X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=5f268ae440eb30280622e36ccdda8340a1505438;hb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;hp=144ec2c6ea14328cb69c066c38a6d06b9663f2ee;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 144ec2c..5f268ae 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,28 +1,43 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.scoremodels.ScoreModels;
+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.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!
@@ -32,7 +47,16 @@ import jalview.util.*;
*/
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;
SequenceI[] sequence;
@@ -46,29 +70,29 @@ public class NJTree
int noClus;
- float[][] distance;
+ MatrixI distance;
int mini;
int minj;
- float ri;
+ double ri;
- float rj;
+ double rj;
- Vector groups = new Vector();
+ Vector groups = new Vector();
SequenceNode maxdist;
SequenceNode top;
- float maxDistValue;
+ double maxDistValue;
- float maxheight;
+ double maxheight;
int ycount;
- Vector node;
+ Vector node;
String type;
@@ -76,8 +100,6 @@ public class NJTree
Object found = null;
- Object leaves = null;
-
boolean hasDistances = true; // normal case for jalview trees
boolean hasBootstrap = false; // normal case for jalview trees
@@ -139,8 +161,7 @@ public class NJTree
SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
- Vector leaves = new Vector();
- findLeaves(top, leaves);
+ Vector leaves = findLeaves(top);
int i = 0;
int namesleft = seqs.length;
@@ -148,11 +169,11 @@ public class NJTree
SequenceNode j;
SequenceI nam;
String realnam;
- Vector one2many = new Vector();
+ Vector one2many = new Vector();
int countOne2Many = 0;
while (i < leaves.size())
{
- j = (SequenceNode) leaves.elementAt(i++);
+ j = leaves.elementAt(i++);
realnam = j.getName();
nam = null;
@@ -196,25 +217,25 @@ public class NJTree
*
* @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();
+ this.type = treeType;
+ this.pwtype = modelType;
+ if (seqView != null)
{
- this.seqData = seqData;
+ this.seqData = seqView;
}
else
{
@@ -228,16 +249,16 @@ public class NJTree
this.seqData = new AlignmentView(sdata, start);
}
// System.err.println("Made seqData");// dbg
- if (!(type.equals("NJ")))
+ if (!(treeType.equals(NEIGHBOUR_JOINING)))
{
- type = "AV";
+ treeType = AVERAGE_DISTANCE;
}
- 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";
}
}
@@ -253,8 +274,22 @@ public class NJTree
noseqs = i++;
- distance = findDistances(this.seqData
- .getSequenceStrings(Comparison.GapChars.charAt(0)));
+ if (sm instanceof DistanceScoreModelI)
+ {
+ distance = ((DistanceScoreModelI) sm).findDistances(seqData);
+ }
+ else if (sm instanceof SimilarityScoreModelI)
+ {
+ /*
+ * compute similarity and invert it to give a distance measure
+ */
+ MatrixI result = ((SimilarityScoreModelI) sm)
+ .findSimilarities(seqData);
+ double maxScore = result.getMaxValue();
+ result.subtractAllFrom(maxScore);
+ distance = result;
+ }
+
// System.err.println("Made distances");// dbg
makeLeaves();
// System.err.println("Made leaves");// dbg
@@ -271,6 +306,7 @@ public class NJTree
*
* @return Newick File with all tree data available
*/
+ @Override
public String toString()
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
@@ -288,8 +324,7 @@ public class NJTree
*/
public void UpdatePlaceHolders(List list)
{
- Vector leaves = new Vector();
- findLeaves(top, leaves);
+ Vector leaves = findLeaves(top);
int sz = leaves.size();
SequenceIdMatcher seqmatcher = null;
@@ -297,7 +332,7 @@ public class NJTree
while (i < sz)
{
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+ SequenceNode leaf = leaves.elementAt(i++);
if (list.contains(leaf.element()))
{
@@ -312,7 +347,7 @@ public class NJTree
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) list.get(j);
+ seqs[j] = list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
@@ -358,12 +393,12 @@ public class NJTree
{
@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());
}
}
});
@@ -376,7 +411,7 @@ public class NJTree
{
while (noClus > 2)
{
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findMinNJDistance();
}
@@ -417,7 +452,7 @@ public class NJTree
}
joinClusters(one, two);
- top = (SequenceNode) (node.elementAt(one));
+ top = (node.elementAt(one));
reCount(top);
findHeight(top);
@@ -436,21 +471,21 @@ public class NJTree
*/
public 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);
@@ -458,7 +493,7 @@ public class NJTree
ri = findr(i, j);
rj = findr(j, i);
- if (type.equals("NJ"))
+ if (type.equals(NEIGHBOUR_JOINING))
{
findClusterNJDistance(i, j);
}
@@ -469,13 +504,13 @@ public class NJTree
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);
}
@@ -503,7 +538,7 @@ public class NJTree
* DOCUMENT ME!
*/
public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
+ double dist)
{
tmpi.dist = ((dist + ri) - rj) / 2;
@@ -531,10 +566,10 @@ public class NJTree
* DOCUMENT ME!
*/
public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
+ double dist)
{
- float ih = 0;
- float jh = 0;
+ double ih = 0;
+ double jh = 0;
SequenceNode sni = tmpi;
SequenceNode snj = tmpj;
@@ -565,17 +600,20 @@ public class NJTree
*/
public 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
@@ -586,8 +624,10 @@ public class NJTree
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]);
}
}
@@ -603,13 +643,16 @@ public class NJTree
{
// 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
{
@@ -619,8 +662,10 @@ public class NJTree
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]);
}
}
@@ -634,15 +679,16 @@ public class NJTree
*
* @return DOCUMENT ME!
*/
- public float findr(int i, int j)
+ public 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);
}
}
@@ -659,9 +705,9 @@ public class NJTree
*
* @return DOCUMENT ME!
*/
- public float findMinNJDistance()
+ public double findMinNJDistance()
{
- float min = 100000;
+ double min = Double.MAX_VALUE;
for (int i = 0; i < (noseqs - 1); i++)
{
@@ -669,7 +715,9 @@ public class NJTree
{
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)
{
@@ -690,9 +738,9 @@ public class NJTree
*
* @return DOCUMENT ME!
*/
- public float findMinDistance()
+ public double findMinDistance()
{
- float min = 100000;
+ double min = Double.MAX_VALUE;
for (int i = 0; i < (noseqs - 1); i++)
{
@@ -700,12 +748,14 @@ public class NJTree
{
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);
}
}
}
@@ -715,100 +765,44 @@ public class NJTree
}
/**
- * DOCUMENT ME!
+ * Calculate a distance matrix given the sequence input data and score model
*
- * @return DOCUMENT ME!
+ * @return
*/
- public float[][] findDistances(String[] sequenceString)
+ public MatrixI findDistances(ScoreModelI scoreModel)
{
- float[][] distance = new float[noseqs][noseqs];
+ MatrixI result = null;
- if (pwtype.equals("PID"))
+ if (scoreModel == null)
{
- for (int i = 0; i < (noseqs - 1); i++)
+ // Resolve substitution model
+ scoreModel = ScoreModels.getInstance().forName(pwtype);
+ if (scoreModel == null)
{
- for (int j = i; j < noseqs; j++)
- {
- if (j == i)
- {
- distance[i][i] = 0;
- }
- else
- {
- distance[i][j] = 100 - Comparison.PID(sequenceString[i],
- sequenceString[j]);
-
- distance[j][i] = distance[i][j];
- }
- }
+ scoreModel = ScoreModels.getInstance().forName("BLOSUM62");
}
}
+ if (scoreModel instanceof DistanceScoreModelI)
+ {
+ result = ((DistanceScoreModelI) scoreModel).findDistances(seqData);
+ }
+ else if (scoreModel instanceof SimilarityScoreModelI)
+ {
+ /*
+ * compute similarity and invert it to give a distance measure
+ */
+ result = ((SimilarityScoreModelI) scoreModel)
+ .findSimilarities(seqData);
+ double maxScore = result.getMaxValue();
+ result.subtractAllFrom(maxScore);
+ }
else
{
- // Pairwise substitution score (with no gap penalties)
- ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
- if (pwmatrix == null)
- {
- pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- int maxscore = 0;
- int end = sequenceString[0].length();
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- int score = 0;
-
- for (int k = 0; k < end; k++)
- {
- try
- {
- score += pwmatrix.getPairwiseScore(
- sequenceString[i].charAt(k),
- sequenceString[j].charAt(k));
- } catch (Exception ex)
- {
- System.err.println("err creating BLOSUM62 tree");
- ex.printStackTrace();
- }
- }
-
- distance[i][j] = (float) score;
-
- if (score > maxscore)
- {
- maxscore = score;
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = (float) maxscore - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
-
+ System.err
+ .println("Unexpected type of score model, can't compute distances");
}
- return distance;
- // else
- /*
- * else if (pwtype.equals("SW")) { float max = -1;
- *
- * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- * { AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
- * as.calcScoreMatrix(); as.traceAlignment(); as.printAlignment(System.out);
- * distance[i][j] = (float) as.maxscore;
- *
- * if (max < distance[i][j]) { max = distance[i][j]; } } }
- *
- * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
- * { distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j];
- * } } }/
- */
+ return result;
}
/**
@@ -816,7 +810,7 @@ public class NJTree
*/
public void makeLeaves()
{
- cluster = new Vector();
+ cluster = new Vector();
for (int i = 0; i < noseqs; i++)
{
@@ -835,26 +829,42 @@ public class NJTree
}
/**
+ * Search for leaf nodes below (or at) the given node
+ *
+ * @param nd
+ * root node to search from
+ *
+ * @return
+ */
+ public Vector findLeaves(SequenceNode nd)
+ {
+ Vector leaves = new Vector();
+ 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 findLeaves(SequenceNode nd,
+ Vector 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;
}
@@ -864,8 +874,8 @@ public class NJTree
* 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;
@@ -874,16 +884,16 @@ public class NJTree
/**
* Find the leaf node with a particular ycount
*
- * @param node
+ * @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 node, int count)
+ public Object findLeaf(SequenceNode nd, int count)
{
- found = _findLeaf(node, count);
+ found = _findLeaf(nd, count);
return found;
}
@@ -891,23 +901,23 @@ public class NJTree
/*
* #see findLeaf(SequenceNode node, count)
*/
- public Object _findLeaf(SequenceNode node, int count)
+ public Object _findLeaf(SequenceNode nd, int count)
{
- if (node == null)
+ if (nd == null)
{
return null;
}
- if (node.ycount == count)
+ if (nd.ycount == count)
{
- found = node.element();
+ found = nd.element();
return found;
}
else
{
- _findLeaf((SequenceNode) node.left(), count);
- _findLeaf((SequenceNode) node.right(), count);
+ _findLeaf((SequenceNode) nd.left(), count);
+ _findLeaf((SequenceNode) nd.right(), count);
}
return found;
@@ -916,58 +926,57 @@ public class NJTree
/**
* printNode is mainly for debugging purposes.
*
- * @param node
+ * @param nd
* SequenceNode
*/
- public void printNode(SequenceNode node)
+ public 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)
+ public 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());
}
}
@@ -976,7 +985,7 @@ public class NJTree
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ public Vector getGroups()
{
return groups;
}
@@ -986,7 +995,7 @@ public class NJTree
*
* @return DOCUMENT ME!
*/
- public float getMaxHeight()
+ public double getMaxHeight()
{
return maxheight;
}
@@ -994,51 +1003,51 @@ public class NJTree
/**
* 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
{
@@ -1047,18 +1056,18 @@ public class NJTree
}
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;
@@ -1075,7 +1084,7 @@ public class NJTree
{
ycount = 0;
- float tmpdist = maxdist.dist;
+ double tmpdist = maxdist.dist;
// New top
SequenceNode sn = new SequenceNode();
@@ -1141,44 +1150,42 @@ public class NJTree
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void printN(SequenceNode node)
+ public 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;
@@ -1186,37 +1193,37 @@ public class NJTree
/**
* DOCUMENT ME!
*
- * @param node
+ * @param nd
* DOCUMENT ME!
*/
- public void _reCount(SequenceNode node)
+ public 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--;
}
@@ -1224,80 +1231,80 @@ public class NJTree
/**
* 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)
+ public 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());
}
}
}
@@ -1353,9 +1360,12 @@ public class NJTree
*/
public void applyToNodes(NodeTransformI nodeTransformI)
{
- for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
- .transform((BinaryNode) nodes.nextElement()))
+ for (Enumeration nodes = node.elements(); nodes
+ .hasMoreElements(); nodeTransformI.transform(nodes
+ .nextElement()))
+ {
;
+ }
}
}
@@ -1365,6 +1375,7 @@ public class NJTree
* @author $author$
* @version $Revision$
*/
+// TODO what does this class have that int[] doesn't have already?
class Cluster
{
int[] value;