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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63 boolean hasDistances = true; // normal case for jalview trees
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64 boolean hasBootstrap = false; // normal case for jalview trees
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66 private boolean hasRootDistance = true;
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69 * Creates a new NJTree object.
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71 * @param node DOCUMENT ME!
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73 public NJTree(SequenceNode node)
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76 maxheight = findHeight(top);
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80 * Creates a new NJTree object.
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82 * @param seqs DOCUMENT ME!
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83 * @param treefile DOCUMENT ME!
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85 public NJTree(SequenceI[] seqs, NewickFile treefile)
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87 top = treefile.getTree();
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89 hasDistances = treefile.HasDistances();
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90 hasBootstrap = treefile.HasBootstrap();
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91 hasRootDistance = treefile.HasRootDistance();
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93 maxheight = findHeight(top);
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95 SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
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97 Vector leaves = new Vector();
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98 findLeaves(top, leaves);
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101 int namesleft = seqs.length;
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107 while (i < leaves.size())
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109 j = (SequenceNode) leaves.elementAt(i++);
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110 realnam = j.getName();
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113 if (namesleft > -1)
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115 nam = algnIds.findIdMatch(realnam);
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125 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
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126 j.setPlaceholder(true);
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132 * Creates a new NJTree object.
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134 * @param sequence DOCUMENT ME!
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135 * @param start DOCUMENT ME!
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136 * @param end DOCUMENT ME!
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138 public NJTree(SequenceI[] sequence, int start, int end)
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140 this(sequence, "NJ", "BL", start, end);
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144 * Creates a new NJTree object.
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146 * @param sequence DOCUMENT ME!
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147 * @param type DOCUMENT ME!
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148 * @param pwtype DOCUMENT ME!
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149 * @param start DOCUMENT ME!
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150 * @param end DOCUMENT ME!
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152 public NJTree(SequenceI[] sequence, String type, String pwtype, int start,
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155 this.sequence = sequence;
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156 this.node = new Vector();
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158 this.pwtype = pwtype;
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159 this.start = start;
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162 if (!(type.equals("NJ")))
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167 if (!(pwtype.equals("PID")))
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174 done = new int[sequence.length];
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176 while ((i < sequence.length) && (sequence[i] != null))
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184 distance = findDistances();
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188 noClus = cluster.size();
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196 * @return DOCUMENT ME!
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198 public String toString()
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200 jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
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202 return fout.print(false, true); // distances only
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207 * used when the alignment associated to a tree has changed.
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209 * @param alignment Vector
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211 public void UpdatePlaceHolders(Vector alignment)
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213 Vector leaves = new Vector();
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214 findLeaves(top, leaves);
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216 int sz = leaves.size();
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217 SequenceIdMatcher seqmatcher = null;
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222 SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
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224 if (alignment.contains(leaf.element()))
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226 leaf.setPlaceholder(false);
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230 if (seqmatcher == null)
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232 // Only create this the first time we need it
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233 SequenceI[] seqs = new SequenceI[alignment.size()];
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235 for (int j = 0; j < seqs.length; j++)
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236 seqs[j] = (SequenceI) alignment.elementAt(j);
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238 seqmatcher = new SequenceIdMatcher(seqs);
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241 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
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245 leaf.setPlaceholder(false);
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246 leaf.setElement(nam);
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250 leaf.setPlaceholder(true);
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259 public void cluster()
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263 if (type.equals("NJ"))
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265 findMinNJDistance();
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272 Cluster c = joinClusters(mini, minj);
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276 cluster.setElementAt(null, minj);
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277 cluster.setElementAt(c, mini);
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282 boolean onefound = false;
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287 for (int i = 0; i < noseqs; i++)
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291 if (onefound == false)
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303 joinClusters(one, two);
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304 top = (SequenceNode) (node.elementAt(one));
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314 * @param i DOCUMENT ME!
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315 * @param j DOCUMENT ME!
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317 * @return DOCUMENT ME!
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319 public Cluster joinClusters(int i, int j)
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321 float dist = distance[i][j];
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323 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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324 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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326 int[] value = new int[noi + noj];
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328 for (int ii = 0; ii < noi; ii++)
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330 value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
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333 for (int ii = noi; ii < (noi + noj); ii++)
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335 value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
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338 Cluster c = new Cluster(value);
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343 if (type.equals("NJ"))
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345 findClusterNJDistance(i, j);
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349 findClusterDistance(i, j);
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352 SequenceNode sn = new SequenceNode();
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354 sn.setLeft((SequenceNode) (node.elementAt(i)));
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355 sn.setRight((SequenceNode) (node.elementAt(j)));
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357 SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
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358 SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
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360 if (type.equals("NJ"))
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362 findNewNJDistances(tmpi, tmpj, dist);
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366 findNewDistances(tmpi, tmpj, dist);
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369 tmpi.setParent(sn);
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370 tmpj.setParent(sn);
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372 node.setElementAt(sn, i);
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380 * @param tmpi DOCUMENT ME!
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381 * @param tmpj DOCUMENT ME!
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382 * @param dist DOCUMENT ME!
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384 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
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388 tmpi.dist = ((dist + ri) - rj) / 2;
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389 tmpj.dist = (dist - tmpi.dist);
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405 * @param tmpi DOCUMENT ME!
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406 * @param tmpj DOCUMENT ME!
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407 * @param dist DOCUMENT ME!
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409 public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
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415 SequenceNode sni = tmpi;
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416 SequenceNode snj = tmpj;
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418 while (sni != null)
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420 ih = ih + sni.dist;
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421 sni = (SequenceNode) sni.left();
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424 while (snj != null)
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426 jh = jh + snj.dist;
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427 snj = (SequenceNode) snj.left();
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430 tmpi.dist = ((dist / 2) - ih);
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431 tmpj.dist = ((dist / 2) - jh);
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437 * @param i DOCUMENT ME!
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438 * @param j DOCUMENT ME!
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440 public void findClusterDistance(int i, int j)
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442 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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443 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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445 // New distances from cluster to others
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446 float[] newdist = new float[noseqs];
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448 for (int l = 0; l < noseqs; l++)
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450 if ((l != i) && (l != j))
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452 newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
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461 for (int ii = 0; ii < noseqs; ii++)
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463 distance[i][ii] = newdist[ii];
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464 distance[ii][i] = newdist[ii];
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471 * @param i DOCUMENT ME!
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472 * @param j DOCUMENT ME!
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474 public void findClusterNJDistance(int i, int j)
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477 // New distances from cluster to others
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478 float[] newdist = new float[noseqs];
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480 for (int l = 0; l < noseqs; l++)
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482 if ((l != i) && (l != j))
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484 newdist[l] = ((distance[i][l] + distance[j][l]) -
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485 distance[i][j]) / 2;
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493 for (int ii = 0; ii < noseqs; ii++)
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495 distance[i][ii] = newdist[ii];
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496 distance[ii][i] = newdist[ii];
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503 * @param i DOCUMENT ME!
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504 * @param j DOCUMENT ME!
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506 * @return DOCUMENT ME!
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508 public float findr(int i, int j)
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512 for (int k = 0; k < noseqs; k++)
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514 if ((k != i) && (k != j) && (done[k] != 1))
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516 tmp = tmp + distance[i][k];
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522 tmp = tmp / (noClus - 2);
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531 * @return DOCUMENT ME!
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533 public float findMinNJDistance()
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535 float min = 100000;
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537 for (int i = 0; i < (noseqs - 1); i++)
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539 for (int j = i + 1; j < noseqs; j++)
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541 if ((done[i] != 1) && (done[j] != 1))
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543 float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
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562 * @return DOCUMENT ME!
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564 public float findMinDistance()
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566 float min = 100000;
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568 for (int i = 0; i < (noseqs - 1); i++)
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570 for (int j = i + 1; j < noseqs; j++)
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572 if ((done[i] != 1) && (done[j] != 1))
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574 if (distance[i][j] < min)
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579 min = distance[i][j];
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591 * @return DOCUMENT ME!
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593 public float[][] findDistances()
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595 float[][] distance = new float[noseqs][noseqs];
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597 if (pwtype.equals("PID"))
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599 for (int i = 0; i < (noseqs - 1); i++)
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601 for (int j = i; j < noseqs; j++)
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605 distance[i][i] = 0;
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609 distance[i][j] = 100 -
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610 Comparison.PID(sequence[i], sequence[j], start, end);
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611 distance[j][i] = distance[i][j];
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616 else if (pwtype.equals("BL"))
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620 for (int i = 0; i < (noseqs - 1); i++)
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622 for (int j = i; j < noseqs; j++)
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626 for (int k = start; k < end; k++)
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630 score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(
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631 k, k + 1), sequence[j].getSequence(k, k +
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634 catch (Exception ex)
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636 System.err.println("err creating BLOSUM62 tree");
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637 ex.printStackTrace();
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641 distance[i][j] = (float) score;
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643 if (score > maxscore)
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650 for (int i = 0; i < (noseqs - 1); i++)
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652 for (int j = i; j < noseqs; j++)
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654 distance[i][j] = (float) maxscore - distance[i][j];
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655 distance[j][i] = distance[i][j];
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659 else if (pwtype.equals("SW"))
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663 for (int i = 0; i < (noseqs - 1); i++)
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665 for (int j = i; j < noseqs; j++)
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667 AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
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668 as.calcScoreMatrix();
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669 as.traceAlignment();
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670 as.printAlignment(System.out);
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671 distance[i][j] = (float) as.maxscore;
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673 if (max < distance[i][j])
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675 max = distance[i][j];
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680 for (int i = 0; i < (noseqs - 1); i++)
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682 for (int j = i; j < noseqs; j++)
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684 distance[i][j] = max - distance[i][j];
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685 distance[j][i] = distance[i][j];
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696 public void makeLeaves()
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698 cluster = new Vector();
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700 for (int i = 0; i < noseqs; i++)
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702 SequenceNode sn = new SequenceNode();
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704 sn.setElement(sequence[i]);
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705 sn.setName(sequence[i].getName());
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706 node.addElement(sn);
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708 int[] value = new int[1];
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711 Cluster c = new Cluster(value);
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712 cluster.addElement(c);
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719 * @param node DOCUMENT ME!
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720 * @param leaves DOCUMENT ME!
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722 * @return DOCUMENT ME!
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724 public Vector findLeaves(SequenceNode node, Vector leaves)
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731 if ((node.left() == null) && (node.right() == null))
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733 leaves.addElement(node);
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739 findLeaves((SequenceNode) node.left(), leaves);
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740 findLeaves((SequenceNode) node.right(), leaves);
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749 * @param node DOCUMENT ME!
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750 * @param count DOCUMENT ME!
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752 * @return DOCUMENT ME!
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754 public Object findLeaf(SequenceNode node, int count)
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756 found = _findLeaf(node, count);
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764 * @param node DOCUMENT ME!
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765 * @param count DOCUMENT ME!
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767 * @return DOCUMENT ME!
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769 public Object _findLeaf(SequenceNode node, int count)
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776 if (node.ycount == count)
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778 found = node.element();
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784 _findLeaf((SequenceNode) node.left(), count);
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785 _findLeaf((SequenceNode) node.right(), count);
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792 * printNode is mainly for debugging purposes.
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794 * @param node SequenceNode
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796 public void printNode(SequenceNode node)
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803 if ((node.left() == null) && (node.right() == null))
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805 System.out.println("Leaf = " +
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806 ((SequenceI) node.element()).getName());
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807 System.out.println("Dist " + ((SequenceNode) node).dist);
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808 System.out.println("Boot " + node.getBootstrap());
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812 System.out.println("Dist " + ((SequenceNode) node).dist);
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813 printNode((SequenceNode) node.left());
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814 printNode((SequenceNode) node.right());
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821 * @param node DOCUMENT ME!
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823 public void findMaxDist(SequenceNode node)
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830 if ((node.left() == null) && (node.right() == null))
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832 float dist = ((SequenceNode) node).dist;
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834 if (dist > maxDistValue)
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836 maxdist = (SequenceNode) node;
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837 maxDistValue = dist;
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842 findMaxDist((SequenceNode) node.left());
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843 findMaxDist((SequenceNode) node.right());
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850 * @return DOCUMENT ME!
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852 public Vector getGroups()
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860 * @return DOCUMENT ME!
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862 public float getMaxHeight()
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870 * @param node DOCUMENT ME!
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871 * @param threshold DOCUMENT ME!
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873 public void groupNodes(SequenceNode node, float threshold)
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880 if ((node.height / maxheight) > threshold)
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882 groups.addElement(node);
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886 groupNodes((SequenceNode) node.left(), threshold);
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887 groupNodes((SequenceNode) node.right(), threshold);
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894 * @param node DOCUMENT ME!
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896 * @return DOCUMENT ME!
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898 public float findHeight(SequenceNode node)
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905 if ((node.left() == null) && (node.right() == null))
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907 node.height = ((SequenceNode) node.parent()).height + node.dist;
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909 if (node.height > maxheight)
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911 return node.height;
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920 if (node.parent() != null)
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922 node.height = ((SequenceNode) node.parent()).height +
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928 node.height = (float) 0.0;
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931 maxheight = findHeight((SequenceNode) (node.left()));
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932 maxheight = findHeight((SequenceNode) (node.right()));
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941 * @return DOCUMENT ME!
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943 public SequenceNode reRoot()
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945 if (maxdist != null)
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949 float tmpdist = maxdist.dist;
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952 SequenceNode sn = new SequenceNode();
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953 sn.setParent(null);
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955 // New right hand of top
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956 SequenceNode snr = (SequenceNode) maxdist.parent();
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957 changeDirection(snr, maxdist);
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958 System.out.println("Printing reversed tree");
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960 snr.dist = tmpdist / 2;
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961 maxdist.dist = tmpdist / 2;
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964 maxdist.setParent(sn);
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967 sn.setLeft(maxdist);
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982 * @param node DOCUMENT ME!
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984 public static void printN(SequenceNode node)
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991 if ((node.left() != null) && (node.right() != null))
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993 printN((SequenceNode) node.left());
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994 printN((SequenceNode) node.right());
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998 System.out.println(" name = " +
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999 ((SequenceI) node.element()).getName());
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1002 System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
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1003 ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
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1009 * @param node DOCUMENT ME!
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1011 public void reCount(SequenceNode node)
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1020 * @param node DOCUMENT ME!
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1022 public void _reCount(SequenceNode node)
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1029 if ((node.left() != null) && (node.right() != null))
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1031 _reCount((SequenceNode) node.left());
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1032 _reCount((SequenceNode) node.right());
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1034 SequenceNode l = (SequenceNode) node.left();
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1035 SequenceNode r = (SequenceNode) node.right();
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1037 ((SequenceNode) node).count = l.count + r.count;
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1038 ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
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1042 ((SequenceNode) node).count = 1;
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1043 ((SequenceNode) node).ycount = ycount++;
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1050 * @param node DOCUMENT ME!
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1052 public void swapNodes(SequenceNode node)
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1059 SequenceNode tmp = (SequenceNode) node.left();
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1061 node.setLeft(node.right());
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1062 node.setRight(tmp);
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1068 * @param node DOCUMENT ME!
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1069 * @param dir DOCUMENT ME!
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1071 public void changeDirection(SequenceNode node, SequenceNode dir)
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1078 if (node.parent() != top)
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1080 changeDirection((SequenceNode) node.parent(), node);
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1082 SequenceNode tmp = (SequenceNode) node.parent();
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1084 if (dir == node.left())
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1086 node.setParent(dir);
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1087 node.setLeft(tmp);
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1089 else if (dir == node.right())
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1091 node.setParent(dir);
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1092 node.setRight(tmp);
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1097 if (dir == node.left())
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1099 node.setParent(node.left());
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1101 if (top.left() == node)
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1103 node.setRight(top.right());
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1107 node.setRight(top.left());
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1112 node.setParent(node.right());
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1114 if (top.left() == node)
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1116 node.setLeft(top.right());
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1120 node.setLeft(top.left());
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1130 * @return DOCUMENT ME!
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1132 public SequenceNode getMaxDist()
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1140 * @return DOCUMENT ME!
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1142 public SequenceNode getTopNode()
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1148 * @return true if tree has real distances
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1150 public boolean isHasDistances() {
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1151 return hasDistances;
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1156 * @return true if tree has real bootstrap values
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1158 public boolean isHasBootstrap() {
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1159 return hasBootstrap;
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1162 public boolean isHasRootDistance()
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1164 return hasRootDistance;
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1173 * @author $author$
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1174 * @version $Revision$
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1181 * Creates a new Cluster object.
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1183 * @param value DOCUMENT ME!
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1185 public Cluster(int[] value)
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1187 this.value = value;
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