X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=82e028456f693c4cbf427a463838f3779dbc9fb7;hb=567c2595554096f10feab130153f97286f3f7d80;hp=4d0bb9352d7b17fafe38a118b1a755f1eed1bd6c;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java old mode 100755 new mode 100644 index 4d0bb93..82e0284 --- a/src/jalview/analysis/NJTree.java +++ b/src/jalview/analysis/NJTree.java @@ -1,455 +1,104 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; +import jalview.datamodel.SequenceNode; +import jalview.viewmodel.AlignmentViewport; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class NJTree +public class NJTree extends TreeBuilder { - 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! + * Constructor given a viewport, tree type and score model + * + * @param av + * the current alignment viewport + * @param sm + * a distance or similarity score model to use to compute the tree + * @param scoreParameters */ - public NJTree(SequenceI[] sequence, - AlignmentView seqData, - String type, - String pwtype, - int start, int end) + public NJTree(AlignmentViewport av, ScoreModelI sm, + SimilarityParamsI scoreParameters) { - 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); - } - - if (! (type.equals("NJ"))) - { - type = "AV"; - } - - if (! (pwtype.equals("PID"))) - { - if (ResidueProperties.getScoreMatrix(pwtype) == null) - { - type = "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))); - - makeLeaves(); - - noClus = cluster.size(); - - cluster(); + super(av, sm, scoreParameters); } + // private long _lycount = 0, _lylimit = 0; /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public String toString() - { - jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode()); - - return fout.print(false, true); // distances only - } - - /** - * - * used when the alignment associated to a tree has changed. - * - * @param alignment Vector - */ - public void UpdatePlaceHolders(Vector alignment) + @Override + protected + double findMinDistance() { - Vector leaves = new Vector(); - findLeaves(top, leaves); + double min = Double.MAX_VALUE; - int sz = leaves.size(); - SequenceIdMatcher seqmatcher = null; - int i = 0; - - while (i < sz) + for (int i = 0; i < (noseqs - 1); i++) { - SequenceNode leaf = (SequenceNode) leaves.elementAt(i++); - - if (alignment.contains(leaf.element())) - { - leaf.setPlaceholder(false); - } - else + for (int j = i + 1; j < noseqs; j++) { - if (seqmatcher == null) + if (!done.get(i) && !done.get(j)) { - // Only create this the first time we need it - SequenceI[] seqs = new SequenceI[alignment.size()]; + double tmp = distances.getValue(i, j) + - (findr(i, j) + findr(j, i)); - for (int j = 0; j < seqs.length; j++) + if (tmp < min) { - seqs[j] = (SequenceI) alignment.elementAt(j); - } - - seqmatcher = new SequenceIdMatcher(seqs); - } - - SequenceI nam = seqmatcher.findIdMatch(leaf.getName()); + mini = i; + minj = j; - 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")); + min = tmp; } - leaf.setPlaceholder(true); - - } - } - } - } - - /** - * 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; + return min; } /** * DOCUMENT ME! - * - * @param tmpi DOCUMENT ME! - * @param tmpj DOCUMENT ME! - * @param dist DOCUMENT ME! + * + * @param tmpi + * DOCUMENT ME! + * @param tmpj + * DOCUMENT ME! + * @param dist + * DOCUMENT ME! */ - public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, - float dist) + @Override + protected + void findNewDistances(SequenceNode tmpi, SequenceNode tmpj, double dist) { - tmpi.dist = ( (dist + ri) - rj) / 2; + tmpi.dist = ((dist + ri) - rj) / 2; tmpj.dist = (dist - tmpi.dist); if (tmpi.dist < 0) @@ -463,834 +112,41 @@ public class NJTree } } - /** - * 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! + * Calculates and saves the distance between the combination of cluster(i) and + * cluster(j) and all other clusters. The new distance to cluster k is + * calculated as the average of the distances from i to k and from j to k, + * less half the distance from i to j. + * + * @param i + * @param j */ - public void findClusterNJDistance(int i, int j) + @Override + protected + void findClusterDistance(int i, int j) { - - // New distances from cluster to others - float[] newdist = new float[noseqs]; - + // New distances from cluster i to others + double[] newdist = new double[noseqs]; + + double ijDistance = distances.getValue(i, j); for (int l = 0; l < noseqs; l++) { - if ( (l != i) && (l != j)) + if ((l != i) && (l != j)) { - newdist[l] = ( (distance[i][l] + distance[j][l]) - - distance[i][j]) / 2; + newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l) - ijDistance) / 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; - } - } - } + distances.setValue(i, ii, newdist[ii]); + distances.setValue(ii, i, newdist[ii]); } - - 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); - } - } - - /** - * DOCUMENT ME! - * - * @param node DOCUMENT ME! - * @param leaves DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - 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; - } - - /** - * DOCUMENT ME! - * - * @param node DOCUMENT ME! - * @param count DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Object findLeaf(SequenceNode node, int count) - { - found = _findLeaf(node, count); - - return found; - } - - /** - * DOCUMENT ME! - * - * @param node DOCUMENT ME! - * @param count DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - 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; - _reCount(node); - } - - /** - * DOCUMENT ME! - * - * @param node DOCUMENT ME! - */ - 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++; - } - } - - /** - * 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; - } - -} - -/** - * 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; } }