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 public class NJTree {
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11 SequenceI[] sequence;
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24 Vector groups = new Vector();
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25 SequenceNode maxdist;
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38 Object found = null;
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39 Object leaves = null;
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44 public NJTree(SequenceNode node) {
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46 maxheight = findHeight(top);
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49 public NJTree(SequenceI[] sequence,int start, int end) {
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50 this(sequence,"NJ","BL",start,end);
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53 public NJTree(SequenceI[] sequence,String type,String pwtype,int start, int end ) {
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55 this.sequence = sequence;
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56 this.node = new Vector();
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58 this.pwtype = pwtype;
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62 if (!(type.equals("NJ"))) {
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66 if (!(pwtype.equals("PID"))) {
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72 done = new int[sequence.length];
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75 while (i < sequence.length && sequence[i] != null) {
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82 distance = findDistances();
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86 noClus = cluster.size();
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93 public void cluster() {
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95 while (noClus > 2) {
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96 if (type.equals("NJ")) {
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97 float mind = findMinNJDistance();
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99 float mind = findMinDistance();
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102 Cluster c = joinClusters(mini,minj);
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107 cluster.setElementAt(null,minj);
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108 cluster.setElementAt(c,mini);
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113 boolean onefound = false;
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118 for (int i=0; i < noseqs; i++) {
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119 if (done[i] != 1) {
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120 if (onefound == false) {
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129 Cluster c = joinClusters(one,two);
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130 top = (SequenceNode)(node.elementAt(one));
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138 public Cluster joinClusters(int i, int j) {
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140 float dist = distance[i][j];
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142 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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143 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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145 int[] value = new int[noi + noj];
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147 for (int ii = 0; ii < noi;ii++) {
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148 value[ii] = ((Cluster)cluster.elementAt(i)).value[ii];
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151 for (int ii = noi; ii < noi+ noj;ii++) {
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152 value[ii] = ((Cluster)cluster.elementAt(j)).value[ii-noi];
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155 Cluster c = new Cluster(value);
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160 if (type.equals("NJ")) {
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161 findClusterNJDistance(i,j);
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163 findClusterDistance(i,j);
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166 SequenceNode sn = new SequenceNode();
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168 sn.setLeft((SequenceNode)(node.elementAt(i)));
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169 sn.setRight((SequenceNode)(node.elementAt(j)));
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171 SequenceNode tmpi = (SequenceNode)(node.elementAt(i));
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172 SequenceNode tmpj = (SequenceNode)(node.elementAt(j));
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174 if (type.equals("NJ")) {
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175 findNewNJDistances(tmpi,tmpj,dist);
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177 findNewDistances(tmpi,tmpj,dist);
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180 tmpi.setParent(sn);
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181 tmpj.setParent(sn);
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183 node.setElementAt(sn,i);
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187 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) {
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192 SequenceNode sni = tmpi;
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193 SequenceNode snj = tmpj;
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195 tmpi.dist = (dist + ri - rj)/2;
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196 tmpj.dist = (dist - tmpi.dist);
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198 if (tmpi.dist < 0) {
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201 if (tmpj.dist < 0) {
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206 public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) {
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211 SequenceNode sni = tmpi;
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212 SequenceNode snj = tmpj;
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214 while (sni != null) {
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215 ih = ih + sni.dist;
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216 sni = (SequenceNode)sni.left();
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219 while (snj != null) {
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220 jh = jh + snj.dist;
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221 snj = (SequenceNode)snj.left();
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224 tmpi.dist = (dist/2 - ih);
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225 tmpj.dist = (dist/2 - jh);
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230 public void findClusterDistance(int i, int j) {
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232 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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233 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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235 // New distances from cluster to others
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236 float[] newdist = new float[noseqs];
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238 for (int l = 0; l < noseqs; l++) {
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239 if ( l != i && l != j) {
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240 newdist[l] = (distance[i][l] * noi + distance[j][l] * noj)/(noi + noj);
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246 for (int ii=0; ii < noseqs;ii++) {
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247 distance[i][ii] = newdist[ii];
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248 distance[ii][i] = newdist[ii];
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252 public void findClusterNJDistance(int i, int j) {
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254 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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255 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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257 // New distances from cluster to others
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258 float[] newdist = new float[noseqs];
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260 for (int l = 0; l < noseqs; l++) {
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261 if ( l != i && l != j) {
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262 newdist[l] = (distance[i][l] + distance[j][l] - distance[i][j])/2;
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268 for (int ii=0; ii < noseqs;ii++) {
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269 distance[i][ii] = newdist[ii];
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270 distance[ii][i] = newdist[ii];
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274 public float findr(int i, int j) {
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277 for (int k=0; k < noseqs;k++) {
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278 if (k!= i && k!= j && done[k] != 1) {
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279 tmp = tmp + distance[i][k];
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284 tmp = tmp/(noClus - 2);
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290 public float findMinNJDistance() {
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292 float min = 100000;
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294 for (int i=0; i < noseqs-1; i++) {
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295 for (int j=i+1;j < noseqs;j++) {
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296 if (done[i] != 1 && done[j] != 1) {
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297 float tmp = distance[i][j] - (findr(i,j) + findr(j,i));
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312 public float findMinDistance() {
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314 float min = 100000;
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316 for (int i=0; i < noseqs-1;i++) {
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317 for (int j = i+1; j < noseqs;j++) {
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318 if (done[i] != 1 && done[j] != 1) {
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319 if (distance[i][j] < min) {
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323 min = distance[i][j];
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331 public float[][] findDistances() {
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333 float[][] distance = new float[noseqs][noseqs];
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335 if (pwtype.equals("PID")) {
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336 for (int i = 0; i < noseqs-1; i++) {
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337 for (int j = i; j < noseqs; j++) {
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339 distance[i][i] = 0;
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341 distance[i][j] = 100-Comparison.compare(sequence[i],sequence[j],start,end);
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342 distance[j][i] = distance[i][j];
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346 } else if (pwtype.equals("BL")) {
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349 for (int i = 0; i < noseqs-1; i++) {
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350 for (int j = i; j < noseqs; j++) {
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352 for (int k=0; k < sequence[i].getLength(); k++) {
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355 ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,
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357 sequence[j].getSequence(k,
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359 }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}
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361 distance[i][j] = (float)score;
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362 if (score > maxscore) {
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367 for (int i = 0; i < noseqs-1; i++) {
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368 for (int j = i; j < noseqs; j++) {
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369 distance[i][j] = (float)maxscore - distance[i][j];
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370 distance[j][i] = distance[i][j];
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373 } else if (pwtype.equals("SW")) {
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375 for (int i = 0; i < noseqs-1; i++) {
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376 for (int j = i; j < noseqs; j++) {
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377 AlignSeq as = new AlignSeq(sequence[i],sequence[j],"pep");
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378 as.calcScoreMatrix();
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379 as.traceAlignment();
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380 as.printAlignment();
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381 distance[i][j] = (float)as.maxscore;
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382 if (max < distance[i][j]) {
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383 max = distance[i][j];
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387 for (int i = 0; i < noseqs-1; i++) {
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388 for (int j = i; j < noseqs; j++) {
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389 distance[i][j] = max - distance[i][j];
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390 distance[j][i] = distance[i][j];
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398 public void makeLeaves() {
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399 cluster = new Vector();
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401 for (int i=0; i < noseqs; i++) {
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402 SequenceNode sn = new SequenceNode();
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404 sn.setElement(sequence[i]);
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405 sn.setName(sequence[i].getName());
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406 node.addElement(sn);
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408 int[] value = new int[1];
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411 Cluster c = new Cluster(value);
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412 cluster.addElement(c);
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416 public Vector findLeaves(SequenceNode node, Vector leaves) {
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417 if (node == null) {
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421 if (node.left() == null && node.right() == null) {
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422 leaves.addElement(node);
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425 findLeaves((SequenceNode)node.left(),leaves);
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426 findLeaves((SequenceNode)node.right(),leaves);
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431 public Object findLeaf(SequenceNode node, int count) {
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432 found = _findLeaf(node,count);
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436 public Object _findLeaf(SequenceNode node,int count) {
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437 if (node == null) {
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440 if (node.ycount == count) {
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441 found = node.element();
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444 _findLeaf((SequenceNode)node.left(),count);
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445 _findLeaf((SequenceNode)node.right(),count);
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451 public void printNode(SequenceNode node) {
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452 if (node == null) {
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455 if (node.left() == null && node.right() == null) {
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456 System.out.println("Leaf = " + ((SequenceI)node.element()).getName());
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457 System.out.println("Dist " + ((SequenceNode)node).dist);
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458 System.out.println("Boot " + node.getBootstrap());
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460 System.out.println("Dist " + ((SequenceNode)node).dist);
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461 printNode((SequenceNode)node.left());
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462 printNode((SequenceNode)node.right());
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465 public void findMaxDist(SequenceNode node) {
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466 if (node == null) {
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469 if (node.left() == null && node.right() == null) {
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471 float dist = ((SequenceNode)node).dist;
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472 if (dist > maxDistValue) {
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473 maxdist = (SequenceNode)node;
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474 maxDistValue = dist;
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477 findMaxDist((SequenceNode)node.left());
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478 findMaxDist((SequenceNode)node.right());
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481 public Vector getGroups() {
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484 public float getMaxHeight() {
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487 public void groupNodes(SequenceNode node, float threshold) {
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488 if (node == null) {
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492 if (node.height/maxheight > threshold) {
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493 groups.addElement(node);
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495 groupNodes((SequenceNode)node.left(),threshold);
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496 groupNodes((SequenceNode)node.right(),threshold);
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500 public float findHeight(SequenceNode node) {
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502 if (node == null) {
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506 if (node.left() == null && node.right() == null) {
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507 node.height = ((SequenceNode)node.parent()).height + node.dist;
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509 if (node.height > maxheight) {
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510 return node.height;
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515 if (node.parent() != null) {
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516 node.height = ((SequenceNode)node.parent()).height + node.dist;
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519 node.height = (float)0.0;
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522 maxheight = findHeight((SequenceNode)(node.left()));
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523 maxheight = findHeight((SequenceNode)(node.right()));
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527 public SequenceNode reRoot() {
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528 if (maxdist != null) {
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530 float tmpdist = maxdist.dist;
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533 SequenceNode sn = new SequenceNode();
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534 sn.setParent(null);
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536 // New right hand of top
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537 SequenceNode snr = (SequenceNode)maxdist.parent();
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538 changeDirection(snr,maxdist);
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539 System.out.println("Printing reversed tree");
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541 snr.dist = tmpdist/2;
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542 maxdist.dist = tmpdist/2;
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545 maxdist.setParent(sn);
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548 sn.setLeft(maxdist);
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559 public static void printN(SequenceNode node) {
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560 if (node == null) {
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564 if (node.left() != null && node.right() != null) {
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565 printN((SequenceNode)node.left());
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566 printN((SequenceNode)node.right());
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568 System.out.println(" name = " + ((SequenceI)node.element()).getName());
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570 System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height);
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573 public void reCount(SequenceNode node) {
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577 public void _reCount(SequenceNode node) {
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578 if (node == null) {
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582 if (node.left() != null && node.right() != null) {
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583 _reCount((SequenceNode)node.left());
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584 _reCount((SequenceNode)node.right());
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586 SequenceNode l = (SequenceNode)node.left();
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587 SequenceNode r = (SequenceNode)node.right();
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589 ((SequenceNode)node).count = l.count + r.count;
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590 ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2;
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593 ((SequenceNode)node).count = 1;
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594 ((SequenceNode)node).ycount = ycount++;
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598 public void swapNodes(SequenceNode node) {
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599 if (node == null) {
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602 SequenceNode tmp = (SequenceNode)node.left();
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604 node.setLeft(node.right());
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605 node.setRight(tmp);
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607 public void changeDirection(SequenceNode node, SequenceNode dir) {
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608 if (node == null) {
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611 if (node.parent() != top) {
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612 changeDirection((SequenceNode)node.parent(), node);
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614 SequenceNode tmp = (SequenceNode)node.parent();
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616 if (dir == node.left()) {
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617 node.setParent(dir);
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619 } else if (dir == node.right()) {
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620 node.setParent(dir);
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621 node.setRight(tmp);
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625 if (dir == node.left()) {
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626 node.setParent(node.left());
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628 if (top.left() == node) {
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629 node.setRight(top.right());
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631 node.setRight(top.left());
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634 node.setParent(node.right());
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636 if (top.left() == node) {
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637 node.setLeft(top.right());
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639 node.setLeft(top.left());
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644 public void setMaxDist(SequenceNode node) {
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645 this.maxdist = maxdist;
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647 public SequenceNode getMaxDist() {
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650 public SequenceNode getTopNode() {
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662 public Cluster(int[] value) {
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663 this.value = value;
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