X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=67ce460bb5ba8b158528c421641a603a5495382b;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=75d36c18018ec156aabbcc2d01c61724c60bc3a7;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java old mode 100755 new mode 100644 index 75d36c1..67ce460 --- a/src/jalview/analysis/NJTree.java +++ b/src/jalview/analysis/NJTree.java @@ -1,765 +1,1377 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program 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 2 -* of the License, or (at your option) any later version. -* -* This program 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 this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ - -package jalview.analysis; - -import jalview.datamodel.*; -import jalview.util.*; -import jalview.schemes.ResidueProperties; -import java.util.*; - -import jalview.io.NewickFile; - -public class NJTree { - - Vector cluster; - SequenceI[] sequence; - - int done[]; - int noseqs; - int noClus; - - float distance[][]; - - int mini; - int minj; - float ri; - float rj; - - Vector groups = new Vector(); - SequenceNode maxdist; - SequenceNode top; - - float maxDistValue; - float maxheight; - - int ycount; - - Vector node; - - String type; - String pwtype; - - Object found = null; - Object leaves = null; - - int start; - int end; - - public NJTree(SequenceNode node) { - top = node; - maxheight = findHeight(top); - } - - public String toString() - { - jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode()); - return fout.print(false,true); // distances only - } - - public NJTree(SequenceI[] seqs, NewickFile treefile) { - top = treefile.getTree(); - maxheight = findHeight(top); - SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs); - - Vector leaves = new Vector(); - findLeaves(top, leaves); - - int i = 0; - int namesleft = seqs.length; - - SequenceNode j; - SequenceI nam; - String realnam; - while (i < leaves.size()) - { - j = (SequenceNode) leaves.elementAt(i++); - realnam = j.getName(); - nam = null; - if (namesleft>-1) - nam = algnIds.findIdMatch(realnam); - if (nam != null) { - j.setElement(nam); - namesleft--; - } else { - j.setElement(new Sequence(realnam, "THISISAPLACEHLDER")); - j.setPlaceholder(true); - - } - } - } - - /** - * - * used when the alignment associated to a tree has changed. - * - * @param alignment Vector - */ - public void UpdatePlaceHolders(Vector alignment) { - Vector leaves = new Vector(); - findLeaves(top, leaves); - int sz = leaves.size(); - SequenceIdMatcher seqmatcher=null; - int i=0; - while (i 2) { - if (type.equals("NJ")) { - float mind = findMinNJDistance(); - } else { - float mind = findMinDistance(); - } - - Cluster c = joinClusters(mini,minj); - - - done[minj] = 1; - - cluster.setElementAt(null,minj); - cluster.setElementAt(c,mini); - - noClus--; - } - - boolean onefound = false; - - int one = -1; - int two = -1; - - for (int i=0; i < noseqs; i++) { - if (done[i] != 1) { - if (onefound == false) { - two = i; - onefound = true; - } else { - one = i; - } - } - } - - Cluster c = joinClusters(one,two); - top = (SequenceNode)(node.elementAt(one)); - - reCount(top); - findHeight(top); - findMaxDist(top); - - } - - public Cluster joinClusters(int i, int j) { - - float dist = distance[i][j]; - - int noi = ((Cluster)cluster.elementAt(i)).value.length; - int noj = ((Cluster)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]; - } - - for (int ii = noi; ii < noi+ noj;ii++) { - value[ii] = ((Cluster)cluster.elementAt(j)).value[ii-noi]; - } - - Cluster c = new Cluster(value); - - ri = findr(i,j); - rj = findr(j,i); - - if (type.equals("NJ")) { - findClusterNJDistance(i,j); - } else { - findClusterDistance(i,j); - } - - SequenceNode sn = new SequenceNode(); - - sn.setLeft((SequenceNode)(node.elementAt(i))); - sn.setRight((SequenceNode)(node.elementAt(j))); - - SequenceNode tmpi = (SequenceNode)(node.elementAt(i)); - SequenceNode tmpj = (SequenceNode)(node.elementAt(j)); - - if (type.equals("NJ")) { - findNewNJDistances(tmpi,tmpj,dist); - } else { - findNewDistances(tmpi,tmpj,dist); - } - - tmpi.setParent(sn); - tmpj.setParent(sn); - - node.setElementAt(sn,i); - return c; - } - - public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) { - - float ih = 0; - float jh = 0; - - SequenceNode sni = tmpi; - SequenceNode snj = tmpj; - - tmpi.dist = (dist + ri - rj)/2; - tmpj.dist = (dist - tmpi.dist); - - if (tmpi.dist < 0) { - tmpi.dist = 0; - } - if (tmpj.dist < 0) { - tmpj.dist = 0; - } - } - - public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) { - - float ih = 0; - float jh = 0; - - SequenceNode sni = tmpi; - SequenceNode snj = tmpj; - - while (sni != null) { - ih = ih + sni.dist; - sni = (SequenceNode)sni.left(); - } - - while (snj != null) { - jh = jh + snj.dist; - snj = (SequenceNode)snj.left(); - } - - tmpi.dist = (dist/2 - ih); - tmpj.dist = (dist/2 - jh); - } - - - - public void findClusterDistance(int i, int j) { - - int noi = ((Cluster)cluster.elementAt(i)).value.length; - int noj = ((Cluster)cluster.elementAt(j)).value.length; - - // New distances from cluster to others - float[] newdist = new float[noseqs]; - - for (int l = 0; l < noseqs; l++) { - if ( l != i && l != j) { - newdist[l] = (distance[i][l] * noi + distance[j][l] * noj)/(noi + noj); - } else { - newdist[l] = 0; - } - } - - for (int ii=0; ii < noseqs;ii++) { - distance[i][ii] = newdist[ii]; - distance[ii][i] = newdist[ii]; - } - } - - public void findClusterNJDistance(int i, int j) { - - int noi = ((Cluster)cluster.elementAt(i)).value.length; - int noj = ((Cluster)cluster.elementAt(j)).value.length; - - // New distances from cluster to others - float[] newdist = new float[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; - } else { - newdist[l] = 0; - } - } - - for (int ii=0; ii < noseqs;ii++) { - distance[i][ii] = newdist[ii]; - distance[ii][i] = newdist[ii]; - } - } - - public float findr(int i, int j) { - - float tmp = 1; - for (int k=0; k < noseqs;k++) { - if (k!= i && k!= j && done[k] != 1) { - tmp = tmp + distance[i][k]; - } - } - - if (noClus > 2) { - tmp = tmp/(noClus - 2); - } - - return tmp; - } - - public float findMinNJDistance() { - - float min = 100000; - - for (int i=0; i < noseqs-1; i++) { - for (int j=i+1;j < noseqs;j++) { - if (done[i] != 1 && done[j] != 1) { - float tmp = distance[i][j] - (findr(i,j) + findr(j,i)); - if (tmp < min) { - - mini = i; - minj = j; - - min = tmp; - - } - } - } - } - return min; - } - - public float findMinDistance() { - - float min = 100000; - - for (int i=0; i < noseqs-1;i++) { - for (int j = i+1; j < noseqs;j++) { - if (done[i] != 1 && done[j] != 1) { - if (distance[i][j] < min) { - mini = i; - minj = j; - - min = distance[i][j]; - } - } - } - } - return min; - } - - public float[][] findDistances() { - - float[][] distance = new float[noseqs][noseqs]; - if (pwtype.equals("PID")) { - for (int i = 0; i < noseqs-1; i++) { - for (int j = i; j < noseqs; j++) { - if (j==i) { - distance[i][i] = 0; - } else { - distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j], start, end); - distance[j][i] = distance[i][j]; - } - } - } - } else if (pwtype.equals("BL")) { - int maxscore = 0; - - for (int i = 0; i < noseqs-1; i++) { - for (int j = i; j < noseqs; j++) { - int score = 0; - for (int k=start; k < end; k++) { - try{ - score += - ResidueProperties.getBLOSUM62(sequence[i].getSequence(k, - k + 1), - sequence[j].getSequence(k, - k + 1)); - }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]; - } - } - } 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(); - 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 distance; - } - - public void makeLeaves() { - cluster = new Vector(); - - for (int i=0; i < noseqs; i++) { - SequenceNode sn = new SequenceNode(); - - sn.setElement(sequence[i]); - sn.setName(sequence[i].getName()); - node.addElement(sn); - - int[] value = new int[1]; - value[0] = i; - - Cluster c = new Cluster(value); - cluster.addElement(c); - } - } - - public Vector findLeaves(SequenceNode node, Vector leaves) { - if (node == null) { - return leaves; - } - - if (node.left() == null && node.right() == null) { - leaves.addElement(node); - return leaves; - } else { - findLeaves((SequenceNode)node.left(),leaves); - findLeaves((SequenceNode)node.right(),leaves); - } - return leaves; - } - - public Object findLeaf(SequenceNode node, int count) { - found = _findLeaf(node,count); - - return found; - } - 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 SequenceNode - */ - public void printNode(SequenceNode node) { - if (node == null) { - return; - } - if (node.left() == null && node.right() == null) { - System.out.println("Leaf = " + ((SequenceI)node.element()).getName()); - System.out.println("Dist " + ((SequenceNode)node).dist); - System.out.println("Boot " + node.getBootstrap()); - } else { - System.out.println("Dist " + ((SequenceNode)node).dist); - printNode((SequenceNode)node.left()); - printNode((SequenceNode)node.right()); - } - } - public void findMaxDist(SequenceNode node) { - if (node == null) { - return; - } - if (node.left() == null && node.right() == null) { - - float dist = ((SequenceNode)node).dist; - if (dist > maxDistValue) { - maxdist = (SequenceNode)node; - maxDistValue = dist; - } - } else { - findMaxDist((SequenceNode)node.left()); - findMaxDist((SequenceNode)node.right()); - } - } - public Vector getGroups() { - return groups; - } - public float getMaxHeight() { - return maxheight; - } - public void groupNodes(SequenceNode node, float threshold) { - if (node == null) { - return; - } - - if (node.height/maxheight > threshold) { - groups.addElement(node); - } else { - groupNodes((SequenceNode)node.left(),threshold); - groupNodes((SequenceNode)node.right(),threshold); - } - } - - public float findHeight(SequenceNode node) { - - if (node == null) { - return maxheight; - } - - if (node.left() == null && node.right() == null) { - node.height = ((SequenceNode)node.parent()).height + node.dist; - - if (node.height > maxheight) { - return node.height; - } else { - return maxheight; - } - } else { - if (node.parent() != null) { - node.height = ((SequenceNode)node.parent()).height + node.dist; - } else { - maxheight = 0; - node.height = (float)0.0; - } - - maxheight = findHeight((SequenceNode)(node.left())); - maxheight = findHeight((SequenceNode)(node.right())); - } - return maxheight; - } - public SequenceNode reRoot() { - if (maxdist != null) { - ycount = 0; - float tmpdist = maxdist.dist; - - // New top - SequenceNode sn = new SequenceNode(); - sn.setParent(null); - - // New right hand of top - SequenceNode snr = (SequenceNode)maxdist.parent(); - changeDirection(snr,maxdist); - System.out.println("Printing reversed tree"); - printN(snr); - snr.dist = tmpdist/2; - maxdist.dist = tmpdist/2; - - snr.setParent(sn); - maxdist.setParent(sn); - - sn.setRight(snr); - sn.setLeft(maxdist); - - top = sn; - - ycount = 0; - reCount(top); - findHeight(top); - - } - return top; - } - public static void printN(SequenceNode node) { - if (node == null) { - return; - } - - if (node.left() != null && node.right() != null) { - printN((SequenceNode)node.left()); - printN((SequenceNode)node.right()); - } else { - System.out.println(" name = " + ((SequenceI)node.element()).getName()); - } - System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height); - } - - public void reCount(SequenceNode node) { - ycount = 0; - _reCount(node); - } - public void _reCount(SequenceNode node) { - if (node == null) { - return; - } - - if (node.left() != null && node.right() != null) { - _reCount((SequenceNode)node.left()); - _reCount((SequenceNode)node.right()); - - SequenceNode l = (SequenceNode)node.left(); - SequenceNode r = (SequenceNode)node.right(); - - ((SequenceNode)node).count = l.count + r.count; - ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2; - - } else { - ((SequenceNode)node).count = 1; - ((SequenceNode)node).ycount = ycount++; - } - - } - public void swapNodes(SequenceNode node) { - if (node == null) { - return; - } - SequenceNode tmp = (SequenceNode)node.left(); - - node.setLeft(node.right()); - node.setRight(tmp); - } - public void changeDirection(SequenceNode node, SequenceNode dir) { - if (node == null) { - return; - } - if (node.parent() != top) { - changeDirection((SequenceNode)node.parent(), node); - - SequenceNode tmp = (SequenceNode)node.parent(); - - if (dir == node.left()) { - node.setParent(dir); - node.setLeft(tmp); - } else if (dir == node.right()) { - node.setParent(dir); - node.setRight(tmp); - } - - } else { - if (dir == node.left()) { - node.setParent(node.left()); - - if (top.left() == node) { - node.setRight(top.right()); - } else { - node.setRight(top.left()); - } - } else { - node.setParent(node.right()); - - if (top.left() == node) { - node.setLeft(top.right()); - } else { - node.setLeft(top.left()); - } - } - } - } - public void setMaxDist(SequenceNode node) { - this.maxdist = maxdist; - } - public SequenceNode getMaxDist() { - return maxdist; - } - public SequenceNode getTopNode() { - return top; - } - -} - - - -class Cluster { - - int[] value; - - public Cluster(int[] value) { - this.value = value; - } - -} - +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.analysis; + +import java.util.*; + +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; +import jalview.util.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class NJTree +{ + Vector cluster; + + SequenceI[] sequence; + + // SequenceData is a string representation of what the user + // sees. The display may contain hidden columns. + public AlignmentView seqData = null; + + int[] done; + + int noseqs; + + int noClus; + + float[][] distance; + + int mini; + + int minj; + + float ri; + + float rj; + + Vector groups = new Vector(); + + SequenceNode maxdist; + + SequenceNode top; + + float maxDistValue; + + float maxheight; + + int ycount; + + Vector node; + + String type; + + String pwtype; + + Object found = null; + + Object leaves = null; + + boolean hasDistances = true; // normal case for jalview trees + + boolean hasBootstrap = false; // normal case for jalview trees + + private boolean hasRootDistance = true; + + /** + * Create a new NJTree object with leaves associated with sequences in seqs, + * and original alignment data represented by Cigar strings. + * + * @param seqs + * SequenceI[] + * @param odata + * Cigar[] + * @param treefile + * NewickFile + */ + public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) + { + this(seqs, treefile); + if (odata != null) + { + seqData = odata; + } + /* + * sequenceString = new String[odata.length]; char gapChar = + * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i < + * odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar); + * sequenceString[i] = oseq_aligned.getSequence(); } + */ + } + + /** + * Creates a new NJTree object from a tree from an external source + * + * @param seqs + * SequenceI which should be associated with leafs of treefile + * @param treefile + * A parsed tree + */ + public NJTree(SequenceI[] seqs, NewickFile treefile) + { + this.sequence = seqs; + top = treefile.getTree(); + + /** + * There is no dependent alignment to be recovered from an imported tree. + * + * if (sequenceString == null) { sequenceString = new String[seqs.length]; + * for (int i = 0; i < seqs.length; i++) { sequenceString[i] = + * seqs[i].getSequence(); } } + */ + + hasDistances = treefile.HasDistances(); + hasBootstrap = treefile.HasBootstrap(); + hasRootDistance = treefile.HasRootDistance(); + + maxheight = findHeight(top); + + SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs); + + Vector leaves = new Vector(); + findLeaves(top, leaves); + + int i = 0; + int namesleft = seqs.length; + + SequenceNode j; + SequenceI nam; + String realnam; + Vector one2many = new Vector(); + int countOne2Many = 0; + while (i < leaves.size()) + { + j = (SequenceNode) leaves.elementAt(i++); + realnam = j.getName(); + nam = null; + + if (namesleft > -1) + { + nam = algnIds.findIdMatch(realnam); + } + + if (nam != null) + { + j.setElement(nam); + if (one2many.contains(nam)) + { + countOne2Many++; + // if (jalview.bin.Cache.log.isDebugEnabled()) + // jalview.bin.Cache.log.debug("One 2 many relationship for + // "+nam.getName()); + } + else + { + one2many.addElement(nam); + namesleft--; + } + } + else + { + j.setElement(new Sequence(realnam, "THISISAPLACEHLDER")); + j.setPlaceholder(true); + } + } + // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) { + // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment + // sequence ids (out of "+one2many.size()+" unique ids) linked to two or + // more leaves."); + // } + // one2many.clear(); + } + + /** + * Creates a new NJTree object. + * + * @param sequence + * DOCUMENT ME! + * @param type + * DOCUMENT ME! + * @param pwtype + * DOCUMENT ME! + * @param start + * DOCUMENT ME! + * @param end + * DOCUMENT ME! + */ + public NJTree(SequenceI[] sequence, AlignmentView seqData, String type, + String pwtype, int start, int end) + { + this.sequence = sequence; + this.node = new Vector(); + this.type = type; + this.pwtype = pwtype; + if (seqData != null) + { + this.seqData = seqData; + } + else + { + SeqCigar[] seqs = new SeqCigar[sequence.length]; + for (int i = 0; i < sequence.length; i++) + { + seqs[i] = new SeqCigar(sequence[i], start, end); + } + CigarArray sdata = new CigarArray(seqs); + 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 (ResidueProperties.getScoreMatrix(pwtype) == null) + { + pwtype = "BLOSUM62"; + } + } + + int i = 0; + + done = new int[sequence.length]; + + while ((i < sequence.length) && (sequence[i] != null)) + { + done[i] = 0; + i++; + } + + noseqs = i++; + + distance = findDistances(this.seqData + .getSequenceStrings(Comparison.GapChars.charAt(0))); + // System.err.println("Made distances");// dbg + makeLeaves(); + // System.err.println("Made leaves");// dbg + + noClus = cluster.size(); + + cluster(); + // System.err.println("Made clusters");// dbg + + } + + /** + * Generate a string representation of the Tree + * + * @return Newick File with all tree data available + */ + public String toString() + { + jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode()); + + return fout.print(isHasBootstrap(), + isHasDistances(), isHasRootDistance()); // output all data available for tree + } + + /** + * + * used when the alignment associated to a tree has changed. + * + * @param alignment + * Vector + */ + public void UpdatePlaceHolders(Vector alignment) + { + Vector leaves = new Vector(); + findLeaves(top, leaves); + + int sz = leaves.size(); + SequenceIdMatcher seqmatcher = null; + int i = 0; + + while (i < sz) + { + SequenceNode leaf = (SequenceNode) leaves.elementAt(i++); + + if (alignment.contains(leaf.element())) + { + leaf.setPlaceholder(false); + } + else + { + if (seqmatcher == null) + { + // Only create this the first time we need it + SequenceI[] seqs = new SequenceI[alignment.size()]; + + for (int j = 0; j < seqs.length; j++) + { + seqs[j] = (SequenceI) alignment.elementAt(j); + } + + seqmatcher = new SequenceIdMatcher(seqs); + } + + SequenceI nam = seqmatcher.findIdMatch(leaf.getName()); + + if (nam != null) + { + if (!leaf.isPlaceholder()) + { + // remapping the node to a new sequenceI - should remove any refs to + // old one. + // TODO - make many sequenceI to one leaf mappings possible! + // (JBPNote) + } + leaf.setPlaceholder(false); + leaf.setElement(nam); + } + else + { + if (!leaf.isPlaceholder()) + { + // Construct a new placeholder sequence object for this leaf + leaf.setElement(new Sequence(leaf.getName(), + "THISISAPLACEHLDER")); + } + leaf.setPlaceholder(true); + + } + } + } + } + /** + * rename any nodes according to their associated sequence. + * This will modify the tree's metadata! (ie the original NewickFile or newly generated BinaryTree's label data) + */ + public void renameAssociatedNodes() { + applyToNodes(new NodeTransformI() { + + @Override + public void transform(BinaryNode node) + { + Object el = node.element(); + if (el!=null && el instanceof SequenceI) + { + node.setName(((SequenceI)el).getName()); + } + } + }); + } + /** + * DOCUMENT ME! + */ + public void cluster() + { + while (noClus > 2) + { + if (type.equals("NJ")) + { + findMinNJDistance(); + } + else + { + findMinDistance(); + } + + Cluster c = joinClusters(mini, minj); + + done[minj] = 1; + + cluster.setElementAt(null, minj); + cluster.setElementAt(c, mini); + + noClus--; + } + + boolean onefound = false; + + int one = -1; + int two = -1; + + for (int i = 0; i < noseqs; i++) + { + if (done[i] != 1) + { + if (onefound == false) + { + two = i; + onefound = true; + } + else + { + one = i; + } + } + } + + joinClusters(one, two); + top = (SequenceNode) (node.elementAt(one)); + + reCount(top); + findHeight(top); + findMaxDist(top); + } + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Cluster joinClusters(int i, int j) + { + float dist = distance[i][j]; + + int noi = ((Cluster) cluster.elementAt(i)).value.length; + int noj = ((Cluster) 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]; + } + + for (int ii = noi; ii < (noi + noj); ii++) + { + value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi]; + } + + Cluster c = new Cluster(value); + + ri = findr(i, j); + rj = findr(j, i); + + if (type.equals("NJ")) + { + findClusterNJDistance(i, j); + } + else + { + findClusterDistance(i, j); + } + + SequenceNode sn = new SequenceNode(); + + sn.setLeft((SequenceNode) (node.elementAt(i))); + sn.setRight((SequenceNode) (node.elementAt(j))); + + SequenceNode tmpi = (SequenceNode) (node.elementAt(i)); + SequenceNode tmpj = (SequenceNode) (node.elementAt(j)); + + if (type.equals("NJ")) + { + findNewNJDistances(tmpi, tmpj, dist); + } + else + { + findNewDistances(tmpi, tmpj, dist); + } + + tmpi.setParent(sn); + tmpj.setParent(sn); + + node.setElementAt(sn, i); + + return c; + } + + /** + * DOCUMENT ME! + * + * @param tmpi + * DOCUMENT ME! + * @param tmpj + * DOCUMENT ME! + * @param dist + * DOCUMENT ME! + */ + public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, + float dist) + { + + tmpi.dist = ((dist + ri) - rj) / 2; + tmpj.dist = (dist - tmpi.dist); + + if (tmpi.dist < 0) + { + tmpi.dist = 0; + } + + if (tmpj.dist < 0) + { + tmpj.dist = 0; + } + } + + /** + * DOCUMENT ME! + * + * @param tmpi + * DOCUMENT ME! + * @param tmpj + * DOCUMENT ME! + * @param dist + * DOCUMENT ME! + */ + public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj, + float dist) + { + float ih = 0; + float jh = 0; + + SequenceNode sni = tmpi; + SequenceNode snj = tmpj; + + while (sni != null) + { + ih = ih + sni.dist; + sni = (SequenceNode) sni.left(); + } + + while (snj != null) + { + jh = jh + snj.dist; + snj = (SequenceNode) snj.left(); + } + + tmpi.dist = ((dist / 2) - ih); + tmpj.dist = ((dist / 2) - jh); + } + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + */ + public void findClusterDistance(int i, int j) + { + int noi = ((Cluster) cluster.elementAt(i)).value.length; + int noj = ((Cluster) cluster.elementAt(j)).value.length; + + // New distances from cluster to others + float[] newdist = new float[noseqs]; + + for (int l = 0; l < noseqs; l++) + { + if ((l != i) && (l != j)) + { + newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) + / (noi + noj); + } + else + { + newdist[l] = 0; + } + } + + for (int ii = 0; ii < noseqs; ii++) + { + distance[i][ii] = newdist[ii]; + distance[ii][i] = newdist[ii]; + } + } + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + */ + public void findClusterNJDistance(int i, int j) + { + + // New distances from cluster to others + float[] newdist = new float[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; + } + else + { + newdist[l] = 0; + } + } + + for (int ii = 0; ii < noseqs; ii++) + { + distance[i][ii] = newdist[ii]; + distance[ii][i] = newdist[ii]; + } + } + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float findr(int i, int j) + { + float tmp = 1; + + for (int k = 0; k < noseqs; k++) + { + if ((k != i) && (k != j) && (done[k] != 1)) + { + tmp = tmp + distance[i][k]; + } + } + + if (noClus > 2) + { + tmp = tmp / (noClus - 2); + } + + return tmp; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float findMinNJDistance() + { + float min = 100000; + + for (int i = 0; i < (noseqs - 1); i++) + { + for (int j = i + 1; j < noseqs; j++) + { + if ((done[i] != 1) && (done[j] != 1)) + { + float tmp = distance[i][j] - (findr(i, j) + findr(j, i)); + + if (tmp < min) + { + mini = i; + minj = j; + + min = tmp; + } + } + } + } + + return min; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float findMinDistance() + { + float min = 100000; + + for (int i = 0; i < (noseqs - 1); i++) + { + for (int j = i + 1; j < noseqs; j++) + { + if ((done[i] != 1) && (done[j] != 1)) + { + if (distance[i][j] < min) + { + mini = i; + minj = j; + + min = distance[i][j]; + } + } + } + } + + return min; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float[][] findDistances(String[] sequenceString) + { + float[][] distance = new float[noseqs][noseqs]; + + if (pwtype.equals("PID")) + { + for (int i = 0; i < (noseqs - 1); i++) + { + 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]; + } + } + } + } + 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]; + } + } + + } + 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]; + * } } }/ + */ + } + + /** + * DOCUMENT ME! + */ + public void makeLeaves() + { + cluster = new Vector(); + + for (int i = 0; i < noseqs; i++) + { + SequenceNode sn = new SequenceNode(); + + sn.setElement(sequence[i]); + sn.setName(sequence[i].getName()); + node.addElement(sn); + + int[] value = new int[1]; + value[0] = i; + + Cluster c = new Cluster(value); + cluster.addElement(c); + } + } + + /** + * Search for leaf nodes. + * + * @param node + * 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) + { + if (node == null) + { + return leaves; + } + + if ((node.left() == null) && (node.right() == null)) // Interior node + // detection + { + leaves.addElement(node); + + return leaves; + } + else + { + /* + * TODO: Identify internal nodes... if (node.isSequenceLabel()) { + * leaves.addElement(node); } + */ + findLeaves((SequenceNode) node.left(), leaves); + findLeaves((SequenceNode) node.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 + * SequenceNode + */ + public void printNode(SequenceNode node) + { + if (node == null) + { + return; + } + + if ((node.left() == null) && (node.right() == null)) + { + System.out + .println("Leaf = " + ((SequenceI) node.element()).getName()); + System.out.println("Dist " + ((SequenceNode) node).dist); + System.out.println("Boot " + node.getBootstrap()); + } + else + { + System.out.println("Dist " + ((SequenceNode) node).dist); + printNode((SequenceNode) node.left()); + printNode((SequenceNode) node.right()); + } + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + */ + public void findMaxDist(SequenceNode node) + { + if (node == null) + { + return; + } + + if ((node.left() == null) && (node.right() == null)) + { + float dist = ((SequenceNode) node).dist; + + if (dist > maxDistValue) + { + maxdist = (SequenceNode) node; + maxDistValue = dist; + } + } + else + { + findMaxDist((SequenceNode) node.left()); + findMaxDist((SequenceNode) node.right()); + } + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public Vector getGroups() + { + return groups; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float getMaxHeight() + { + return maxheight; + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + * @param threshold + * DOCUMENT ME! + */ + public void groupNodes(SequenceNode node, float threshold) + { + if (node == null) + { + return; + } + + if ((node.height / maxheight) > threshold) + { + groups.addElement(node); + } + else + { + groupNodes((SequenceNode) node.left(), threshold); + groupNodes((SequenceNode) node.right(), threshold); + } + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float findHeight(SequenceNode node) + { + if (node == null) + { + return maxheight; + } + + if ((node.left() == null) && (node.right() == null)) + { + node.height = ((SequenceNode) node.parent()).height + node.dist; + + if (node.height > maxheight) + { + return node.height; + } + else + { + return maxheight; + } + } + else + { + if (node.parent() != null) + { + node.height = ((SequenceNode) node.parent()).height + node.dist; + } + else + { + maxheight = 0; + node.height = (float) 0.0; + } + + maxheight = findHeight((SequenceNode) (node.left())); + maxheight = findHeight((SequenceNode) (node.right())); + } + + return maxheight; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceNode reRoot() + { + if (maxdist != null) + { + ycount = 0; + + float tmpdist = maxdist.dist; + + // New top + SequenceNode sn = new SequenceNode(); + sn.setParent(null); + + // New right hand of top + SequenceNode snr = (SequenceNode) maxdist.parent(); + changeDirection(snr, maxdist); + System.out.println("Printing reversed tree"); + printN(snr); + snr.dist = tmpdist / 2; + maxdist.dist = tmpdist / 2; + + snr.setParent(sn); + maxdist.setParent(sn); + + sn.setRight(snr); + sn.setLeft(maxdist); + + top = sn; + + ycount = 0; + reCount(top); + findHeight(top); + } + + return top; + } + + /** + * + * @return true if original sequence data can be recovered + */ + public boolean hasOriginalSequenceData() + { + return seqData != null; + } + + /** + * Returns original alignment data used for calculation - or null where not + * available. + * + * @return null or cut'n'pasteable alignment + */ + public String printOriginalSequenceData(char gapChar) + { + if (seqData == null) + { + return null; + } + + StringBuffer sb = new StringBuffer(); + String[] seqdatas = seqData.getSequenceStrings(gapChar); + for (int i = 0; i < seqdatas.length; i++) + { + sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i] + .getName())); + sb.append(" " + seqdatas[i] + "\n"); + } + return sb.toString(); + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + */ + public void printN(SequenceNode node) + { + if (node == null) + { + return; + } + + if ((node.left() != null) && (node.right() != null)) + { + printN((SequenceNode) node.left()); + printN((SequenceNode) node.right()); + } + else + { + System.out.println(" name = " + + ((SequenceI) node.element()).getName()); + } + + System.out.println(" dist = " + ((SequenceNode) node).dist + " " + + ((SequenceNode) node).count + " " + + ((SequenceNode) node).height); + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + */ + public void reCount(SequenceNode node) + { + ycount = 0; + _lycount = 0; + // _lylimit = this.node.size(); + _reCount(node); + } + + private long _lycount = 0, _lylimit = 0; + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + */ + public void _reCount(SequenceNode node) + { + // if (_lycount<_lylimit) + // { + // System.err.println("Warning: depth of _recount greater than number of nodes."); + // } + if (node == null) + { + return; + } + _lycount++; + + if ((node.left() != null) && (node.right() != null)) + { + + _reCount((SequenceNode) node.left()); + _reCount((SequenceNode) node.right()); + + SequenceNode l = (SequenceNode) node.left(); + SequenceNode r = (SequenceNode) node.right(); + + ((SequenceNode) node).count = l.count + r.count; + ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2; + } + else + { + ((SequenceNode) node).count = 1; + ((SequenceNode) node).ycount = ycount++; + } + _lycount--; + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + */ + public void swapNodes(SequenceNode node) + { + if (node == null) + { + return; + } + + SequenceNode tmp = (SequenceNode) node.left(); + + node.setLeft(node.right()); + node.setRight(tmp); + } + + /** + * DOCUMENT ME! + * + * @param node + * DOCUMENT ME! + * @param dir + * DOCUMENT ME! + */ + public void changeDirection(SequenceNode node, SequenceNode dir) + { + if (node == null) + { + return; + } + + if (node.parent() != top) + { + changeDirection((SequenceNode) node.parent(), node); + + SequenceNode tmp = (SequenceNode) node.parent(); + + if (dir == node.left()) + { + node.setParent(dir); + node.setLeft(tmp); + } + else if (dir == node.right()) + { + node.setParent(dir); + node.setRight(tmp); + } + } + else + { + if (dir == node.left()) + { + node.setParent(node.left()); + + if (top.left() == node) + { + node.setRight(top.right()); + } + else + { + node.setRight(top.left()); + } + } + else + { + node.setParent(node.right()); + + if (top.left() == node) + { + node.setLeft(top.right()); + } + else + { + node.setLeft(top.left()); + } + } + } + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceNode getMaxDist() + { + return maxdist; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceNode getTopNode() + { + return top; + } + + /** + * + * @return true if tree has real distances + */ + public boolean isHasDistances() + { + return hasDistances; + } + + /** + * + * @return true if tree has real bootstrap values + */ + public boolean isHasBootstrap() + { + return hasBootstrap; + } + + public boolean isHasRootDistance() + { + return hasRootDistance; + } + + /** + * apply the given transform to all the nodes in the tree. + * + * @param nodeTransformI + */ + public void applyToNodes(NodeTransformI nodeTransformI) + { + for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI + .transform((BinaryNode) nodes.nextElement())) + ; + } +} + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +class Cluster +{ + int[] value; + + /** + * Creates a new Cluster object. + * + * @param value + * DOCUMENT ME! + */ + public Cluster(int[] value) + { + this.value = value; + } +}