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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43 //SequenceData is a string representation of what the user
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44 //sees. The display may contain hidden columns.
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45 String [] sequenceString;
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55 Vector groups = new Vector();
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56 SequenceNode maxdist;
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64 Object found = null;
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65 Object leaves = null;
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67 boolean hasDistances = true; // normal case for jalview trees
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68 boolean hasBootstrap = false; // normal case for jalview trees
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70 private boolean hasRootDistance = true;
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74 * Creates a new NJTree object.
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76 * @param seqs DOCUMENT ME!
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77 * @param treefile DOCUMENT ME!
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79 public NJTree(SequenceI[] seqs, NewickFile treefile)
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81 this.sequence = seqs;
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82 top = treefile.getTree();
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84 if (sequenceString == null)
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86 sequenceString = new String[seqs.length];
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87 for (int i = 0; i < seqs.length; i++)
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89 sequenceString[i] = seqs[i].getSequence();
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94 hasDistances = treefile.HasDistances();
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95 hasBootstrap = treefile.HasBootstrap();
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96 hasRootDistance = treefile.HasRootDistance();
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98 maxheight = findHeight(top);
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100 SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
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102 Vector leaves = new Vector();
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103 findLeaves(top, leaves);
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106 int namesleft = seqs.length;
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112 while (i < leaves.size())
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114 j = (SequenceNode) leaves.elementAt(i++);
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115 realnam = j.getName();
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118 if (namesleft > -1)
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120 nam = algnIds.findIdMatch(realnam);
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130 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
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131 j.setPlaceholder(true);
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137 * Creates a new NJTree object.
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139 * @param sequence DOCUMENT ME!
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140 * @param type DOCUMENT ME!
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141 * @param pwtype DOCUMENT ME!
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142 * @param start DOCUMENT ME!
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143 * @param end DOCUMENT ME!
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145 public NJTree(SequenceI[] sequence,
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146 String [] sequenceString,
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149 int start, int end)
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151 this.sequence = sequence;
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152 this.node = new Vector();
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154 this.pwtype = pwtype;
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156 if (sequenceString == null)
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158 this.sequenceString = new String[sequence.length];
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159 for(int i=0; i<sequence.length; i++)
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161 this.sequenceString[i] = sequence[i].getSequence(start, end);
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165 this.sequenceString = sequenceString;
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168 if (!(type.equals("NJ")))
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173 if (!(pwtype.equals("PID")))
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180 done = new int[sequence.length];
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182 while ((i < sequence.length) && (sequence[i] != null))
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190 distance = findDistances();
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194 noClus = cluster.size();
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202 * @return DOCUMENT ME!
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204 public String toString()
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206 jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
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208 return fout.print(false, true); // distances only
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213 * used when the alignment associated to a tree has changed.
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215 * @param alignment Vector
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217 public void UpdatePlaceHolders(Vector alignment)
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219 Vector leaves = new Vector();
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220 findLeaves(top, leaves);
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222 int sz = leaves.size();
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223 SequenceIdMatcher seqmatcher = null;
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228 SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
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230 if (alignment.contains(leaf.element()))
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232 leaf.setPlaceholder(false);
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236 if (seqmatcher == null)
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238 // Only create this the first time we need it
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239 SequenceI[] seqs = new SequenceI[alignment.size()];
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241 for (int j = 0; j < seqs.length; j++)
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242 seqs[j] = (SequenceI) alignment.elementAt(j);
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244 seqmatcher = new SequenceIdMatcher(seqs);
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247 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
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251 leaf.setPlaceholder(false);
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252 leaf.setElement(nam);
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256 leaf.setPlaceholder(true);
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265 public void cluster()
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269 if (type.equals("NJ"))
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271 findMinNJDistance();
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278 Cluster c = joinClusters(mini, minj);
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282 cluster.setElementAt(null, minj);
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283 cluster.setElementAt(c, mini);
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288 boolean onefound = false;
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293 for (int i = 0; i < noseqs; i++)
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297 if (onefound == false)
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309 joinClusters(one, two);
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310 top = (SequenceNode) (node.elementAt(one));
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320 * @param i DOCUMENT ME!
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321 * @param j DOCUMENT ME!
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323 * @return DOCUMENT ME!
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325 public Cluster joinClusters(int i, int j)
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327 float dist = distance[i][j];
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329 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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330 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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332 int[] value = new int[noi + noj];
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334 for (int ii = 0; ii < noi; ii++)
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336 value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
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339 for (int ii = noi; ii < (noi + noj); ii++)
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341 value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
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344 Cluster c = new Cluster(value);
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349 if (type.equals("NJ"))
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351 findClusterNJDistance(i, j);
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355 findClusterDistance(i, j);
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358 SequenceNode sn = new SequenceNode();
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360 sn.setLeft((SequenceNode) (node.elementAt(i)));
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361 sn.setRight((SequenceNode) (node.elementAt(j)));
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363 SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
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364 SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
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366 if (type.equals("NJ"))
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368 findNewNJDistances(tmpi, tmpj, dist);
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372 findNewDistances(tmpi, tmpj, dist);
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375 tmpi.setParent(sn);
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376 tmpj.setParent(sn);
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378 node.setElementAt(sn, i);
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386 * @param tmpi DOCUMENT ME!
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387 * @param tmpj DOCUMENT ME!
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388 * @param dist DOCUMENT ME!
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390 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
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394 tmpi.dist = ((dist + ri) - rj) / 2;
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395 tmpj.dist = (dist - tmpi.dist);
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411 * @param tmpi DOCUMENT ME!
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412 * @param tmpj DOCUMENT ME!
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413 * @param dist DOCUMENT ME!
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415 public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
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421 SequenceNode sni = tmpi;
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422 SequenceNode snj = tmpj;
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424 while (sni != null)
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426 ih = ih + sni.dist;
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427 sni = (SequenceNode) sni.left();
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430 while (snj != null)
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432 jh = jh + snj.dist;
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433 snj = (SequenceNode) snj.left();
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436 tmpi.dist = ((dist / 2) - ih);
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437 tmpj.dist = ((dist / 2) - jh);
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443 * @param i DOCUMENT ME!
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444 * @param j DOCUMENT ME!
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446 public void findClusterDistance(int i, int j)
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448 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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449 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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451 // New distances from cluster to others
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452 float[] newdist = new float[noseqs];
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454 for (int l = 0; l < noseqs; l++)
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456 if ((l != i) && (l != j))
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458 newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
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467 for (int ii = 0; ii < noseqs; ii++)
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469 distance[i][ii] = newdist[ii];
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470 distance[ii][i] = newdist[ii];
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477 * @param i DOCUMENT ME!
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478 * @param j DOCUMENT ME!
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480 public void findClusterNJDistance(int i, int j)
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483 // New distances from cluster to others
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484 float[] newdist = new float[noseqs];
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486 for (int l = 0; l < noseqs; l++)
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488 if ((l != i) && (l != j))
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490 newdist[l] = ((distance[i][l] + distance[j][l]) -
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491 distance[i][j]) / 2;
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499 for (int ii = 0; ii < noseqs; ii++)
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501 distance[i][ii] = newdist[ii];
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502 distance[ii][i] = newdist[ii];
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509 * @param i DOCUMENT ME!
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510 * @param j DOCUMENT ME!
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512 * @return DOCUMENT ME!
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514 public float findr(int i, int j)
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518 for (int k = 0; k < noseqs; k++)
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520 if ((k != i) && (k != j) && (done[k] != 1))
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522 tmp = tmp + distance[i][k];
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528 tmp = tmp / (noClus - 2);
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537 * @return DOCUMENT ME!
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539 public float findMinNJDistance()
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541 float min = 100000;
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543 for (int i = 0; i < (noseqs - 1); i++)
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545 for (int j = i + 1; j < noseqs; j++)
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547 if ((done[i] != 1) && (done[j] != 1))
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549 float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
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568 * @return DOCUMENT ME!
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570 public float findMinDistance()
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572 float min = 100000;
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574 for (int i = 0; i < (noseqs - 1); i++)
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576 for (int j = i + 1; j < noseqs; j++)
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578 if ((done[i] != 1) && (done[j] != 1))
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580 if (distance[i][j] < min)
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585 min = distance[i][j];
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597 * @return DOCUMENT ME!
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599 public float[][] findDistances()
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601 float[][] distance = new float[noseqs][noseqs];
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603 if (pwtype.equals("PID"))
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605 for (int i = 0; i < (noseqs - 1); i++)
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607 for (int j = i; j < noseqs; j++)
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611 distance[i][i] = 0;
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615 distance[i][j] = 100 -
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616 Comparison.PID(sequenceString[i], sequenceString[j]);
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618 distance[j][i] = distance[i][j];
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623 else if (pwtype.equals("BL"))
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626 int end = sequenceString[0].length();
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627 for (int i = 0; i < (noseqs - 1); i++)
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629 for (int j = i; j < noseqs; j++)
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633 for (int k = 0; k < end; k++)
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637 score += ResidueProperties.getBLOSUM62(
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638 sequenceString[i].substring(k, k + 1),
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639 sequenceString[j].substring(k, k + 1));
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641 catch (Exception ex)
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643 System.err.println("err creating BLOSUM62 tree");
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644 ex.printStackTrace();
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648 distance[i][j] = (float) score;
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650 if (score > maxscore)
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657 for (int i = 0; i < (noseqs - 1); i++)
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659 for (int j = i; j < noseqs; j++)
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661 distance[i][j] = (float) maxscore - distance[i][j];
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662 distance[j][i] = distance[i][j];
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666 /* else if (pwtype.equals("SW"))
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670 for (int i = 0; i < (noseqs - 1); i++)
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672 for (int j = i; j < noseqs; j++)
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674 AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
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675 as.calcScoreMatrix();
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676 as.traceAlignment();
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677 as.printAlignment(System.out);
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678 distance[i][j] = (float) as.maxscore;
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680 if (max < distance[i][j])
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682 max = distance[i][j];
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687 for (int i = 0; i < (noseqs - 1); i++)
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689 for (int j = i; j < noseqs; j++)
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691 distance[i][j] = max - distance[i][j];
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692 distance[j][i] = distance[i][j];
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703 public void makeLeaves()
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705 cluster = new Vector();
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707 for (int i = 0; i < noseqs; i++)
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709 SequenceNode sn = new SequenceNode();
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711 sn.setElement(sequence[i]);
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712 sn.setName(sequence[i].getName());
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713 node.addElement(sn);
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715 int[] value = new int[1];
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718 Cluster c = new Cluster(value);
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719 cluster.addElement(c);
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726 * @param node DOCUMENT ME!
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727 * @param leaves DOCUMENT ME!
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729 * @return DOCUMENT ME!
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731 public Vector findLeaves(SequenceNode node, Vector leaves)
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738 if ((node.left() == null) && (node.right() == null))
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740 leaves.addElement(node);
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746 findLeaves((SequenceNode) node.left(), leaves);
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747 findLeaves((SequenceNode) node.right(), leaves);
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756 * @param node DOCUMENT ME!
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757 * @param count DOCUMENT ME!
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759 * @return DOCUMENT ME!
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761 public Object findLeaf(SequenceNode node, int count)
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763 found = _findLeaf(node, count);
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771 * @param node DOCUMENT ME!
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772 * @param count DOCUMENT ME!
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774 * @return DOCUMENT ME!
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776 public Object _findLeaf(SequenceNode node, int count)
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783 if (node.ycount == count)
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785 found = node.element();
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791 _findLeaf((SequenceNode) node.left(), count);
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792 _findLeaf((SequenceNode) node.right(), count);
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799 * printNode is mainly for debugging purposes.
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801 * @param node SequenceNode
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803 public void printNode(SequenceNode node)
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810 if ((node.left() == null) && (node.right() == null))
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812 System.out.println("Leaf = " +
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813 ((SequenceI) node.element()).getName());
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814 System.out.println("Dist " + ((SequenceNode) node).dist);
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815 System.out.println("Boot " + node.getBootstrap());
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819 System.out.println("Dist " + ((SequenceNode) node).dist);
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820 printNode((SequenceNode) node.left());
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821 printNode((SequenceNode) node.right());
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828 * @param node DOCUMENT ME!
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830 public void findMaxDist(SequenceNode node)
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837 if ((node.left() == null) && (node.right() == null))
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839 float dist = ((SequenceNode) node).dist;
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841 if (dist > maxDistValue)
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843 maxdist = (SequenceNode) node;
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844 maxDistValue = dist;
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849 findMaxDist((SequenceNode) node.left());
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850 findMaxDist((SequenceNode) node.right());
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857 * @return DOCUMENT ME!
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859 public Vector getGroups()
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867 * @return DOCUMENT ME!
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869 public float getMaxHeight()
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877 * @param node DOCUMENT ME!
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878 * @param threshold DOCUMENT ME!
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880 public void groupNodes(SequenceNode node, float threshold)
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887 if ((node.height / maxheight) > threshold)
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889 groups.addElement(node);
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893 groupNodes((SequenceNode) node.left(), threshold);
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894 groupNodes((SequenceNode) node.right(), threshold);
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901 * @param node DOCUMENT ME!
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903 * @return DOCUMENT ME!
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905 public float findHeight(SequenceNode node)
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912 if ((node.left() == null) && (node.right() == null))
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914 node.height = ((SequenceNode) node.parent()).height + node.dist;
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916 if (node.height > maxheight)
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918 return node.height;
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927 if (node.parent() != null)
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929 node.height = ((SequenceNode) node.parent()).height +
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935 node.height = (float) 0.0;
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938 maxheight = findHeight((SequenceNode) (node.left()));
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939 maxheight = findHeight((SequenceNode) (node.right()));
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948 * @return DOCUMENT ME!
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950 public SequenceNode reRoot()
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952 if (maxdist != null)
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956 float tmpdist = maxdist.dist;
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959 SequenceNode sn = new SequenceNode();
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960 sn.setParent(null);
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962 // New right hand of top
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963 SequenceNode snr = (SequenceNode) maxdist.parent();
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964 changeDirection(snr, maxdist);
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965 System.out.println("Printing reversed tree");
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967 snr.dist = tmpdist / 2;
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968 maxdist.dist = tmpdist / 2;
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971 maxdist.setParent(sn);
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974 sn.setLeft(maxdist);
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986 public String printOriginalSequenceData()
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988 StringBuffer sb = new StringBuffer();
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989 for(int i=0; i<sequenceString.length; i++)
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991 sb.append(new jalview.util.Format("%-" + 15 + "s").form(
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992 sequence[i].getName()));
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993 sb.append(" "+sequenceString[i]+"\n");
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995 return sb.toString();
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1001 * @param node DOCUMENT ME!
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1003 public void printN(SequenceNode node)
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1010 if ((node.left() != null) && (node.right() != null))
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1012 printN((SequenceNode) node.left());
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1013 printN((SequenceNode) node.right());
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1017 System.out.println(" name = " +
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1018 ((SequenceI) node.element()).getName());
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1021 System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
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1022 ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
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1028 * @param node DOCUMENT ME!
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1030 public void reCount(SequenceNode node)
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1039 * @param node DOCUMENT ME!
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1041 public void _reCount(SequenceNode node)
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1048 if ((node.left() != null) && (node.right() != null))
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1050 _reCount((SequenceNode) node.left());
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1051 _reCount((SequenceNode) node.right());
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1053 SequenceNode l = (SequenceNode) node.left();
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1054 SequenceNode r = (SequenceNode) node.right();
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1056 ((SequenceNode) node).count = l.count + r.count;
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1057 ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
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1061 ((SequenceNode) node).count = 1;
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1062 ((SequenceNode) node).ycount = ycount++;
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1069 * @param node DOCUMENT ME!
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1071 public void swapNodes(SequenceNode node)
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1078 SequenceNode tmp = (SequenceNode) node.left();
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1080 node.setLeft(node.right());
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1081 node.setRight(tmp);
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1087 * @param node DOCUMENT ME!
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1088 * @param dir DOCUMENT ME!
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1090 public void changeDirection(SequenceNode node, SequenceNode dir)
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1097 if (node.parent() != top)
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1099 changeDirection((SequenceNode) node.parent(), node);
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1101 SequenceNode tmp = (SequenceNode) node.parent();
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1103 if (dir == node.left())
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1105 node.setParent(dir);
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1106 node.setLeft(tmp);
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1108 else if (dir == node.right())
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1110 node.setParent(dir);
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1111 node.setRight(tmp);
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1116 if (dir == node.left())
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1118 node.setParent(node.left());
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1120 if (top.left() == node)
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1122 node.setRight(top.right());
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1126 node.setRight(top.left());
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1131 node.setParent(node.right());
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1133 if (top.left() == node)
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1135 node.setLeft(top.right());
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1139 node.setLeft(top.left());
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1149 * @return DOCUMENT ME!
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1151 public SequenceNode getMaxDist()
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1159 * @return DOCUMENT ME!
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1161 public SequenceNode getTopNode()
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1167 * @return true if tree has real distances
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1169 public boolean isHasDistances() {
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1170 return hasDistances;
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1175 * @return true if tree has real bootstrap values
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1177 public boolean isHasBootstrap() {
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1178 return hasBootstrap;
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1181 public boolean isHasRootDistance()
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1183 return hasRootDistance;
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1192 * @author $author$
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1193 * @version $Revision$
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1200 * Creates a new Cluster object.
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1202 * @param value DOCUMENT ME!
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1204 public Cluster(int[] value)
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1206 this.value = value;
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