/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.analysis;
-import java.util.*;
-
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.api.analysis.SimilarityScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+import jalview.math.MatrixI;
+
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
*/
public class NJTree
{
- Vector cluster;
+ /*
+ * 'methods'
+ */
+ public static final String AVERAGE_DISTANCE = "AV";
+
+ public static final String NEIGHBOUR_JOINING = "NJ";
+
+ public static final String FROM_FILE = "FromFile";
+
+ Vector<Cluster> cluster;
SequenceI[] sequence;
int noClus;
- float[][] distance;
+ MatrixI distance;
int mini;
int minj;
- float ri;
+ double ri;
- float rj;
+ double rj;
- Vector groups = new Vector();
+ Vector<SequenceNode> groups = new Vector<SequenceNode>();
SequenceNode maxdist;
SequenceNode top;
- float maxDistValue;
+ double maxDistValue;
- float maxheight;
+ double maxheight;
int ycount;
- Vector node;
+ Vector<SequenceNode> node;
String type;
Object found = null;
- Object leaves = null;
-
boolean hasDistances = true; // normal case for jalview trees
boolean hasBootstrap = false; // normal case for jalview trees
SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
- Vector leaves = new Vector();
- findLeaves(top, leaves);
+ Vector<SequenceNode> leaves = findLeaves(top);
int i = 0;
int namesleft = seqs.length;
SequenceNode j;
SequenceI nam;
String realnam;
- Vector one2many = new Vector();
+ Vector<SequenceI> one2many = new Vector<SequenceI>();
int countOne2Many = 0;
while (i < leaves.size())
{
- j = (SequenceNode) leaves.elementAt(i++);
+ j = leaves.elementAt(i++);
realnam = j.getName();
nam = null;
*
* @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, int start, int end)
+ public NJTree(SequenceI[] sqs, AlignmentView seqView, String treeType,
+ String modelType, ScoreModelI sm, int start, int end)
{
- this.sequence = sequence;
- this.node = new Vector();
- this.type = type;
- this.pwtype = pwtype;
- if (seqData != null)
+ this.sequence = sqs;
+ this.node = new Vector<SequenceNode>();
+ if (!(treeType.equals(NEIGHBOUR_JOINING)))
+ {
+ treeType = AVERAGE_DISTANCE;
+ }
+ this.type = treeType;
+ this.pwtype = modelType;
+ if (seqView != null)
{
- this.seqData = seqData;
+ 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("NJ")))
- {
- type = "AV";
- }
- if (!(pwtype.equals("PID")))
+ if (sm == null && !(modelType.equals("PID")))
{
- if (ResidueProperties.getScoreMatrix(pwtype) == null)
+ if (ScoreModels.getInstance().forName(modelType) == null)
{
- pwtype = "BLOSUM62";
+ modelType = "BLOSUM62";
}
}
noseqs = i++;
- distance = findDistances();
- // 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
-
}
/**
*
* @return Newick File with all tree data available
*/
+ @Override
public String toString()
{
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 leaves = new Vector();
- findLeaves(top, leaves);
+ Vector<SequenceNode> leaves = findLeaves(top);
int sz = leaves.size();
SequenceIdMatcher seqmatcher = null;
while (i < sz)
{
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+ SequenceNode leaf = leaves.elementAt(i++);
if (list.contains(leaf.element()))
{
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) list.get(j);
+ seqs[j] = list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
{
@Override
- public void transform(BinaryNode node)
+ public void transform(BinaryNode nd)
{
- Object el = node.element();
+ Object el = nd.element();
if (el != null && el instanceof SequenceI)
{
- node.setName(((SequenceI) el).getName());
+ nd.setName(((SequenceI) el).getName());
}
}
});
/**
* DOCUMENT ME!
*/
- public void cluster()
+ void cluster()
{
while (noClus > 2)
{
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findMinNJDistance();
}
}
joinClusters(one, two);
- top = (SequenceNode) (node.elementAt(one));
+ top = (node.elementAt(one));
reCount(top);
findHeight(top);
*
* @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) cluster.elementAt(i)).value.length;
- int noj = ((Cluster) cluster.elementAt(j)).value.length;
+ int noi = cluster.elementAt(i).value.length;
+ int noj = cluster.elementAt(j).value.length;
int[] value = new int[noi + noj];
for (int ii = 0; ii < noi; ii++)
{
- value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
+ value[ii] = cluster.elementAt(i).value[ii];
}
for (int ii = noi; ii < (noi + noj); ii++)
{
- value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
+ value[ii] = cluster.elementAt(j).value[ii - noi];
}
Cluster c = new Cluster(value);
ri = findr(i, j);
rj = findr(j, i);
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findClusterNJDistance(i, j);
}
SequenceNode sn = new SequenceNode();
- sn.setLeft((SequenceNode) (node.elementAt(i)));
- sn.setRight((SequenceNode) (node.elementAt(j)));
+ sn.setLeft((node.elementAt(i)));
+ sn.setRight((node.elementAt(j)));
- SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
- SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
+ SequenceNode tmpi = (node.elementAt(i));
+ SequenceNode tmpj = (node.elementAt(j));
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findNewNJDistances(tmpi, tmpj, dist);
}
* @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) cluster.elementAt(i)).value.length;
- int noj = ((Cluster) cluster.elementAt(j)).value.length;
+ 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()
- {
-
- float[][] distance = new float[noseqs][noseqs];
-
- // Pairwise substitution score (with no gap penalties)
- ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
- if (_pwmatrix == null)
- {
- _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- distance = _pwmatrix.findDistances(seqData);
- return distance;
-
- }
-
- /**
* DOCUMENT ME!
*/
- public void makeLeaves()
+ void makeLeaves()
{
- cluster = new Vector();
+ cluster = new Vector<Cluster>();
for (int i = 0; i < noseqs; i++)
{
}
/**
+ * Search for leaf nodes below (or at) the given node
+ *
+ * @param nd
+ * root node to search from
+ *
+ * @return
+ */
+ public Vector<SequenceNode> findLeaves(SequenceNode nd)
+ {
+ Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+ findLeaves(nd, leaves);
+ return leaves;
+ }
+
+ /**
* Search for leaf nodes.
*
- * @param node
+ * @param nd
* root node to search from
* @param leaves
* Vector of leaves to add leaf node objects too.
*
* @return Vector of leaf nodes on binary tree
*/
- public Vector findLeaves(SequenceNode node, Vector leaves)
+ Vector<SequenceNode> findLeaves(SequenceNode nd,
+ Vector<SequenceNode> leaves)
{
- if (node == null)
+ if (nd == null)
{
return leaves;
}
- if ((node.left() == null) && (node.right() == null)) // Interior node
+ if ((nd.left() == null) && (nd.right() == null)) // Interior node
// detection
{
- leaves.addElement(node);
+ leaves.addElement(nd);
return leaves;
}
* TODO: Identify internal nodes... if (node.isSequenceLabel()) {
* leaves.addElement(node); }
*/
- findLeaves((SequenceNode) node.left(), leaves);
- findLeaves((SequenceNode) node.right(), leaves);
+ findLeaves((SequenceNode) nd.left(), leaves);
+ findLeaves((SequenceNode) nd.right(), leaves);
}
return leaves;
}
/**
- * Find the leaf node with a particular ycount
- *
- * @param node
- * 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 node, int count)
- {
- found = _findLeaf(node, count);
-
- return found;
- }
-
- /*
- * #see findLeaf(SequenceNode node, count)
- */
- public Object _findLeaf(SequenceNode node, int count)
- {
- if (node == null)
- {
- return null;
- }
-
- if (node.ycount == count)
- {
- found = node.element();
-
- return found;
- }
- else
- {
- _findLeaf((SequenceNode) node.left(), count);
- _findLeaf((SequenceNode) node.right(), count);
- }
-
- return found;
- }
-
- /**
* printNode is mainly for debugging purposes.
*
- * @param node
+ * @param nd
* SequenceNode
*/
- public void printNode(SequenceNode node)
+ void printNode(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ((node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null))
{
- System.out
- .println("Leaf = " + ((SequenceI) node.element()).getName());
- System.out.println("Dist " + ((SequenceNode) node).dist);
- System.out.println("Boot " + node.getBootstrap());
+ System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
+ System.out.println("Dist " + nd.dist);
+ System.out.println("Boot " + nd.getBootstrap());
}
else
{
- System.out.println("Dist " + ((SequenceNode) node).dist);
- printNode((SequenceNode) node.left());
- printNode((SequenceNode) node.right());
+ System.out.println("Dist " + nd.dist);
+ printNode((SequenceNode) nd.left());
+ printNode((SequenceNode) nd.right());
}
}
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void findMaxDist(SequenceNode node)
+ void findMaxDist(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ((node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null))
{
- float dist = ((SequenceNode) node).dist;
+ double dist = nd.dist;
if (dist > maxDistValue)
{
- maxdist = (SequenceNode) node;
+ maxdist = nd;
maxDistValue = dist;
}
}
else
{
- findMaxDist((SequenceNode) node.left());
- findMaxDist((SequenceNode) node.right());
+ findMaxDist((SequenceNode) nd.left());
+ findMaxDist((SequenceNode) nd.right());
}
}
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ public Vector<SequenceNode> getGroups()
{
return groups;
}
*
* @return DOCUMENT ME!
*/
- public float getMaxHeight()
+ public double getMaxHeight()
{
return maxheight;
}
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
* @param threshold
* DOCUMENT ME!
*/
- public void groupNodes(SequenceNode node, float threshold)
+ public void groupNodes(SequenceNode nd, float threshold)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ((node.height / maxheight) > threshold)
+ if ((nd.height / maxheight) > threshold)
{
- groups.addElement(node);
+ groups.addElement(nd);
}
else
{
- groupNodes((SequenceNode) node.left(), threshold);
- groupNodes((SequenceNode) node.right(), threshold);
+ groupNodes((SequenceNode) nd.left(), threshold);
+ groupNodes((SequenceNode) nd.right(), threshold);
}
}
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public float findHeight(SequenceNode node)
+ public double findHeight(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return maxheight;
}
- if ((node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null))
{
- node.height = ((SequenceNode) node.parent()).height + node.dist;
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
- if (node.height > maxheight)
+ if (nd.height > maxheight)
{
- return node.height;
+ return nd.height;
}
else
{
}
else
{
- if (node.parent() != null)
+ if (nd.parent() != null)
{
- node.height = ((SequenceNode) node.parent()).height + node.dist;
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
}
else
{
maxheight = 0;
- node.height = (float) 0.0;
+ nd.height = (float) 0.0;
}
- maxheight = findHeight((SequenceNode) (node.left()));
- maxheight = findHeight((SequenceNode) (node.right()));
+ maxheight = findHeight((SequenceNode) (nd.left()));
+ maxheight = findHeight((SequenceNode) (nd.right()));
}
return maxheight;
*
* @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();
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void printN(SequenceNode node)
+ void printN(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ((node.left() != null) && (node.right() != null))
+ if ((nd.left() != null) && (nd.right() != null))
{
- printN((SequenceNode) node.left());
- printN((SequenceNode) node.right());
+ printN((SequenceNode) nd.left());
+ printN((SequenceNode) nd.right());
}
else
{
- System.out.println(" name = "
- + ((SequenceI) node.element()).getName());
+ System.out.println(" name = " + ((SequenceI) nd.element()).getName());
}
- System.out.println(" dist = " + ((SequenceNode) node).dist + " "
- + ((SequenceNode) node).count + " "
- + ((SequenceNode) node).height);
+ System.out.println(" dist = " + nd.dist + " " + nd.count + " "
+ + nd.height);
}
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void reCount(SequenceNode node)
+ public void reCount(SequenceNode nd)
{
ycount = 0;
_lycount = 0;
// _lylimit = this.node.size();
- _reCount(node);
+ _reCount(nd);
}
private long _lycount = 0, _lylimit = 0;
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void _reCount(SequenceNode node)
+ void _reCount(SequenceNode nd)
{
// if (_lycount<_lylimit)
// {
// System.err.println("Warning: depth of _recount greater than number of nodes.");
// }
- if (node == null)
+ if (nd == null)
{
return;
}
_lycount++;
- if ((node.left() != null) && (node.right() != null))
+ if ((nd.left() != null) && (nd.right() != null))
{
- _reCount((SequenceNode) node.left());
- _reCount((SequenceNode) node.right());
+ _reCount((SequenceNode) nd.left());
+ _reCount((SequenceNode) nd.right());
- SequenceNode l = (SequenceNode) node.left();
- SequenceNode r = (SequenceNode) node.right();
+ SequenceNode l = (SequenceNode) nd.left();
+ SequenceNode r = (SequenceNode) nd.right();
- ((SequenceNode) node).count = l.count + r.count;
- ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+ nd.count = l.count + r.count;
+ nd.ycount = (l.ycount + r.ycount) / 2;
}
else
{
- ((SequenceNode) node).count = 1;
- ((SequenceNode) node).ycount = ycount++;
+ nd.count = 1;
+ nd.ycount = ycount++;
}
_lycount--;
}
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void swapNodes(SequenceNode node)
+ public void swapNodes(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- SequenceNode tmp = (SequenceNode) node.left();
+ SequenceNode tmp = (SequenceNode) nd.left();
- node.setLeft(node.right());
- node.setRight(tmp);
+ nd.setLeft(nd.right());
+ nd.setRight(tmp);
}
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
* @param dir
* DOCUMENT ME!
*/
- public void changeDirection(SequenceNode node, SequenceNode dir)
+ void changeDirection(SequenceNode nd, SequenceNode dir)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if (node.parent() != top)
+ if (nd.parent() != top)
{
- changeDirection((SequenceNode) node.parent(), node);
+ changeDirection((SequenceNode) nd.parent(), nd);
- SequenceNode tmp = (SequenceNode) node.parent();
+ SequenceNode tmp = (SequenceNode) nd.parent();
- if (dir == node.left())
+ if (dir == nd.left())
{
- node.setParent(dir);
- node.setLeft(tmp);
+ nd.setParent(dir);
+ nd.setLeft(tmp);
}
- else if (dir == node.right())
+ else if (dir == nd.right())
{
- node.setParent(dir);
- node.setRight(tmp);
+ nd.setParent(dir);
+ nd.setRight(tmp);
}
}
else
{
- if (dir == node.left())
+ if (dir == nd.left())
{
- node.setParent(node.left());
+ nd.setParent(nd.left());
- if (top.left() == node)
+ if (top.left() == nd)
{
- node.setRight(top.right());
+ nd.setRight(top.right());
}
else
{
- node.setRight(top.left());
+ nd.setRight(top.left());
}
}
else
{
- node.setParent(node.right());
+ nd.setParent(nd.right());
- if (top.left() == node)
+ if (top.left() == nd)
{
- node.setLeft(top.right());
+ nd.setLeft(top.right());
}
else
{
- node.setLeft(top.left());
+ nd.setLeft(top.left());
}
}
}
*
* @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;
}
*/
public void applyToNodes(NodeTransformI nodeTransformI)
{
- for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
- .transform((BinaryNode) nodes.nextElement()))
+ for (Enumeration<SequenceNode> nodes = node.elements(); nodes
+ .hasMoreElements(); nodeTransformI.transform(nodes
+ .nextElement()))
+ {
;
+ }
}
}
* @author $author$
* @version $Revision$
*/
+// TODO what does this class have that int[] doesn't have already?
class Cluster
{
int[] value;