2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.analysis;
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21 import jalview.datamodel.*;
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23 import jalview.io.NewickFile;
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25 import jalview.schemes.ResidueProperties;
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27 import jalview.util.*;
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36 * @version $Revision$
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41 SequenceI[] sequence;
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50 Vector groups = new Vector();
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51 SequenceNode maxdist;
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59 Object found = null;
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60 Object leaves = null;
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65 * Creates a new NJTree object.
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67 * @param node DOCUMENT ME!
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69 public NJTree(SequenceNode node)
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72 maxheight = findHeight(top);
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76 * Creates a new NJTree object.
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78 * @param seqs DOCUMENT ME!
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79 * @param treefile DOCUMENT ME!
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81 public NJTree(SequenceI[] seqs, NewickFile treefile)
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83 top = treefile.getTree();
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84 maxheight = findHeight(top);
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86 SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
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88 Vector leaves = new Vector();
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89 findLeaves(top, leaves);
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92 int namesleft = seqs.length;
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98 while (i < leaves.size())
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100 j = (SequenceNode) leaves.elementAt(i++);
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101 realnam = j.getName();
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104 if (namesleft > -1)
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106 nam = algnIds.findIdMatch(realnam);
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116 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
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117 j.setPlaceholder(true);
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123 * Creates a new NJTree object.
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125 * @param sequence DOCUMENT ME!
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126 * @param start DOCUMENT ME!
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127 * @param end DOCUMENT ME!
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129 public NJTree(SequenceI[] sequence, int start, int end)
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131 this(sequence, "NJ", "BL", start, end);
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135 * Creates a new NJTree object.
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137 * @param sequence DOCUMENT ME!
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138 * @param type DOCUMENT ME!
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139 * @param pwtype DOCUMENT ME!
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140 * @param start DOCUMENT ME!
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141 * @param end DOCUMENT ME!
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143 public NJTree(SequenceI[] sequence, String type, String pwtype, int start,
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146 this.sequence = sequence;
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147 this.node = new Vector();
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149 this.pwtype = pwtype;
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150 this.start = start;
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153 if (!(type.equals("NJ")))
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158 if (!(pwtype.equals("PID")))
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165 done = new int[sequence.length];
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167 while ((i < sequence.length) && (sequence[i] != null))
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175 distance = findDistances();
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179 noClus = cluster.size();
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187 * @return DOCUMENT ME!
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189 public String toString()
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191 jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
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193 return fout.print(false, true); // distances only
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198 * used when the alignment associated to a tree has changed.
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200 * @param alignment Vector
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202 public void UpdatePlaceHolders(Vector alignment)
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204 Vector leaves = new Vector();
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205 findLeaves(top, leaves);
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207 int sz = leaves.size();
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208 SequenceIdMatcher seqmatcher = null;
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213 SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
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215 if (alignment.contains(leaf.element()))
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217 leaf.setPlaceholder(false);
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221 if (seqmatcher == null)
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223 // Only create this the first time we need it
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224 SequenceI[] seqs = new SequenceI[alignment.size()];
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226 for (int j = 0; j < seqs.length; j++)
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227 seqs[j] = (SequenceI) alignment.elementAt(j);
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229 seqmatcher = new SequenceIdMatcher(seqs);
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232 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
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236 leaf.setPlaceholder(false);
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237 leaf.setElement(nam);
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241 leaf.setPlaceholder(true);
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250 public void cluster()
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254 if (type.equals("NJ"))
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256 findMinNJDistance();
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263 Cluster c = joinClusters(mini, minj);
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267 cluster.setElementAt(null, minj);
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268 cluster.setElementAt(c, mini);
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273 boolean onefound = false;
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278 for (int i = 0; i < noseqs; i++)
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282 if (onefound == false)
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294 joinClusters(one, two);
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295 top = (SequenceNode) (node.elementAt(one));
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305 * @param i DOCUMENT ME!
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306 * @param j DOCUMENT ME!
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308 * @return DOCUMENT ME!
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310 public Cluster joinClusters(int i, int j)
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312 float dist = distance[i][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 int[] value = new int[noi + noj];
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319 for (int ii = 0; ii < noi; ii++)
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321 value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
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324 for (int ii = noi; ii < (noi + noj); ii++)
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326 value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
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329 Cluster c = new Cluster(value);
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334 if (type.equals("NJ"))
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336 findClusterNJDistance(i, j);
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340 findClusterDistance(i, j);
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343 SequenceNode sn = new SequenceNode();
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345 sn.setLeft((SequenceNode) (node.elementAt(i)));
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346 sn.setRight((SequenceNode) (node.elementAt(j)));
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348 SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
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349 SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
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351 if (type.equals("NJ"))
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353 findNewNJDistances(tmpi, tmpj, dist);
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357 findNewDistances(tmpi, tmpj, dist);
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360 tmpi.setParent(sn);
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361 tmpj.setParent(sn);
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363 node.setElementAt(sn, i);
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371 * @param tmpi DOCUMENT ME!
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372 * @param tmpj DOCUMENT ME!
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373 * @param dist DOCUMENT ME!
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375 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
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379 tmpi.dist = ((dist + ri) - rj) / 2;
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380 tmpj.dist = (dist - tmpi.dist);
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396 * @param tmpi DOCUMENT ME!
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397 * @param tmpj DOCUMENT ME!
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398 * @param dist DOCUMENT ME!
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400 public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
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406 SequenceNode sni = tmpi;
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407 SequenceNode snj = tmpj;
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409 while (sni != null)
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411 ih = ih + sni.dist;
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412 sni = (SequenceNode) sni.left();
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415 while (snj != null)
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417 jh = jh + snj.dist;
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418 snj = (SequenceNode) snj.left();
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421 tmpi.dist = ((dist / 2) - ih);
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422 tmpj.dist = ((dist / 2) - jh);
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428 * @param i DOCUMENT ME!
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429 * @param j DOCUMENT ME!
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431 public void findClusterDistance(int i, int j)
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433 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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434 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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436 // New distances from cluster to others
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437 float[] newdist = new float[noseqs];
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439 for (int l = 0; l < noseqs; l++)
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441 if ((l != i) && (l != j))
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443 newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
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452 for (int ii = 0; ii < noseqs; ii++)
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454 distance[i][ii] = newdist[ii];
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455 distance[ii][i] = newdist[ii];
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462 * @param i DOCUMENT ME!
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463 * @param j DOCUMENT ME!
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465 public void findClusterNJDistance(int i, int j)
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468 // New distances from cluster to others
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469 float[] newdist = new float[noseqs];
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471 for (int l = 0; l < noseqs; l++)
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473 if ((l != i) && (l != j))
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475 newdist[l] = ((distance[i][l] + distance[j][l]) -
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476 distance[i][j]) / 2;
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484 for (int ii = 0; ii < noseqs; ii++)
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486 distance[i][ii] = newdist[ii];
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487 distance[ii][i] = newdist[ii];
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494 * @param i DOCUMENT ME!
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495 * @param j DOCUMENT ME!
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497 * @return DOCUMENT ME!
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499 public float findr(int i, int j)
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503 for (int k = 0; k < noseqs; k++)
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505 if ((k != i) && (k != j) && (done[k] != 1))
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507 tmp = tmp + distance[i][k];
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513 tmp = tmp / (noClus - 2);
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522 * @return DOCUMENT ME!
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524 public float findMinNJDistance()
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526 float min = 100000;
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528 for (int i = 0; i < (noseqs - 1); i++)
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530 for (int j = i + 1; j < noseqs; j++)
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532 if ((done[i] != 1) && (done[j] != 1))
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534 float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
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553 * @return DOCUMENT ME!
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555 public float findMinDistance()
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557 float min = 100000;
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559 for (int i = 0; i < (noseqs - 1); i++)
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561 for (int j = i + 1; j < noseqs; j++)
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563 if ((done[i] != 1) && (done[j] != 1))
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565 if (distance[i][j] < min)
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570 min = distance[i][j];
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582 * @return DOCUMENT ME!
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584 public float[][] findDistances()
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586 float[][] distance = new float[noseqs][noseqs];
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588 if (pwtype.equals("PID"))
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590 for (int i = 0; i < (noseqs - 1); i++)
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592 for (int j = i; j < noseqs; j++)
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596 distance[i][i] = 0;
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600 distance[i][j] = 100 -
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601 Comparison.PID(sequence[i], sequence[j], start, end);
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602 distance[j][i] = distance[i][j];
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607 else if (pwtype.equals("BL"))
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611 for (int i = 0; i < (noseqs - 1); i++)
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613 for (int j = i; j < noseqs; j++)
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617 for (int k = start; k < end; k++)
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621 score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(
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622 k, k + 1), sequence[j].getSequence(k, k +
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625 catch (Exception ex)
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627 System.err.println("err creating BLOSUM62 tree");
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628 ex.printStackTrace();
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632 distance[i][j] = (float) score;
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634 if (score > maxscore)
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641 for (int i = 0; i < (noseqs - 1); i++)
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643 for (int j = i; j < noseqs; j++)
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645 distance[i][j] = (float) maxscore - distance[i][j];
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646 distance[j][i] = distance[i][j];
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650 else if (pwtype.equals("SW"))
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654 for (int i = 0; i < (noseqs - 1); i++)
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656 for (int j = i; j < noseqs; j++)
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658 AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
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659 as.calcScoreMatrix();
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660 as.traceAlignment();
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661 as.printAlignment(System.out);
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662 distance[i][j] = (float) as.maxscore;
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664 if (max < distance[i][j])
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666 max = distance[i][j];
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671 for (int i = 0; i < (noseqs - 1); i++)
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673 for (int j = i; j < noseqs; j++)
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675 distance[i][j] = max - distance[i][j];
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676 distance[j][i] = distance[i][j];
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687 public void makeLeaves()
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689 cluster = new Vector();
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691 for (int i = 0; i < noseqs; i++)
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693 SequenceNode sn = new SequenceNode();
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695 sn.setElement(sequence[i]);
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696 sn.setName(sequence[i].getName());
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697 node.addElement(sn);
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699 int[] value = new int[1];
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702 Cluster c = new Cluster(value);
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703 cluster.addElement(c);
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710 * @param node DOCUMENT ME!
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711 * @param leaves DOCUMENT ME!
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713 * @return DOCUMENT ME!
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715 public Vector findLeaves(SequenceNode node, Vector leaves)
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722 if ((node.left() == null) && (node.right() == null))
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724 leaves.addElement(node);
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730 findLeaves((SequenceNode) node.left(), leaves);
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731 findLeaves((SequenceNode) node.right(), leaves);
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740 * @param node DOCUMENT ME!
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741 * @param count DOCUMENT ME!
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743 * @return DOCUMENT ME!
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745 public Object findLeaf(SequenceNode node, int count)
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747 found = _findLeaf(node, count);
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755 * @param node DOCUMENT ME!
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756 * @param count DOCUMENT ME!
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758 * @return DOCUMENT ME!
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760 public Object _findLeaf(SequenceNode node, int count)
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767 if (node.ycount == count)
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769 found = node.element();
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775 _findLeaf((SequenceNode) node.left(), count);
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776 _findLeaf((SequenceNode) node.right(), count);
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783 * printNode is mainly for debugging purposes.
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785 * @param node SequenceNode
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787 public void printNode(SequenceNode node)
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794 if ((node.left() == null) && (node.right() == null))
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796 System.out.println("Leaf = " +
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797 ((SequenceI) node.element()).getName());
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798 System.out.println("Dist " + ((SequenceNode) node).dist);
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799 System.out.println("Boot " + node.getBootstrap());
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803 System.out.println("Dist " + ((SequenceNode) node).dist);
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804 printNode((SequenceNode) node.left());
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805 printNode((SequenceNode) node.right());
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812 * @param node DOCUMENT ME!
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814 public void findMaxDist(SequenceNode node)
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821 if ((node.left() == null) && (node.right() == null))
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823 float dist = ((SequenceNode) node).dist;
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825 if (dist > maxDistValue)
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827 maxdist = (SequenceNode) node;
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828 maxDistValue = dist;
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833 findMaxDist((SequenceNode) node.left());
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834 findMaxDist((SequenceNode) node.right());
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841 * @return DOCUMENT ME!
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843 public Vector getGroups()
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851 * @return DOCUMENT ME!
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853 public float getMaxHeight()
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861 * @param node DOCUMENT ME!
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862 * @param threshold DOCUMENT ME!
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864 public void groupNodes(SequenceNode node, float threshold)
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871 if ((node.height / maxheight) > threshold)
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873 groups.addElement(node);
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877 groupNodes((SequenceNode) node.left(), threshold);
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878 groupNodes((SequenceNode) node.right(), threshold);
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885 * @param node DOCUMENT ME!
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887 * @return DOCUMENT ME!
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889 public float findHeight(SequenceNode node)
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896 if ((node.left() == null) && (node.right() == null))
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898 node.height = ((SequenceNode) node.parent()).height + node.dist;
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900 if (node.height > maxheight)
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902 return node.height;
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911 if (node.parent() != null)
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913 node.height = ((SequenceNode) node.parent()).height +
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919 node.height = (float) 0.0;
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922 maxheight = findHeight((SequenceNode) (node.left()));
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923 maxheight = findHeight((SequenceNode) (node.right()));
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932 * @return DOCUMENT ME!
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934 public SequenceNode reRoot()
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936 if (maxdist != null)
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940 float tmpdist = maxdist.dist;
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943 SequenceNode sn = new SequenceNode();
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944 sn.setParent(null);
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946 // New right hand of top
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947 SequenceNode snr = (SequenceNode) maxdist.parent();
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948 changeDirection(snr, maxdist);
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949 System.out.println("Printing reversed tree");
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951 snr.dist = tmpdist / 2;
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952 maxdist.dist = tmpdist / 2;
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955 maxdist.setParent(sn);
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958 sn.setLeft(maxdist);
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973 * @param node DOCUMENT ME!
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975 public static void printN(SequenceNode node)
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982 if ((node.left() != null) && (node.right() != null))
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984 printN((SequenceNode) node.left());
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985 printN((SequenceNode) node.right());
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989 System.out.println(" name = " +
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990 ((SequenceI) node.element()).getName());
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993 System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
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994 ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
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1000 * @param node DOCUMENT ME!
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1002 public void reCount(SequenceNode node)
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1011 * @param node DOCUMENT ME!
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1013 public void _reCount(SequenceNode node)
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1020 if ((node.left() != null) && (node.right() != null))
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1022 _reCount((SequenceNode) node.left());
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1023 _reCount((SequenceNode) node.right());
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1025 SequenceNode l = (SequenceNode) node.left();
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1026 SequenceNode r = (SequenceNode) node.right();
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1028 ((SequenceNode) node).count = l.count + r.count;
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1029 ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
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1033 ((SequenceNode) node).count = 1;
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1034 ((SequenceNode) node).ycount = ycount++;
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1041 * @param node DOCUMENT ME!
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1043 public void swapNodes(SequenceNode node)
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1050 SequenceNode tmp = (SequenceNode) node.left();
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1052 node.setLeft(node.right());
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1053 node.setRight(tmp);
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1059 * @param node DOCUMENT ME!
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1060 * @param dir DOCUMENT ME!
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1062 public void changeDirection(SequenceNode node, SequenceNode dir)
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1069 if (node.parent() != top)
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1071 changeDirection((SequenceNode) node.parent(), node);
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1073 SequenceNode tmp = (SequenceNode) node.parent();
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1075 if (dir == node.left())
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1077 node.setParent(dir);
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1078 node.setLeft(tmp);
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1080 else if (dir == node.right())
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1082 node.setParent(dir);
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1083 node.setRight(tmp);
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1088 if (dir == node.left())
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1090 node.setParent(node.left());
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1092 if (top.left() == node)
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1094 node.setRight(top.right());
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1098 node.setRight(top.left());
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1103 node.setParent(node.right());
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1105 if (top.left() == node)
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1107 node.setLeft(top.right());
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1111 node.setLeft(top.left());
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1121 * @return DOCUMENT ME!
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1123 public SequenceNode getMaxDist()
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1131 * @return DOCUMENT ME!
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1133 public SequenceNode getTopNode()
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1143 * @author $author$
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1144 * @version $Revision$
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1151 * Creates a new Cluster object.
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1153 * @param value DOCUMENT ME!
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1155 public Cluster(int[] value)
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1157 this.value = value;
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