1 package jalview.analysis;
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3 import jalview.datamodel.*;
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4 import jalview.util.*;
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5 import jalview.schemes.ResidueProperties;
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8 import jalview.io.NewickFile;
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10 public class NJTree {
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13 SequenceI[] sequence;
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26 Vector groups = new Vector();
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27 SequenceNode maxdist;
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40 Object found = null;
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41 Object leaves = null;
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46 public NJTree(SequenceNode node) {
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48 maxheight = findHeight(top);
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51 public String toString()
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53 jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
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54 return fout.print(false,true); // distances only
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57 public NJTree(SequenceI[] seqs, NewickFile treefile) {
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58 top = treefile.getTree();
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59 maxheight = findHeight(top);
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60 SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
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62 Vector leaves = new Vector();
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63 findLeaves(top, leaves);
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66 int namesleft = seqs.length;
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71 while (i < leaves.size())
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73 j = (SequenceNode) leaves.elementAt(i++);
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74 realnam = j.getName();
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77 nam = algnIds.findIdMatch(realnam);
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82 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
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83 j.setPlaceholder(true);
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91 * used when the alignment associated to a tree has changed.
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93 * @param alignment Vector
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95 public void UpdatePlaceHolders(Vector alignment) {
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96 Vector leaves = new Vector();
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97 findLeaves(top, leaves);
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98 int sz = leaves.size();
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99 SequenceIdMatcher seqmatcher=null;
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102 SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
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103 if (alignment.contains(leaf.element()))
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104 leaf.setPlaceholder(false);
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106 if (seqmatcher==null) {
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107 // Only create this the first time we need it
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108 SequenceI[] seqs = new SequenceI[alignment.size()];
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109 for (int j=0; j<seqs.length; j++)
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110 seqs[j] = (SequenceI) alignment.elementAt(j);
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111 seqmatcher = new SequenceIdMatcher(seqs);
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113 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
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115 leaf.setPlaceholder(false);
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116 leaf.setElement(nam);
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118 leaf.setPlaceholder(true);
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124 public NJTree(SequenceI[] sequence,int start, int end) {
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125 this(sequence,"NJ","BL",start,end);
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128 public NJTree(SequenceI[] sequence,String type,String pwtype,int start, int end ) {
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130 this.sequence = sequence;
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131 this.node = new Vector();
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133 this.pwtype = pwtype;
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134 this.start = start;
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137 if (!(type.equals("NJ"))) {
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141 if (!(pwtype.equals("PID"))) {
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147 done = new int[sequence.length];
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150 while (i < sequence.length && sequence[i] != null) {
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157 distance = findDistances();
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161 noClus = cluster.size();
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168 public void cluster() {
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170 while (noClus > 2) {
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171 if (type.equals("NJ")) {
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172 float mind = findMinNJDistance();
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174 float mind = findMinDistance();
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177 Cluster c = joinClusters(mini,minj);
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182 cluster.setElementAt(null,minj);
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183 cluster.setElementAt(c,mini);
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188 boolean onefound = false;
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193 for (int i=0; i < noseqs; i++) {
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194 if (done[i] != 1) {
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195 if (onefound == false) {
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204 Cluster c = joinClusters(one,two);
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205 top = (SequenceNode)(node.elementAt(one));
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213 public Cluster joinClusters(int i, int j) {
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215 float dist = distance[i][j];
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217 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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218 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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220 int[] value = new int[noi + noj];
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222 for (int ii = 0; ii < noi;ii++) {
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223 value[ii] = ((Cluster)cluster.elementAt(i)).value[ii];
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226 for (int ii = noi; ii < noi+ noj;ii++) {
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227 value[ii] = ((Cluster)cluster.elementAt(j)).value[ii-noi];
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230 Cluster c = new Cluster(value);
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235 if (type.equals("NJ")) {
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236 findClusterNJDistance(i,j);
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238 findClusterDistance(i,j);
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241 SequenceNode sn = new SequenceNode();
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243 sn.setLeft((SequenceNode)(node.elementAt(i)));
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244 sn.setRight((SequenceNode)(node.elementAt(j)));
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246 SequenceNode tmpi = (SequenceNode)(node.elementAt(i));
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247 SequenceNode tmpj = (SequenceNode)(node.elementAt(j));
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249 if (type.equals("NJ")) {
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250 findNewNJDistances(tmpi,tmpj,dist);
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252 findNewDistances(tmpi,tmpj,dist);
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255 tmpi.setParent(sn);
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256 tmpj.setParent(sn);
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258 node.setElementAt(sn,i);
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262 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) {
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267 SequenceNode sni = tmpi;
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268 SequenceNode snj = tmpj;
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270 tmpi.dist = (dist + ri - rj)/2;
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271 tmpj.dist = (dist - tmpi.dist);
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273 if (tmpi.dist < 0) {
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276 if (tmpj.dist < 0) {
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281 public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) {
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286 SequenceNode sni = tmpi;
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287 SequenceNode snj = tmpj;
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289 while (sni != null) {
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290 ih = ih + sni.dist;
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291 sni = (SequenceNode)sni.left();
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294 while (snj != null) {
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295 jh = jh + snj.dist;
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296 snj = (SequenceNode)snj.left();
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299 tmpi.dist = (dist/2 - ih);
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300 tmpj.dist = (dist/2 - jh);
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305 public void findClusterDistance(int i, int j) {
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307 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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308 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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310 // New distances from cluster to others
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311 float[] newdist = new float[noseqs];
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313 for (int l = 0; l < noseqs; l++) {
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314 if ( l != i && l != j) {
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315 newdist[l] = (distance[i][l] * noi + distance[j][l] * noj)/(noi + noj);
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321 for (int ii=0; ii < noseqs;ii++) {
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322 distance[i][ii] = newdist[ii];
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323 distance[ii][i] = newdist[ii];
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327 public void findClusterNJDistance(int i, int j) {
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329 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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330 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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332 // New distances from cluster to others
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333 float[] newdist = new float[noseqs];
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335 for (int l = 0; l < noseqs; l++) {
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336 if ( l != i && l != j) {
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337 newdist[l] = (distance[i][l] + distance[j][l] - distance[i][j])/2;
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343 for (int ii=0; ii < noseqs;ii++) {
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344 distance[i][ii] = newdist[ii];
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345 distance[ii][i] = newdist[ii];
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349 public float findr(int i, int j) {
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352 for (int k=0; k < noseqs;k++) {
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353 if (k!= i && k!= j && done[k] != 1) {
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354 tmp = tmp + distance[i][k];
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359 tmp = tmp/(noClus - 2);
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365 public float findMinNJDistance() {
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367 float min = 100000;
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369 for (int i=0; i < noseqs-1; i++) {
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370 for (int j=i+1;j < noseqs;j++) {
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371 if (done[i] != 1 && done[j] != 1) {
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372 float tmp = distance[i][j] - (findr(i,j) + findr(j,i));
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387 public float findMinDistance() {
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389 float min = 100000;
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391 for (int i=0; i < noseqs-1;i++) {
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392 for (int j = i+1; j < noseqs;j++) {
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393 if (done[i] != 1 && done[j] != 1) {
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394 if (distance[i][j] < min) {
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398 min = distance[i][j];
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406 public float[][] findDistances() {
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408 float[][] distance = new float[noseqs][noseqs];
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409 if (pwtype.equals("PID")) {
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410 for (int i = 0; i < noseqs-1; i++) {
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411 for (int j = i; j < noseqs; j++) {
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413 distance[i][i] = 0;
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415 distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);
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416 distance[j][i] = distance[i][j];
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420 } else if (pwtype.equals("BL")) {
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423 for (int i = 0; i < noseqs-1; i++) {
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424 for (int j = i; j < noseqs; j++) {
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426 for (int k=0; k < sequence[i].getLength(); k++) {
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429 ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,
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431 sequence[j].getSequence(k,
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433 }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}
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435 distance[i][j] = (float)score;
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436 if (score > maxscore) {
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441 for (int i = 0; i < noseqs-1; i++) {
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442 for (int j = i; j < noseqs; j++) {
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443 distance[i][j] = (float)maxscore - distance[i][j];
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444 distance[j][i] = distance[i][j];
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447 } else if (pwtype.equals("SW")) {
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449 for (int i = 0; i < noseqs-1; i++) {
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450 for (int j = i; j < noseqs; j++) {
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451 AlignSeq as = new AlignSeq(sequence[i],sequence[j],"pep");
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452 as.calcScoreMatrix();
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453 as.traceAlignment();
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454 as.printAlignment();
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455 distance[i][j] = (float)as.maxscore;
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456 if (max < distance[i][j]) {
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457 max = distance[i][j];
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461 for (int i = 0; i < noseqs-1; i++) {
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462 for (int j = i; j < noseqs; j++) {
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463 distance[i][j] = max - distance[i][j];
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464 distance[j][i] = distance[i][j];
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472 public void makeLeaves() {
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473 cluster = new Vector();
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475 for (int i=0; i < noseqs; i++) {
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476 SequenceNode sn = new SequenceNode();
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478 sn.setElement(sequence[i]);
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479 sn.setName(sequence[i].getName());
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480 node.addElement(sn);
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482 int[] value = new int[1];
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485 Cluster c = new Cluster(value);
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486 cluster.addElement(c);
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490 public Vector findLeaves(SequenceNode node, Vector leaves) {
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491 if (node == null) {
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495 if (node.left() == null && node.right() == null) {
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496 leaves.addElement(node);
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499 findLeaves((SequenceNode)node.left(),leaves);
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500 findLeaves((SequenceNode)node.right(),leaves);
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505 public Object findLeaf(SequenceNode node, int count) {
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506 found = _findLeaf(node,count);
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510 public Object _findLeaf(SequenceNode node,int count) {
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511 if (node == null) {
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514 if (node.ycount == count) {
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515 found = node.element();
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518 _findLeaf((SequenceNode)node.left(),count);
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519 _findLeaf((SequenceNode)node.right(),count);
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526 * printNode is mainly for debugging purposes.
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528 * @param node SequenceNode
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530 public void printNode(SequenceNode node) {
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531 if (node == null) {
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534 if (node.left() == null && node.right() == null) {
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535 System.out.println("Leaf = " + ((SequenceI)node.element()).getName());
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536 System.out.println("Dist " + ((SequenceNode)node).dist);
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537 System.out.println("Boot " + node.getBootstrap());
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539 System.out.println("Dist " + ((SequenceNode)node).dist);
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540 printNode((SequenceNode)node.left());
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541 printNode((SequenceNode)node.right());
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544 public void findMaxDist(SequenceNode node) {
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545 if (node == null) {
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548 if (node.left() == null && node.right() == null) {
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550 float dist = ((SequenceNode)node).dist;
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551 if (dist > maxDistValue) {
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552 maxdist = (SequenceNode)node;
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553 maxDistValue = dist;
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556 findMaxDist((SequenceNode)node.left());
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557 findMaxDist((SequenceNode)node.right());
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560 public Vector getGroups() {
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563 public float getMaxHeight() {
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566 public void groupNodes(SequenceNode node, float threshold) {
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567 if (node == null) {
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571 if (node.height/maxheight > threshold) {
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572 groups.addElement(node);
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574 groupNodes((SequenceNode)node.left(),threshold);
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575 groupNodes((SequenceNode)node.right(),threshold);
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579 public float findHeight(SequenceNode node) {
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581 if (node == null) {
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585 if (node.left() == null && node.right() == null) {
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586 node.height = ((SequenceNode)node.parent()).height + node.dist;
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588 if (node.height > maxheight) {
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589 return node.height;
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594 if (node.parent() != null) {
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595 node.height = ((SequenceNode)node.parent()).height + node.dist;
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598 node.height = (float)0.0;
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601 maxheight = findHeight((SequenceNode)(node.left()));
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602 maxheight = findHeight((SequenceNode)(node.right()));
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606 public SequenceNode reRoot() {
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607 if (maxdist != null) {
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609 float tmpdist = maxdist.dist;
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612 SequenceNode sn = new SequenceNode();
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613 sn.setParent(null);
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615 // New right hand of top
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616 SequenceNode snr = (SequenceNode)maxdist.parent();
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617 changeDirection(snr,maxdist);
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618 System.out.println("Printing reversed tree");
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620 snr.dist = tmpdist/2;
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621 maxdist.dist = tmpdist/2;
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624 maxdist.setParent(sn);
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627 sn.setLeft(maxdist);
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638 public static void printN(SequenceNode node) {
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639 if (node == null) {
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643 if (node.left() != null && node.right() != null) {
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644 printN((SequenceNode)node.left());
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645 printN((SequenceNode)node.right());
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647 System.out.println(" name = " + ((SequenceI)node.element()).getName());
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649 System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height);
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652 public void reCount(SequenceNode node) {
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656 public void _reCount(SequenceNode node) {
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657 if (node == null) {
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661 if (node.left() != null && node.right() != null) {
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662 _reCount((SequenceNode)node.left());
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663 _reCount((SequenceNode)node.right());
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665 SequenceNode l = (SequenceNode)node.left();
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666 SequenceNode r = (SequenceNode)node.right();
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668 ((SequenceNode)node).count = l.count + r.count;
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669 ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2;
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672 ((SequenceNode)node).count = 1;
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673 ((SequenceNode)node).ycount = ycount++;
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677 public void swapNodes(SequenceNode node) {
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678 if (node == null) {
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681 SequenceNode tmp = (SequenceNode)node.left();
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683 node.setLeft(node.right());
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684 node.setRight(tmp);
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686 public void changeDirection(SequenceNode node, SequenceNode dir) {
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687 if (node == null) {
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690 if (node.parent() != top) {
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691 changeDirection((SequenceNode)node.parent(), node);
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693 SequenceNode tmp = (SequenceNode)node.parent();
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695 if (dir == node.left()) {
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696 node.setParent(dir);
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698 } else if (dir == node.right()) {
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699 node.setParent(dir);
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700 node.setRight(tmp);
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704 if (dir == node.left()) {
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705 node.setParent(node.left());
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707 if (top.left() == node) {
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708 node.setRight(top.right());
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710 node.setRight(top.left());
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713 node.setParent(node.right());
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715 if (top.left() == node) {
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716 node.setLeft(top.right());
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718 node.setLeft(top.left());
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723 public void setMaxDist(SequenceNode node) {
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724 this.maxdist = maxdist;
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726 public SequenceNode getMaxDist() {
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729 public SequenceNode getTopNode() {
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741 public Cluster(int[] value) {
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742 this.value = value;
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