- public SequenceNode reRoot()
+ SequenceNode reRoot()
{
+ // TODO not used - remove?
if (maxdist != null)
{
ycount = 0;
- float tmpdist = maxdist.dist;
+ double tmpdist = maxdist.dist;
// New top
SequenceNode sn = new SequenceNode();
* @param nd
* DOCUMENT ME!
*/
- public void printN(SequenceNode nd)
+ void printN(SequenceNode nd)
{
if (nd == null)
{
* @param nd
* DOCUMENT ME!
*/
- public void _reCount(SequenceNode nd)
+ void _reCount(SequenceNode nd)
{
// if (_lycount<_lylimit)
// {
* @param dir
* DOCUMENT ME!
*/
- public void changeDirection(SequenceNode nd, SequenceNode dir)
+ void changeDirection(SequenceNode nd, SequenceNode dir)
{
if (nd == null)
{
*
* @return true if tree has real distances
*/
- public boolean isHasDistances()
+ public boolean hasDistances()
{
return hasDistances;
}
*
* @return true if tree has real bootstrap values
*/
- public boolean isHasBootstrap()
+ public boolean hasBootstrap()
{
return hasBootstrap;
}
- public boolean isHasRootDistance()
+ public boolean hasRootDistance()
{
return hasRootDistance;
}
* @author $author$
* @version $Revision$
*/
+// TODO what does this class have that int[] doesn't have already?
class Cluster
{
int[] value;
git://source.jalview.org / jalview.git / blobdiff