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 top = treefile.getTree();
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83 if (sequenceString == null)
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85 sequenceString = new String[seqs.length];
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86 for (int i = 0; i < seqs.length; i++)
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88 sequenceString[i] = seqs[i].getSequence();
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93 hasDistances = treefile.HasDistances();
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94 hasBootstrap = treefile.HasBootstrap();
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95 hasRootDistance = treefile.HasRootDistance();
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97 maxheight = findHeight(top);
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99 SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
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101 Vector leaves = new Vector();
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102 findLeaves(top, leaves);
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105 int namesleft = seqs.length;
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111 while (i < leaves.size())
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113 j = (SequenceNode) leaves.elementAt(i++);
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114 realnam = j.getName();
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117 if (namesleft > -1)
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119 nam = algnIds.findIdMatch(realnam);
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129 j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
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130 j.setPlaceholder(true);
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136 * Creates a new NJTree object.
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138 * @param sequence DOCUMENT ME!
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139 * @param type DOCUMENT ME!
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140 * @param pwtype DOCUMENT ME!
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141 * @param start DOCUMENT ME!
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142 * @param end DOCUMENT ME!
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144 public NJTree(SequenceI[] sequence,
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145 String [] sequenceString,
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148 int start, int end)
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150 this.sequence = sequence;
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151 this.node = new Vector();
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153 this.pwtype = pwtype;
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155 if (sequenceString == null)
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157 this.sequenceString = new String[sequence.length];
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158 for(int i=0; i<sequence.length; i++)
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160 this.sequenceString[i] = sequence[i].getSequence(start, end);
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164 this.sequenceString = sequenceString;
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167 if (!(type.equals("NJ")))
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172 if (!(pwtype.equals("PID")))
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179 done = new int[sequence.length];
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181 while ((i < sequence.length) && (sequence[i] != null))
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189 distance = findDistances();
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193 noClus = cluster.size();
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201 * @return DOCUMENT ME!
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203 public String toString()
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205 jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
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207 return fout.print(false, true); // distances only
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212 * used when the alignment associated to a tree has changed.
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214 * @param alignment Vector
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216 public void UpdatePlaceHolders(Vector alignment)
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218 Vector leaves = new Vector();
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219 findLeaves(top, leaves);
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221 int sz = leaves.size();
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222 SequenceIdMatcher seqmatcher = null;
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227 SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
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229 if (alignment.contains(leaf.element()))
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231 leaf.setPlaceholder(false);
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235 if (seqmatcher == null)
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237 // Only create this the first time we need it
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238 SequenceI[] seqs = new SequenceI[alignment.size()];
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240 for (int j = 0; j < seqs.length; j++)
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241 seqs[j] = (SequenceI) alignment.elementAt(j);
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243 seqmatcher = new SequenceIdMatcher(seqs);
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246 SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
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250 leaf.setPlaceholder(false);
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251 leaf.setElement(nam);
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255 leaf.setPlaceholder(true);
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264 public void cluster()
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268 if (type.equals("NJ"))
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270 findMinNJDistance();
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277 Cluster c = joinClusters(mini, minj);
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281 cluster.setElementAt(null, minj);
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282 cluster.setElementAt(c, mini);
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287 boolean onefound = false;
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292 for (int i = 0; i < noseqs; i++)
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296 if (onefound == false)
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308 joinClusters(one, two);
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309 top = (SequenceNode) (node.elementAt(one));
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319 * @param i DOCUMENT ME!
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320 * @param j DOCUMENT ME!
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322 * @return DOCUMENT ME!
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324 public Cluster joinClusters(int i, int j)
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326 float dist = distance[i][j];
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328 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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329 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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331 int[] value = new int[noi + noj];
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333 for (int ii = 0; ii < noi; ii++)
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335 value[ii] = ((Cluster) cluster.elementAt(i)).value[ii];
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338 for (int ii = noi; ii < (noi + noj); ii++)
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340 value[ii] = ((Cluster) cluster.elementAt(j)).value[ii - noi];
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343 Cluster c = new Cluster(value);
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348 if (type.equals("NJ"))
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350 findClusterNJDistance(i, j);
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354 findClusterDistance(i, j);
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357 SequenceNode sn = new SequenceNode();
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359 sn.setLeft((SequenceNode) (node.elementAt(i)));
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360 sn.setRight((SequenceNode) (node.elementAt(j)));
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362 SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
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363 SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
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365 if (type.equals("NJ"))
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367 findNewNJDistances(tmpi, tmpj, dist);
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371 findNewDistances(tmpi, tmpj, dist);
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374 tmpi.setParent(sn);
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375 tmpj.setParent(sn);
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377 node.setElementAt(sn, i);
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385 * @param tmpi DOCUMENT ME!
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386 * @param tmpj DOCUMENT ME!
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387 * @param dist DOCUMENT ME!
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389 public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
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393 tmpi.dist = ((dist + ri) - rj) / 2;
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394 tmpj.dist = (dist - tmpi.dist);
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410 * @param tmpi DOCUMENT ME!
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411 * @param tmpj DOCUMENT ME!
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412 * @param dist DOCUMENT ME!
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414 public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
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420 SequenceNode sni = tmpi;
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421 SequenceNode snj = tmpj;
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423 while (sni != null)
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425 ih = ih + sni.dist;
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426 sni = (SequenceNode) sni.left();
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429 while (snj != null)
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431 jh = jh + snj.dist;
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432 snj = (SequenceNode) snj.left();
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435 tmpi.dist = ((dist / 2) - ih);
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436 tmpj.dist = ((dist / 2) - jh);
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442 * @param i DOCUMENT ME!
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443 * @param j DOCUMENT ME!
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445 public void findClusterDistance(int i, int j)
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447 int noi = ((Cluster) cluster.elementAt(i)).value.length;
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448 int noj = ((Cluster) cluster.elementAt(j)).value.length;
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450 // New distances from cluster to others
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451 float[] newdist = new float[noseqs];
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453 for (int l = 0; l < noseqs; l++)
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455 if ((l != i) && (l != j))
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457 newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
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466 for (int ii = 0; ii < noseqs; ii++)
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468 distance[i][ii] = newdist[ii];
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469 distance[ii][i] = newdist[ii];
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476 * @param i DOCUMENT ME!
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477 * @param j DOCUMENT ME!
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479 public void findClusterNJDistance(int i, int j)
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482 // New distances from cluster to others
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483 float[] newdist = new float[noseqs];
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485 for (int l = 0; l < noseqs; l++)
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487 if ((l != i) && (l != j))
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489 newdist[l] = ((distance[i][l] + distance[j][l]) -
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490 distance[i][j]) / 2;
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498 for (int ii = 0; ii < noseqs; ii++)
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500 distance[i][ii] = newdist[ii];
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501 distance[ii][i] = newdist[ii];
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508 * @param i DOCUMENT ME!
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509 * @param j DOCUMENT ME!
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511 * @return DOCUMENT ME!
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513 public float findr(int i, int j)
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517 for (int k = 0; k < noseqs; k++)
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519 if ((k != i) && (k != j) && (done[k] != 1))
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521 tmp = tmp + distance[i][k];
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527 tmp = tmp / (noClus - 2);
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536 * @return DOCUMENT ME!
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538 public float findMinNJDistance()
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540 float min = 100000;
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542 for (int i = 0; i < (noseqs - 1); i++)
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544 for (int j = i + 1; j < noseqs; j++)
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546 if ((done[i] != 1) && (done[j] != 1))
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548 float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
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567 * @return DOCUMENT ME!
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569 public float findMinDistance()
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571 float min = 100000;
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573 for (int i = 0; i < (noseqs - 1); i++)
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575 for (int j = i + 1; j < noseqs; j++)
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577 if ((done[i] != 1) && (done[j] != 1))
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579 if (distance[i][j] < min)
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584 min = distance[i][j];
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596 * @return DOCUMENT ME!
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598 public float[][] findDistances()
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600 float[][] distance = new float[noseqs][noseqs];
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602 if (pwtype.equals("PID"))
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604 for (int i = 0; i < (noseqs - 1); i++)
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606 for (int j = i; j < noseqs; j++)
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610 distance[i][i] = 0;
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614 distance[i][j] = 100 -
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615 Comparison.PID(sequenceString[i], sequenceString[j]);
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617 distance[j][i] = distance[i][j];
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622 else if (pwtype.equals("BL"))
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625 int end = sequenceString[0].length();
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626 for (int i = 0; i < (noseqs - 1); i++)
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628 for (int j = i; j < noseqs; j++)
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632 for (int k = 0; k < end; k++)
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636 score += ResidueProperties.getBLOSUM62(
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637 sequenceString[i].substring(k, k + 1),
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638 sequenceString[j].substring(k, k + 1));
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640 catch (Exception ex)
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642 System.err.println("err creating BLOSUM62 tree");
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643 ex.printStackTrace();
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647 distance[i][j] = (float) score;
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649 if (score > maxscore)
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656 for (int i = 0; i < (noseqs - 1); i++)
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658 for (int j = i; j < noseqs; j++)
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660 distance[i][j] = (float) maxscore - distance[i][j];
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661 distance[j][i] = distance[i][j];
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665 /* else if (pwtype.equals("SW"))
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669 for (int i = 0; i < (noseqs - 1); i++)
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671 for (int j = i; j < noseqs; j++)
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673 AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
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674 as.calcScoreMatrix();
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675 as.traceAlignment();
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676 as.printAlignment(System.out);
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677 distance[i][j] = (float) as.maxscore;
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679 if (max < distance[i][j])
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681 max = distance[i][j];
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686 for (int i = 0; i < (noseqs - 1); i++)
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688 for (int j = i; j < noseqs; j++)
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690 distance[i][j] = max - distance[i][j];
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691 distance[j][i] = distance[i][j];
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702 public void makeLeaves()
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704 cluster = new Vector();
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706 for (int i = 0; i < noseqs; i++)
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708 SequenceNode sn = new SequenceNode();
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710 sn.setElement(sequence[i]);
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711 sn.setName(sequence[i].getName());
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712 node.addElement(sn);
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714 int[] value = new int[1];
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717 Cluster c = new Cluster(value);
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718 cluster.addElement(c);
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725 * @param node DOCUMENT ME!
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726 * @param leaves DOCUMENT ME!
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728 * @return DOCUMENT ME!
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730 public Vector findLeaves(SequenceNode node, Vector leaves)
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737 if ((node.left() == null) && (node.right() == null))
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739 leaves.addElement(node);
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745 findLeaves((SequenceNode) node.left(), leaves);
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746 findLeaves((SequenceNode) node.right(), leaves);
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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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762 found = _findLeaf(node, count);
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770 * @param node DOCUMENT ME!
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771 * @param count DOCUMENT ME!
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773 * @return DOCUMENT ME!
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775 public Object _findLeaf(SequenceNode node, int count)
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782 if (node.ycount == count)
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784 found = node.element();
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790 _findLeaf((SequenceNode) node.left(), count);
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791 _findLeaf((SequenceNode) node.right(), count);
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798 * printNode is mainly for debugging purposes.
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800 * @param node SequenceNode
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802 public void printNode(SequenceNode node)
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809 if ((node.left() == null) && (node.right() == null))
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811 System.out.println("Leaf = " +
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812 ((SequenceI) node.element()).getName());
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813 System.out.println("Dist " + ((SequenceNode) node).dist);
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814 System.out.println("Boot " + node.getBootstrap());
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818 System.out.println("Dist " + ((SequenceNode) node).dist);
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819 printNode((SequenceNode) node.left());
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820 printNode((SequenceNode) node.right());
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827 * @param node DOCUMENT ME!
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829 public void findMaxDist(SequenceNode node)
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836 if ((node.left() == null) && (node.right() == null))
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838 float dist = ((SequenceNode) node).dist;
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840 if (dist > maxDistValue)
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842 maxdist = (SequenceNode) node;
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843 maxDistValue = dist;
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848 findMaxDist((SequenceNode) node.left());
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849 findMaxDist((SequenceNode) node.right());
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856 * @return DOCUMENT ME!
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858 public Vector getGroups()
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866 * @return DOCUMENT ME!
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868 public float getMaxHeight()
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876 * @param node DOCUMENT ME!
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877 * @param threshold DOCUMENT ME!
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879 public void groupNodes(SequenceNode node, float threshold)
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886 if ((node.height / maxheight) > threshold)
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888 groups.addElement(node);
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892 groupNodes((SequenceNode) node.left(), threshold);
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893 groupNodes((SequenceNode) node.right(), threshold);
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900 * @param node DOCUMENT ME!
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902 * @return DOCUMENT ME!
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904 public float findHeight(SequenceNode node)
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911 if ((node.left() == null) && (node.right() == null))
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913 node.height = ((SequenceNode) node.parent()).height + node.dist;
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915 if (node.height > maxheight)
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917 return node.height;
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926 if (node.parent() != null)
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928 node.height = ((SequenceNode) node.parent()).height +
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934 node.height = (float) 0.0;
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937 maxheight = findHeight((SequenceNode) (node.left()));
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938 maxheight = findHeight((SequenceNode) (node.right()));
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947 * @return DOCUMENT ME!
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949 public SequenceNode reRoot()
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951 if (maxdist != null)
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955 float tmpdist = maxdist.dist;
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958 SequenceNode sn = new SequenceNode();
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959 sn.setParent(null);
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961 // New right hand of top
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962 SequenceNode snr = (SequenceNode) maxdist.parent();
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963 changeDirection(snr, maxdist);
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964 System.out.println("Printing reversed tree");
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966 snr.dist = tmpdist / 2;
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967 maxdist.dist = tmpdist / 2;
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970 maxdist.setParent(sn);
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973 sn.setLeft(maxdist);
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985 public String printOriginalSequenceData()
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987 StringBuffer sb = new StringBuffer();
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988 for(int i=0; i<sequenceString.length; i++)
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990 sb.append(new jalview.util.Format("%-" + 15 + "s").form(
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991 sequence[i].getName()));
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992 sb.append(" "+sequenceString[i]+"\n");
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994 return sb.toString();
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1000 * @param node DOCUMENT ME!
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1002 public void printN(SequenceNode node)
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1009 if ((node.left() != null) && (node.right() != null))
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1011 printN((SequenceNode) node.left());
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1012 printN((SequenceNode) node.right());
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1016 System.out.println(" name = " +
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1017 ((SequenceI) node.element()).getName());
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1020 System.out.println(" dist = " + ((SequenceNode) node).dist + " " +
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1021 ((SequenceNode) node).count + " " + ((SequenceNode) node).height);
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1027 * @param node DOCUMENT ME!
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1029 public void reCount(SequenceNode node)
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1038 * @param node DOCUMENT ME!
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1040 public void _reCount(SequenceNode node)
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1047 if ((node.left() != null) && (node.right() != null))
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1049 _reCount((SequenceNode) node.left());
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1050 _reCount((SequenceNode) node.right());
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1052 SequenceNode l = (SequenceNode) node.left();
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1053 SequenceNode r = (SequenceNode) node.right();
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1055 ((SequenceNode) node).count = l.count + r.count;
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1056 ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
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1060 ((SequenceNode) node).count = 1;
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1061 ((SequenceNode) node).ycount = ycount++;
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1068 * @param node DOCUMENT ME!
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1070 public void swapNodes(SequenceNode node)
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1077 SequenceNode tmp = (SequenceNode) node.left();
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1079 node.setLeft(node.right());
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1080 node.setRight(tmp);
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1086 * @param node DOCUMENT ME!
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1087 * @param dir DOCUMENT ME!
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1089 public void changeDirection(SequenceNode node, SequenceNode dir)
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1096 if (node.parent() != top)
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1098 changeDirection((SequenceNode) node.parent(), node);
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1100 SequenceNode tmp = (SequenceNode) node.parent();
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1102 if (dir == node.left())
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1104 node.setParent(dir);
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1105 node.setLeft(tmp);
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1107 else if (dir == node.right())
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1109 node.setParent(dir);
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1110 node.setRight(tmp);
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1115 if (dir == node.left())
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1117 node.setParent(node.left());
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1119 if (top.left() == node)
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1121 node.setRight(top.right());
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1125 node.setRight(top.left());
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1130 node.setParent(node.right());
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1132 if (top.left() == node)
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1134 node.setLeft(top.right());
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1138 node.setLeft(top.left());
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1148 * @return DOCUMENT ME!
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1150 public SequenceNode getMaxDist()
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1158 * @return DOCUMENT ME!
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1160 public SequenceNode getTopNode()
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1166 * @return true if tree has real distances
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1168 public boolean isHasDistances() {
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1169 return hasDistances;
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1174 * @return true if tree has real bootstrap values
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1176 public boolean isHasBootstrap() {
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1177 return hasBootstrap;
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1180 public boolean isHasRootDistance()
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1182 return hasRootDistance;
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1191 * @author $author$
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1192 * @version $Revision$
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1199 * Creates a new Cluster object.
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1201 * @param value DOCUMENT ME!
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1203 public Cluster(int[] value)
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1205 this.value = value;
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