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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101 SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
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102 if (alignment.contains(leaf.element()))
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103 leaf.setPlaceholder(false);
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105 leaf.setPlaceholder(true);
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109 public NJTree(SequenceI[] sequence,int start, int end) {
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110 this(sequence,"NJ","BL",start,end);
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113 public NJTree(SequenceI[] sequence,String type,String pwtype,int start, int end ) {
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115 this.sequence = sequence;
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116 this.node = new Vector();
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118 this.pwtype = pwtype;
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119 this.start = start;
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122 if (!(type.equals("NJ"))) {
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126 if (!(pwtype.equals("PID"))) {
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132 done = new int[sequence.length];
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135 while (i < sequence.length && sequence[i] != null) {
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142 distance = findDistances();
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146 noClus = cluster.size();
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153 public void cluster() {
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155 while (noClus > 2) {
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156 if (type.equals("NJ")) {
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157 float mind = findMinNJDistance();
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159 float mind = findMinDistance();
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162 Cluster c = joinClusters(mini,minj);
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167 cluster.setElementAt(null,minj);
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168 cluster.setElementAt(c,mini);
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173 boolean onefound = false;
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178 for (int i=0; i < noseqs; i++) {
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179 if (done[i] != 1) {
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180 if (onefound == false) {
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189 Cluster c = joinClusters(one,two);
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190 top = (SequenceNode)(node.elementAt(one));
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198 public Cluster joinClusters(int i, int j) {
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200 float dist = distance[i][j];
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202 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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203 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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205 int[] value = new int[noi + noj];
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207 for (int ii = 0; ii < noi;ii++) {
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208 value[ii] = ((Cluster)cluster.elementAt(i)).value[ii];
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211 for (int ii = noi; ii < noi+ noj;ii++) {
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212 value[ii] = ((Cluster)cluster.elementAt(j)).value[ii-noi];
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215 Cluster c = new Cluster(value);
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220 if (type.equals("NJ")) {
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221 findClusterNJDistance(i,j);
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223 findClusterDistance(i,j);
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226 SequenceNode sn = new SequenceNode();
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228 sn.setLeft((SequenceNode)(node.elementAt(i)));
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229 sn.setRight((SequenceNode)(node.elementAt(j)));
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231 SequenceNode tmpi = (SequenceNode)(node.elementAt(i));
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232 SequenceNode tmpj = (SequenceNode)(node.elementAt(j));
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234 if (type.equals("NJ")) {
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235 findNewNJDistances(tmpi,tmpj,dist);
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237 findNewDistances(tmpi,tmpj,dist);
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240 tmpi.setParent(sn);
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241 tmpj.setParent(sn);
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243 node.setElementAt(sn,i);
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247 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj, float dist) {
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252 SequenceNode sni = tmpi;
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253 SequenceNode snj = tmpj;
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255 tmpi.dist = (dist + ri - rj)/2;
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256 tmpj.dist = (dist - tmpi.dist);
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258 if (tmpi.dist < 0) {
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261 if (tmpj.dist < 0) {
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266 public void findNewDistances(SequenceNode tmpi,SequenceNode tmpj,float dist) {
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271 SequenceNode sni = tmpi;
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272 SequenceNode snj = tmpj;
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274 while (sni != null) {
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275 ih = ih + sni.dist;
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276 sni = (SequenceNode)sni.left();
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279 while (snj != null) {
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280 jh = jh + snj.dist;
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281 snj = (SequenceNode)snj.left();
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284 tmpi.dist = (dist/2 - ih);
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285 tmpj.dist = (dist/2 - jh);
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290 public void findClusterDistance(int i, int j) {
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292 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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293 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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295 // New distances from cluster to others
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296 float[] newdist = new float[noseqs];
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298 for (int l = 0; l < noseqs; l++) {
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299 if ( l != i && l != j) {
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300 newdist[l] = (distance[i][l] * noi + distance[j][l] * noj)/(noi + noj);
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306 for (int ii=0; ii < noseqs;ii++) {
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307 distance[i][ii] = newdist[ii];
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308 distance[ii][i] = newdist[ii];
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312 public void findClusterNJDistance(int i, int j) {
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314 int noi = ((Cluster)cluster.elementAt(i)).value.length;
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315 int noj = ((Cluster)cluster.elementAt(j)).value.length;
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317 // New distances from cluster to others
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318 float[] newdist = new float[noseqs];
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320 for (int l = 0; l < noseqs; l++) {
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321 if ( l != i && l != j) {
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322 newdist[l] = (distance[i][l] + distance[j][l] - distance[i][j])/2;
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328 for (int ii=0; ii < noseqs;ii++) {
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329 distance[i][ii] = newdist[ii];
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330 distance[ii][i] = newdist[ii];
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334 public float findr(int i, int j) {
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337 for (int k=0; k < noseqs;k++) {
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338 if (k!= i && k!= j && done[k] != 1) {
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339 tmp = tmp + distance[i][k];
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344 tmp = tmp/(noClus - 2);
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350 public float findMinNJDistance() {
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352 float min = 100000;
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354 for (int i=0; i < noseqs-1; i++) {
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355 for (int j=i+1;j < noseqs;j++) {
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356 if (done[i] != 1 && done[j] != 1) {
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357 float tmp = distance[i][j] - (findr(i,j) + findr(j,i));
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372 public float findMinDistance() {
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374 float min = 100000;
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376 for (int i=0; i < noseqs-1;i++) {
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377 for (int j = i+1; j < noseqs;j++) {
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378 if (done[i] != 1 && done[j] != 1) {
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379 if (distance[i][j] < min) {
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383 min = distance[i][j];
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391 public float[][] findDistances() {
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393 float[][] distance = new float[noseqs][noseqs];
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394 if (pwtype.equals("PID")) {
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395 for (int i = 0; i < noseqs-1; i++) {
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396 for (int j = i; j < noseqs; j++) {
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398 distance[i][i] = 0;
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400 distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);
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401 distance[j][i] = distance[i][j];
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405 } else if (pwtype.equals("BL")) {
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408 for (int i = 0; i < noseqs-1; i++) {
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409 for (int j = i; j < noseqs; j++) {
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411 for (int k=0; k < sequence[i].getLength(); k++) {
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414 ResidueProperties.getBLOSUM62(sequence[i].getSequence(k,
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416 sequence[j].getSequence(k,
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418 }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}
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420 distance[i][j] = (float)score;
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421 if (score > maxscore) {
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426 for (int i = 0; i < noseqs-1; i++) {
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427 for (int j = i; j < noseqs; j++) {
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428 distance[i][j] = (float)maxscore - distance[i][j];
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429 distance[j][i] = distance[i][j];
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432 } else if (pwtype.equals("SW")) {
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434 for (int i = 0; i < noseqs-1; i++) {
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435 for (int j = i; j < noseqs; j++) {
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436 AlignSeq as = new AlignSeq(sequence[i],sequence[j],"pep");
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437 as.calcScoreMatrix();
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438 as.traceAlignment();
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439 as.printAlignment();
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440 distance[i][j] = (float)as.maxscore;
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441 if (max < distance[i][j]) {
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442 max = distance[i][j];
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446 for (int i = 0; i < noseqs-1; i++) {
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447 for (int j = i; j < noseqs; j++) {
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448 distance[i][j] = max - distance[i][j];
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449 distance[j][i] = distance[i][j];
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457 public void makeLeaves() {
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458 cluster = new Vector();
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460 for (int i=0; i < noseqs; i++) {
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461 SequenceNode sn = new SequenceNode();
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463 sn.setElement(sequence[i]);
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464 sn.setName(sequence[i].getName());
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465 node.addElement(sn);
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467 int[] value = new int[1];
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470 Cluster c = new Cluster(value);
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471 cluster.addElement(c);
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475 public Vector findLeaves(SequenceNode node, Vector leaves) {
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476 if (node == null) {
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480 if (node.left() == null && node.right() == null) {
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481 leaves.addElement(node);
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484 findLeaves((SequenceNode)node.left(),leaves);
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485 findLeaves((SequenceNode)node.right(),leaves);
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490 public Object findLeaf(SequenceNode node, int count) {
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491 found = _findLeaf(node,count);
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495 public Object _findLeaf(SequenceNode node,int count) {
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496 if (node == null) {
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499 if (node.ycount == count) {
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500 found = node.element();
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503 _findLeaf((SequenceNode)node.left(),count);
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504 _findLeaf((SequenceNode)node.right(),count);
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510 public void printNode(SequenceNode node) {
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511 if (node == null) {
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514 if (node.left() == null && node.right() == null) {
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515 System.out.println("Leaf = " + ((SequenceI)node.element()).getName());
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516 System.out.println("Dist " + ((SequenceNode)node).dist);
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517 System.out.println("Boot " + node.getBootstrap());
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519 System.out.println("Dist " + ((SequenceNode)node).dist);
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520 printNode((SequenceNode)node.left());
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521 printNode((SequenceNode)node.right());
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524 public void findMaxDist(SequenceNode node) {
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525 if (node == null) {
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528 if (node.left() == null && node.right() == null) {
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530 float dist = ((SequenceNode)node).dist;
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531 if (dist > maxDistValue) {
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532 maxdist = (SequenceNode)node;
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533 maxDistValue = dist;
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536 findMaxDist((SequenceNode)node.left());
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537 findMaxDist((SequenceNode)node.right());
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540 public Vector getGroups() {
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543 public float getMaxHeight() {
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546 public void groupNodes(SequenceNode node, float threshold) {
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547 if (node == null) {
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551 if (node.height/maxheight > threshold) {
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552 groups.addElement(node);
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554 groupNodes((SequenceNode)node.left(),threshold);
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555 groupNodes((SequenceNode)node.right(),threshold);
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559 public float findHeight(SequenceNode node) {
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561 if (node == null) {
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565 if (node.left() == null && node.right() == null) {
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566 node.height = ((SequenceNode)node.parent()).height + node.dist;
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568 if (node.height > maxheight) {
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569 return node.height;
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574 if (node.parent() != null) {
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575 node.height = ((SequenceNode)node.parent()).height + node.dist;
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578 node.height = (float)0.0;
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581 maxheight = findHeight((SequenceNode)(node.left()));
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582 maxheight = findHeight((SequenceNode)(node.right()));
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586 public SequenceNode reRoot() {
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587 if (maxdist != null) {
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589 float tmpdist = maxdist.dist;
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592 SequenceNode sn = new SequenceNode();
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593 sn.setParent(null);
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595 // New right hand of top
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596 SequenceNode snr = (SequenceNode)maxdist.parent();
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597 changeDirection(snr,maxdist);
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598 System.out.println("Printing reversed tree");
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600 snr.dist = tmpdist/2;
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601 maxdist.dist = tmpdist/2;
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604 maxdist.setParent(sn);
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607 sn.setLeft(maxdist);
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618 public static void printN(SequenceNode node) {
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619 if (node == null) {
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623 if (node.left() != null && node.right() != null) {
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624 printN((SequenceNode)node.left());
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625 printN((SequenceNode)node.right());
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627 System.out.println(" name = " + ((SequenceI)node.element()).getName());
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629 System.out.println(" dist = " + ((SequenceNode)node).dist + " " + ((SequenceNode)node).count + " " + ((SequenceNode)node).height);
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632 public void reCount(SequenceNode node) {
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636 public void _reCount(SequenceNode node) {
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637 if (node == null) {
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641 if (node.left() != null && node.right() != null) {
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642 _reCount((SequenceNode)node.left());
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643 _reCount((SequenceNode)node.right());
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645 SequenceNode l = (SequenceNode)node.left();
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646 SequenceNode r = (SequenceNode)node.right();
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648 ((SequenceNode)node).count = l.count + r.count;
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649 ((SequenceNode)node).ycount = (l.ycount + r.ycount)/2;
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652 ((SequenceNode)node).count = 1;
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653 ((SequenceNode)node).ycount = ycount++;
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657 public void swapNodes(SequenceNode node) {
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658 if (node == null) {
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661 SequenceNode tmp = (SequenceNode)node.left();
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663 node.setLeft(node.right());
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664 node.setRight(tmp);
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666 public void changeDirection(SequenceNode node, SequenceNode dir) {
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667 if (node == null) {
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670 if (node.parent() != top) {
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671 changeDirection((SequenceNode)node.parent(), node);
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673 SequenceNode tmp = (SequenceNode)node.parent();
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675 if (dir == node.left()) {
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676 node.setParent(dir);
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678 } else if (dir == node.right()) {
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679 node.setParent(dir);
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680 node.setRight(tmp);
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684 if (dir == node.left()) {
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685 node.setParent(node.left());
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687 if (top.left() == node) {
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688 node.setRight(top.right());
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690 node.setRight(top.left());
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693 node.setParent(node.right());
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695 if (top.left() == node) {
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696 node.setLeft(top.right());
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698 node.setLeft(top.left());
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703 public void setMaxDist(SequenceNode node) {
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704 this.maxdist = maxdist;
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706 public SequenceNode getMaxDist() {
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709 public SequenceNode getTopNode() {
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721 public Cluster(int[] value) {
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722 this.value = value;
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