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;