2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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23 import jalview.datamodel.*;
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24 import jalview.util.*;
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26 /** Data structure to hold and manipulate a multiple sequence alignment
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28 public class AlignmentSorter
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30 static boolean sortIdAscending = true;
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31 static int lastGroupHash = 0;
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32 static boolean sortGroupAscending = true;
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33 static AlignmentOrder lastOrder = null;
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34 static boolean sortOrderAscending = true;
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35 static NJTree lastTree = null;
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36 static boolean sortTreeAscending = true;
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39 * Sort by Percentage Identity
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41 * @param align AlignmentI
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42 * @param s SequenceI
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44 public static void sortByPID(AlignmentI align, SequenceI s)
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46 int nSeq = align.getHeight();
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48 float[] scores = new float[nSeq];
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49 SequenceI[] seqs = new SequenceI[nSeq];
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51 for (int i = 0; i < nSeq; i++)
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53 scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
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54 s.getSequenceAsString());
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55 seqs[i] = align.getSequenceAt(i);
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58 QuickSort.sort(scores, 0, scores.length - 1, seqs);
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60 setReverseOrder(align, seqs);
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64 * Reverse the order of the sort
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66 * @param align DOCUMENT ME!
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67 * @param seqs DOCUMENT ME!
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69 private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
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71 int nSeq = seqs.length;
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75 if ( (nSeq % 2) == 0)
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81 len = (nSeq + 1) / 2;
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84 // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
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85 for (int i = 0; i < len; i++)
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87 //SequenceI tmp = seqs[i];
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88 align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
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89 align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
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94 * Sets the Alignment object with the given sequences
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96 * @param align Alignment object to be updated
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97 * @param tmp sequences as a vector
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99 private static void setOrder(AlignmentI align, Vector tmp)
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101 setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
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105 * Sets the Alignment object with the given sequences
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107 * @param align DOCUMENT ME!
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108 * @param seqs sequences as an array
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110 public static void setOrder(AlignmentI align, SequenceI[] seqs)
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112 // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
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113 Vector algn = align.getSequences();
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114 Vector tmp = new Vector();
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116 for (int i = 0; i < seqs.length; i++)
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118 if (algn.contains(seqs[i]))
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120 tmp.addElement(seqs[i]);
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124 algn.removeAllElements();
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125 //User may have hidden seqs, then clicked undo or redo
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126 for (int i = 0; i < tmp.size(); i++)
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128 algn.addElement(tmp.elementAt(i));
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134 * Sorts by ID. Numbers are sorted before letters.
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136 * @param align The alignment object to sort
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138 public static void sortByID(AlignmentI align)
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140 int nSeq = align.getHeight();
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142 String[] ids = new String[nSeq];
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143 SequenceI[] seqs = new SequenceI[nSeq];
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145 for (int i = 0; i < nSeq; i++)
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147 ids[i] = align.getSequenceAt(i).getName();
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148 seqs[i] = align.getSequenceAt(i);
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151 QuickSort.sort(ids, seqs);
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153 if (sortIdAscending)
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155 setReverseOrder(align, seqs);
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159 setOrder(align, seqs);
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162 sortIdAscending = !sortIdAscending;
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166 * Sorts the alignment by size of group.
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167 * <br>Maintains the order of sequences in each group
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168 * by order in given alignment object.
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170 * @param align sorts the given alignment object by group
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172 public static void sortByGroup(AlignmentI align)
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174 //MAINTAINS ORIGNAL SEQUENCE ORDER,
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175 //ORDERS BY GROUP SIZE
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176 Vector groups = new Vector();
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178 if (groups.hashCode() != lastGroupHash)
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180 sortGroupAscending = true;
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181 lastGroupHash = groups.hashCode();
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185 sortGroupAscending = !sortGroupAscending;
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188 //SORTS GROUPS BY SIZE
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189 //////////////////////
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190 for (int i = 0; i < align.getGroups().size(); i++)
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192 SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
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194 for (int j = 0; j < groups.size(); j++)
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196 SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
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198 if (sg.getSize() > sg2.getSize())
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200 groups.insertElementAt(sg, j);
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206 if (!groups.contains(sg))
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208 groups.addElement(sg);
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212 //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
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213 ///////////////////////////////////////////////
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214 Vector seqs = new Vector();
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216 for (int i = 0; i < groups.size(); i++)
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218 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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219 SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
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221 for (int j = 0; j < orderedseqs.length; j++)
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223 seqs.addElement(orderedseqs[j]);
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227 if (sortGroupAscending)
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229 setOrder(align, seqs);
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233 setReverseOrder(align,
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234 vectorSubsetToArray(seqs, align.getSequences()));
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239 * Converts Vector to array.
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240 * java 1.18 does not have Vector.toArray()
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242 * @param tmp Vector of SequenceI objects
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244 * @return array of Sequence[]
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246 private static SequenceI[] vectorToArray(Vector tmp)
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248 SequenceI[] seqs = new SequenceI[tmp.size()];
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250 for (int i = 0; i < tmp.size(); i++)
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252 seqs[i] = (SequenceI) tmp.elementAt(i);
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261 * @param tmp DOCUMENT ME!
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262 * @param mask DOCUMENT ME!
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264 * @return DOCUMENT ME!
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266 private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
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268 Vector seqs = new Vector();
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270 boolean[] tmask = new boolean[mask.size()];
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272 for (i = 0; i < mask.size(); i++)
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277 for (i = 0; i < tmp.size(); i++)
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279 Object sq = tmp.elementAt(i);
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281 if (mask.contains(sq) && tmask[mask.indexOf(sq)])
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283 tmask[mask.indexOf(sq)] = false;
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284 seqs.addElement(sq);
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288 for (i = 0; i < tmask.length; i++)
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292 seqs.addElement(mask.elementAt(i));
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296 return vectorToArray(seqs);
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300 * Sorts by a given AlignmentOrder object
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302 * @param align Alignment to order
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303 * @param order specified order for alignment
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305 public static void sortBy(AlignmentI align, AlignmentOrder order)
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307 // Get an ordered vector of sequences which may also be present in align
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308 Vector tmp = order.getOrder();
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310 if (lastOrder == order)
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312 sortOrderAscending = !sortOrderAscending;
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316 sortOrderAscending = true;
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319 if (sortOrderAscending)
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321 setOrder(align, tmp);
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325 setReverseOrder(align,
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326 vectorSubsetToArray(tmp, align.getSequences()));
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333 * @param align alignment to order
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334 * @param tree tree which has
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336 * @return DOCUMENT ME!
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338 private static Vector getOrderByTree(AlignmentI align, NJTree tree)
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340 int nSeq = align.getHeight();
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342 Vector tmp = new Vector();
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344 tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
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346 if (tmp.size() != nSeq)
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348 // TODO: JBPNote - decide if this is always an error
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349 // (eg. not when a tree is associated to another alignment which has more
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351 if (tmp.size() < nSeq)
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353 addStrays(align, tmp);
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356 if (tmp.size() != nSeq)
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358 System.err.println("ERROR: tmp.size()=" + tmp.size() +
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359 " != nseq=" + nSeq + " in getOrderByTree");
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367 * Sorts the alignment by a given tree
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369 * @param align alignment to order
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370 * @param tree tree which has
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372 public static void sortByTree(AlignmentI align, NJTree tree)
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374 Vector tmp = getOrderByTree(align, tree);
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376 // tmp should properly permute align with tree.
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377 if (lastTree != tree)
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379 sortTreeAscending = true;
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384 sortTreeAscending = !sortTreeAscending;
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387 if (sortTreeAscending)
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389 setOrder(align, tmp);
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393 setReverseOrder(align,
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394 vectorSubsetToArray(tmp, align.getSequences()));
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401 * @param align DOCUMENT ME!
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402 * @param seqs DOCUMENT ME!
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404 private static void addStrays(AlignmentI align, Vector seqs)
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406 int nSeq = align.getHeight();
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408 for (int i = 0; i < nSeq; i++)
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410 if (!seqs.contains(align.getSequenceAt(i)))
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412 seqs.addElement(align.getSequenceAt(i));
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416 if (nSeq != seqs.size())
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418 System.err.println(
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419 "ERROR: Size still not right even after addStrays");
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426 * @param node DOCUMENT ME!
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427 * @param tmp DOCUMENT ME!
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428 * @param seqset DOCUMENT ME!
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430 * @return DOCUMENT ME!
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432 private static Vector _sortByTree(SequenceNode node, Vector tmp,
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440 SequenceNode left = (SequenceNode) node.left();
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441 SequenceNode right = (SequenceNode) node.right();
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443 if ( (left == null) && (right == null))
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445 if (!node.isPlaceholder() && (node.element() != null))
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447 if (node.element() instanceof SequenceI)
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449 if (!tmp.contains(node.element()))
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451 tmp.addElement( (SequenceI) node.element());
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460 _sortByTree(left, tmp, seqset);
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461 _sortByTree(right, tmp, seqset);
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467 // Ordering Objects
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468 // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
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472 * recover the order of sequences given by the safe numbering scheme introducd
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473 * SeqsetUtils.uniquify.
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475 public static void recoverOrder(SequenceI[] alignment)
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477 float[] ids = new float[alignment.length];
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479 for (int i = 0; i < alignment.length; i++)
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481 ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
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484 jalview.util.QuickSort.sort(ids, alignment);
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