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  1. Project Clover database Wed Nov 6 2024 14:47:21 GMT
  2. Package jalview.analysis

File AlignmentSorter.java

 

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36% of files have more coverage

Code metrics

144
239
17
1
903
548
100
0.42
14.06
17
5.88

Classes

Class Line # Actions
AlignmentSorter 55 239 100
0.552555.3%
 

Contributing tests

This file is covered by 1 test. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.analysis;
22   
23    import jalview.analysis.scoremodels.PIDModel;
24    import jalview.analysis.scoremodels.SimilarityParams;
25    import jalview.datamodel.AlignmentAnnotation;
26    import jalview.datamodel.AlignmentI;
27    import jalview.datamodel.AlignmentOrder;
28    import jalview.datamodel.BinaryNode;
29    import jalview.datamodel.SequenceFeature;
30    import jalview.datamodel.SequenceGroup;
31    import jalview.datamodel.SequenceI;
32    import jalview.datamodel.SequenceNode;
33    import jalview.util.QuickSort;
34   
35    import java.util.ArrayList;
36    import java.util.Collections;
37    import java.util.Iterator;
38    import java.util.List;
39   
40    /**
41    * Routines for manipulating the order of a multiple sequence alignment TODO:
42    * this class retains some global states concerning sort-order which should be
43    * made attributes for the caller's alignment visualization. TODO: refactor to
44    * allow a subset of selected sequences to be sorted within the context of a
45    * whole alignment. Sort method template is: SequenceI[] tobesorted, [ input
46    * data mapping to each tobesorted element to use ], Alignment context of
47    * tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie
48    * seuqence to be sorted w.r.t.]) sortinplace implies that the sorted vector
49    * resulting from applying the operation to tobesorted should be mapped back to
50    * the original positions in alignment. Otherwise, normal behaviour is to re
51    * order alignment so that tobesorted is sorted and grouped together starting
52    * from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
53    * becomes a,tb1,tb2,tb3,b,c)
54    */
 
55    public class AlignmentSorter
56    {
57    /*
58    * todo: refactor searches to follow a basic pattern: (search property, last
59    * search state, current sort direction)
60    */
61    static boolean sortIdAscending = true;
62   
63    static int lastGroupHash = 0;
64   
65    static boolean sortGroupAscending = true;
66   
67    static AlignmentOrder lastOrder = null;
68   
69    static boolean sortOrderAscending = true;
70   
71    static TreeModel lastTree = null;
72   
73    static boolean sortTreeAscending = true;
74   
75    /*
76    * last Annotation Label used for sort by Annotation score
77    */
78    private static String lastSortByAnnotation;
79   
80    /*
81    * string hash of last arguments to sortByFeature
82    * (sort order toggles if this is unchanged between sorts)
83    */
84    private static String sortByFeatureCriteria;
85   
86    private static boolean sortByFeatureAscending = true;
87   
88    private static boolean sortLengthAscending;
89   
90    /**
91    * Sorts sequences in the alignment by Percentage Identity with the given
92    * reference sequence, sorting the highest identity to the top
93    *
94    * @param align
95    * AlignmentI
96    * @param s
97    * SequenceI
98    * @param end
99    */
 
100  0 toggle public static void sortByPID(AlignmentI align, SequenceI s)
101    {
102  0 int nSeq = align.getHeight();
103   
104  0 float[] scores = new float[nSeq];
105  0 SequenceI[] seqs = new SequenceI[nSeq];
106  0 String refSeq = s.getSequenceAsString();
107   
108  0 SimilarityParams pidParams = new SimilarityParams(true, true, true,
109    true);
110  0 for (int i = 0; i < nSeq; i++)
111    {
112  0 scores[i] = (float) PIDModel.computePID(
113    align.getSequenceAt(i).getSequenceAsString(), refSeq,
114    pidParams);
115  0 seqs[i] = align.getSequenceAt(i);
116    }
117   
118  0 QuickSort.sort(scores, seqs);
119   
120  0 setReverseOrder(align, seqs);
121    }
122   
123    /**
124    * Reverse the order of the sort
125    *
126    * @param align
127    * DOCUMENT ME!
128    * @param seqs
129    * DOCUMENT ME!
130    */
 
131  2 toggle private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
132    {
133  2 int nSeq = seqs.length;
134   
135  2 int len = 0;
136   
137  2 if ((nSeq % 2) == 0)
138    {
139  0 len = nSeq / 2;
140    }
141    else
142    {
143  2 len = (nSeq + 1) / 2;
144    }
145   
146    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
147  2 List<SequenceI> asq = align.getSequences();
148  2 synchronized (asq)
149    {
150  36 for (int i = 0; i < len; i++)
151    {
152    // SequenceI tmp = seqs[i];
153  34 asq.set(i, seqs[nSeq - i - 1]);
154  34 asq.set(nSeq - i - 1, seqs[i]);
155    }
156    }
157    }
158   
159    /**
160    * Sets the Alignment object with the given sequences
161    *
162    * @param align
163    * Alignment object to be updated
164    * @param tmp
165    * sequences as a vector
166    */
 
167  3 toggle private static void setOrder(AlignmentI align, List<SequenceI> tmp)
168    {
169  3 setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
170    }
171   
172    /**
173    * Sets the Alignment object with the given sequences
174    *
175    * @param align
176    * DOCUMENT ME!
177    * @param seqs
178    * sequences as an array
179    */
 
180  9 toggle public static void setOrder(AlignmentI align, SequenceI[] seqs)
181    {
182    // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
183  9 List<SequenceI> algn = align.getSequences();
184  9 synchronized (algn)
185    {
186  9 List<SequenceI> tmp = new ArrayList<>();
187   
188  125 for (int i = 0; i < seqs.length; i++)
189    {
190  116 if (algn.contains(seqs[i]))
191    {
192  116 tmp.add(seqs[i]);
193    }
194    }
195   
196  9 algn.clear();
197    // User may have hidden seqs, then clicked undo or redo
198  125 for (int i = 0; i < tmp.size(); i++)
199    {
200  116 algn.add(tmp.get(i));
201    }
202    }
203    }
204   
205    /**
206    * Sorts by ID. Numbers are sorted before letters.
207    *
208    * @param align
209    * The alignment object to sort
210    */
 
211  0 toggle public static void sortByID(AlignmentI align)
212    {
213  0 int nSeq = align.getHeight();
214   
215  0 String[] ids = new String[nSeq];
216  0 SequenceI[] seqs = new SequenceI[nSeq];
217   
218  0 for (int i = 0; i < nSeq; i++)
219    {
220  0 ids[i] = align.getSequenceAt(i).getName();
221  0 seqs[i] = align.getSequenceAt(i);
222    }
223   
224  0 QuickSort.sort(ids, seqs);
225   
226  0 if (sortIdAscending)
227    {
228  0 setReverseOrder(align, seqs);
229    }
230    else
231    {
232  0 setOrder(align, seqs);
233    }
234   
235  0 sortIdAscending = !sortIdAscending;
236    }
237   
238    /**
239    * Sorts by sequence length
240    *
241    * @param align
242    * The alignment object to sort
243    */
 
244  0 toggle public static void sortByLength(AlignmentI align)
245    {
246  0 int nSeq = align.getHeight();
247   
248  0 float[] length = new float[nSeq];
249  0 SequenceI[] seqs = new SequenceI[nSeq];
250   
251  0 for (int i = 0; i < nSeq; i++)
252    {
253  0 seqs[i] = align.getSequenceAt(i);
254  0 length[i] = (seqs[i].getEnd() - seqs[i].getStart());
255    }
256   
257  0 QuickSort.sort(length, seqs);
258   
259  0 if (sortLengthAscending)
260    {
261  0 setReverseOrder(align, seqs);
262    }
263    else
264    {
265  0 setOrder(align, seqs);
266    }
267   
268  0 sortLengthAscending = !sortLengthAscending;
269    }
270   
271    /**
272    * Sorts the alignment by size of group. <br>
273    * Maintains the order of sequences in each group by order in given alignment
274    * object.
275    *
276    * @param align
277    * sorts the given alignment object by group
278    */
 
279  4 toggle public static void sortByGroup(AlignmentI align)
280    {
281    // MAINTAINS ORIGNAL SEQUENCE ORDER,
282    // ORDERS BY GROUP SIZE
283  4 List<SequenceGroup> groups = new ArrayList<>();
284   
285  4 if (groups.hashCode() != lastGroupHash)
286    {
287  1 sortGroupAscending = true;
288  1 lastGroupHash = groups.hashCode();
289    }
290    else
291    {
292  3 sortGroupAscending = !sortGroupAscending;
293    }
294   
295    // SORTS GROUPS BY SIZE
296    // ////////////////////
297  4 for (SequenceGroup sg : align.getGroups())
298    {
299  44 for (int j = 0; j < groups.size(); j++)
300    {
301  32 SequenceGroup sg2 = groups.get(j);
302   
303  32 if (sg.getSize() > sg2.getSize())
304    {
305  8 groups.add(j, sg);
306   
307  8 break;
308    }
309    }
310   
311  20 if (!groups.contains(sg))
312    {
313  12 groups.add(sg);
314    }
315    }
316   
317    // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
318    // /////////////////////////////////////////////
319  4 List<SequenceI> seqs = new ArrayList<>();
320   
321  24 for (int i = 0; i < groups.size(); i++)
322    {
323  20 SequenceGroup sg = groups.get(i);
324  20 SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
325   
326  152 for (int j = 0; j < orderedseqs.length; j++)
327    {
328  132 seqs.add(orderedseqs[j]);
329    }
330    }
331   
332  4 if (sortGroupAscending)
333    {
334  2 setOrder(align, seqs);
335    }
336    else
337    {
338  2 setReverseOrder(align,
339    vectorSubsetToArray(seqs, align.getSequences()));
340    }
341    }
342   
343    /**
344    * Select sequences in order from tmp that is present in mask, and any
345    * remaining sequences in mask not in tmp
346    *
347    * @param tmp
348    * thread safe collection of sequences
349    * @param mask
350    * thread safe collection of sequences
351    *
352    * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
353    */
 
354  5 toggle private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
355    List<SequenceI> mask)
356    {
357    // or?
358    // tmp2 = tmp.retainAll(mask);
359    // return tmp2.addAll(mask.removeAll(tmp2))
360   
361  5 ArrayList<SequenceI> seqs = new ArrayList<>();
362  5 int i, idx;
363  5 boolean[] tmask = new boolean[mask.size()];
364   
365  152 for (i = 0; i < mask.size(); i++)
366    {
367  147 tmask[i] = true;
368    }
369   
370  152 for (i = 0; i < tmp.size(); i++)
371    {
372  147 SequenceI sq = tmp.get(i);
373  147 idx = mask.indexOf(sq);
374  147 if (idx > -1 && tmask[idx])
375    {
376  147 tmask[idx] = false;
377  147 seqs.add(sq);
378    }
379    }
380   
381  152 for (i = 0; i < tmask.length; i++)
382    {
383  147 if (tmask[i])
384    {
385  0 seqs.add(mask.get(i));
386    }
387    }
388   
389  5 return seqs.toArray(new SequenceI[seqs.size()]);
390    }
391   
392    /**
393    * Sorts by a given AlignmentOrder object
394    *
395    * @param align
396    * Alignment to order
397    * @param order
398    * specified order for alignment
399    */
 
400  0 toggle public static void sortBy(AlignmentI align, AlignmentOrder order)
401    {
402    // Get an ordered vector of sequences which may also be present in align
403  0 List<SequenceI> tmp = order.getOrder();
404   
405  0 if (lastOrder == order)
406    {
407  0 sortOrderAscending = !sortOrderAscending;
408    }
409    else
410    {
411  0 sortOrderAscending = true;
412    }
413   
414  0 if (sortOrderAscending)
415    {
416  0 setOrder(align, tmp);
417    }
418    else
419    {
420  0 setReverseOrder(align,
421    vectorSubsetToArray(tmp, align.getSequences()));
422    }
423    }
424   
425    /**
426    * DOCUMENT ME!
427    *
428    * @param align
429    * alignment to order
430    * @param tree
431    * tree which has
432    *
433    * @return DOCUMENT ME!
434    */
 
435  1 toggle private static List<SequenceI> getOrderByTree(AlignmentI align,
436    TreeModel tree)
437    {
438  1 int nSeq = align.getHeight();
439   
440  1 List<SequenceI> tmp = new ArrayList<>();
441   
442  1 tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
443   
444  1 if (tmp.size() != nSeq)
445    {
446    // TODO: JBPNote - decide if this is always an error
447    // (eg. not when a tree is associated to another alignment which has more
448    // sequences)
449  0 if (tmp.size() != nSeq)
450    {
451  0 addStrays(align, tmp);
452    }
453   
454  0 if (tmp.size() != nSeq)
455    {
456  0 jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size()
457    + " != nseq=" + nSeq
458    + " in getOrderByTree - tree contains sequences not in alignment");
459    }
460    }
461   
462  1 return tmp;
463    }
464   
465    /**
466    * Sorts the alignment by a given tree
467    *
468    * @param align
469    * alignment to order
470    * @param tree
471    * tree which has
472    */
 
473  1 toggle public static void sortByTree(AlignmentI align, TreeModel tree)
474    {
475  1 List<SequenceI> tmp = getOrderByTree(align, tree);
476   
477    // tmp should properly permute align with tree.
478  1 if (lastTree != tree)
479    {
480  1 sortTreeAscending = true;
481  1 lastTree = tree;
482    }
483    else
484    {
485  0 sortTreeAscending = !sortTreeAscending;
486    }
487   
488  1 if (sortTreeAscending)
489    {
490  1 setOrder(align, tmp);
491    }
492    else
493    {
494  0 setReverseOrder(align,
495    vectorSubsetToArray(tmp, align.getSequences()));
496    }
497    }
498   
499    /**
500    * DOCUMENT ME!
501    *
502    * @param align
503    * DOCUMENT ME!
504    * @param tmp
505    * DOCUMENT ME!
506    */
 
507  0 toggle private static void addStrays(AlignmentI align, List<SequenceI> tmp)
508    {
509  0 int nSeq = align.getHeight();
510   
511  0 for (int i = 0; i < nSeq; i++)
512    {
513  0 if (!tmp.contains(align.getSequenceAt(i)))
514    {
515  0 tmp.add(align.getSequenceAt(i));
516    }
517    }
518   
519  0 if (nSeq != tmp.size())
520    {
521  0 System.err
522    .println("ERROR: Size still not right even after addStrays");
523    }
524    }
525   
526    /**
527    * DOCUMENT ME!
528    *
529    * @param node
530    * DOCUMENT ME!
531    * @param tmp
532    * DOCUMENT ME!
533    * @param seqset
534    * DOCUMENT ME!
535    *
536    * @return DOCUMENT ME!
537    */
 
538  29 toggle private static List<SequenceI> _sortByTree(BinaryNode node,
539    List<SequenceI> tmp, List<SequenceI> seqset)
540    {
541  29 if (node == null)
542    {
543  0 return tmp;
544    }
545   
546  29 BinaryNode left = (BinaryNode) node.left();
547  29 BinaryNode right = (BinaryNode) node.right();
548   
549  29 if ((left == null) && (right == null))
550    {
551  15 if (!(node instanceof SequenceNode
552    && ((SequenceNode) node).isPlaceholder())
553    && (node.element() != null))
554    {
555  15 if (node.element() instanceof SequenceI)
556    {
557  15 if (!tmp.contains(node.element())) // && (seqset==null ||
558    // seqset.size()==0 ||
559    // seqset.contains(tmp)))
560    {
561  15 tmp.add((SequenceI) node.element());
562    }
563    }
564    }
565   
566  15 return tmp;
567    }
568    else
569    {
570  14 _sortByTree(left, tmp, seqset);
571  14 _sortByTree(right, tmp, seqset);
572    }
573   
574  14 return tmp;
575    }
576   
577    // Ordering Objects
578    // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
579    // appropriate order
580    //
581   
582    /**
583    * recover the order of sequences given by the safe numbering scheme introducd
584    * SeqsetUtils.uniquify.
585    */
 
586  0 toggle public static void recoverOrder(SequenceI[] alignment)
587    {
588  0 float[] ids = new float[alignment.length];
589   
590  0 for (int i = 0; i < alignment.length; i++)
591    {
592  0 ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
593    .floatValue();
594    }
595   
596  0 jalview.util.QuickSort.sort(ids, alignment);
597    }
598   
599    /**
600    * Sort sequence in order of increasing score attribute for annotation with a
601    * particular scoreLabel. Or reverse if same label was used previously
602    *
603    * @param scoreLabel
604    * exact label for sequence associated AlignmentAnnotation scores to
605    * use for sorting.
606    * @param alignment
607    * sequences to be sorted
608    */
 
609  0 toggle public static void sortByAnnotationScore(String scoreLabel,
610    AlignmentI alignment)
611    {
612  0 SequenceI[] seqs = alignment.getSequencesArray();
613  0 boolean[] hasScore = new boolean[seqs.length]; // per sequence score
614    // presence
615  0 int hasScores = 0; // number of scores present on set
616  0 double[] scores = new double[seqs.length];
617  0 double min = 0, max = 0;
618  0 for (int i = 0; i < seqs.length; i++)
619    {
620  0 AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
621  0 if (scoreAnn != null)
622    {
623  0 hasScores++;
624  0 hasScore[i] = true;
625  0 scores[i] = scoreAnn[0].getScore(); // take the first instance of this
626    // score.
627  0 if (hasScores == 1)
628    {
629  0 max = min = scores[i];
630    }
631    else
632    {
633  0 if (max < scores[i])
634    {
635  0 max = scores[i];
636    }
637  0 if (min > scores[i])
638    {
639  0 min = scores[i];
640    }
641    }
642    }
643    else
644    {
645  0 hasScore[i] = false;
646    }
647    }
648  0 if (hasScores == 0)
649    {
650  0 return; // do nothing - no scores present to sort by.
651    }
652  0 if (hasScores < seqs.length)
653    {
654  0 for (int i = 0; i < seqs.length; i++)
655    {
656  0 if (!hasScore[i])
657    {
658  0 scores[i] = (max + i + 1.0);
659    }
660    }
661    }
662   
663  0 jalview.util.QuickSort.sort(scores, seqs);
664  0 if (lastSortByAnnotation != scoreLabel)
665    {
666  0 lastSortByAnnotation = scoreLabel;
667  0 setOrder(alignment, seqs);
668    }
669    else
670    {
671  0 setReverseOrder(alignment, seqs);
672    }
673    }
674   
675    /**
676    * types of feature ordering: Sort by score : average score - or total score -
677    * over all features in region Sort by feature label text: (or if null -
678    * feature type text) - numerical or alphabetical Sort by feature density:
679    * based on counts - ignoring individual text or scores for each feature
680    */
681    public static String FEATURE_SCORE = "average_score";
682   
683    public static String FEATURE_LABEL = "text";
684   
685    public static String FEATURE_DENSITY = "density";
686   
687    /**
688    * Sort sequences by feature score or density, optionally restricted by
689    * feature types, feature groups, or alignment start/end positions.
690    * <p>
691    * If the sort is repeated for the same combination of types and groups, sort
692    * order is reversed.
693    *
694    * @param featureTypes
695    * a list of feature types to include (or null for all)
696    * @param groups
697    * a list of feature groups to include (or null for all)
698    * @param startCol
699    * start column position to include (base zero)
700    * @param endCol
701    * end column position to include (base zero)
702    * @param alignment
703    * the alignment to be sorted
704    * @param method
705    * either "average_score" or "density" ("text" not yet implemented)
706    */
 
707  6 toggle public static void sortByFeature(List<String> featureTypes,
708    List<String> groups, final int startCol, final int endCol,
709    AlignmentI alignment, String method)
710    {
711  6 if (method != FEATURE_SCORE && method != FEATURE_LABEL
712    && method != FEATURE_DENSITY)
713    {
714  0 String msg = String.format(
715    "Implementation Error - sortByFeature method must be either '%s' or '%s'",
716    FEATURE_SCORE, FEATURE_DENSITY);
717  0 jalview.bin.Console.errPrintln(msg);
718  0 return;
719    }
720   
721  6 flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol,
722    endCol);
723   
724  6 SequenceI[] seqs = alignment.getSequencesArray();
725   
726  6 boolean[] hasScore = new boolean[seqs.length]; // per sequence score
727    // presence
728  6 int hasScores = 0; // number of scores present on set
729  6 double[] scores = new double[seqs.length];
730  6 int[] seqScores = new int[seqs.length];
731  6 Object[][] feats = new Object[seqs.length][];
732  6 double min = 0d;
733  6 double max = 0d;
734   
735  30 for (int i = 0; i < seqs.length; i++)
736    {
737    /*
738    * get sequence residues overlapping column region
739    * and features for residue positions and specified types
740    */
741  24 String[] types = featureTypes == null ? null
742    : featureTypes.toArray(new String[featureTypes.size()]);
743  24 List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
744    endCol + 1, types);
745   
746  24 seqScores[i] = 0;
747  24 scores[i] = 0.0;
748   
749  24 Iterator<SequenceFeature> it = sfs.listIterator();
750  52 while (it.hasNext())
751    {
752  28 SequenceFeature sf = it.next();
753   
754    /*
755    * accept all features with null or empty group, otherwise
756    * check group is one of the currently visible groups
757    */
758  28 String featureGroup = sf.getFeatureGroup();
759  28 if (groups != null && featureGroup != null
760    && !"".equals(featureGroup)
761    && !groups.contains(featureGroup))
762    {
763  1 it.remove();
764    }
765    else
766    {
767  27 float score = sf.getScore();
768  27 if (FEATURE_SCORE.equals(method) && !Float.isNaN(score))
769    {
770  21 if (seqScores[i] == 0)
771    {
772  15 hasScores++;
773    }
774  21 seqScores[i]++;
775  21 hasScore[i] = true;
776  21 scores[i] += score;
777    // take the first instance of this score // ??
778    }
779    }
780    }
781   
782  24 feats[i] = sfs.toArray(new SequenceFeature[sfs.size()]);
783  24 if (!sfs.isEmpty())
784    {
785  18 if (method == FEATURE_LABEL)
786    {
787    // order the labels by alphabet (not yet implemented)
788  0 String[] labs = new String[sfs.size()];
789  0 for (int l = 0; l < sfs.size(); l++)
790    {
791  0 SequenceFeature sf = sfs.get(l);
792  0 String description = sf.getDescription();
793  0 labs[l] = (description != null ? description : sf.getType());
794    }
795  0 QuickSort.sort(labs, feats[i]);
796    }
797    }
798  24 if (hasScore[i])
799    {
800    // compute average score
801  15 scores[i] /= seqScores[i];
802    // update the score bounds.
803  15 if (hasScores == 1)
804    {
805  5 min = scores[i];
806  5 max = min;
807    }
808    else
809    {
810  10 max = Math.max(max, scores[i]);
811  10 min = Math.min(min, scores[i]);
812    }
813    }
814    }
815   
816  6 if (FEATURE_SCORE.equals(method))
817    {
818  6 if (hasScores == 0)
819    {
820  1 return; // do nothing - no scores present to sort by.
821    }
822    // pad score matrix
823  5 if (hasScores < seqs.length)
824    {
825  25 for (int i = 0; i < seqs.length; i++)
826    {
827  20 if (!hasScore[i])
828    {
829  5 scores[i] = (max + 1 + i);
830    }
831    else
832    {
833    // int nf = (feats[i] == null) ? 0
834    // : ((SequenceFeature[]) feats[i]).length;
835    // // jalview.bin.Console.errPrintln("Sorting on Score: seq " +
836    // seqs[i].getName()
837    // + " Feats: " + nf + " Score : " + scores[i]);
838    }
839    }
840    }
841  5 QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
842    }
843  0 else if (FEATURE_DENSITY.equals(method))
844    {
845  0 for (int i = 0; i < seqs.length; i++)
846    {
847  0 int featureCount = feats[i] == null ? 0
848    : ((SequenceFeature[]) feats[i]).length;
849  0 scores[i] = featureCount;
850    // jalview.bin.Console.errPrintln("Sorting on Density: seq
851    // "+seqs[i].getName()+
852    // " Feats: "+featureCount+" Score : "+scores[i]);
853    }
854  0 QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
855    }
856   
857  5 setOrder(alignment, seqs);
858    }
859   
860    /**
861    * Builds a string hash of criteria for sorting, and if unchanged from last
862    * time, reverse the sort order
863    *
864    * @param method
865    * @param featureTypes
866    * @param groups
867    * @param startCol
868    * @param endCol
869    */
 
870  6 toggle protected static void flipFeatureSortIfUnchanged(String method,
871    List<String> featureTypes, List<String> groups,
872    final int startCol, final int endCol)
873    {
874  6 StringBuilder sb = new StringBuilder(64);
875  6 sb.append(startCol).append(method).append(endCol);
876  6 if (featureTypes != null)
877    {
878  2 Collections.sort(featureTypes);
879  2 sb.append(featureTypes.toString());
880    }
881  6 if (groups != null)
882    {
883  1 Collections.sort(groups);
884  1 sb.append(groups.toString());
885    }
886  6 String scoreCriteria = sb.toString();
887   
888    /*
889    * if resorting on the same criteria, toggle sort order
890    */
891  6 if (sortByFeatureCriteria == null
892    || !scoreCriteria.equals(sortByFeatureCriteria))
893    {
894  4 sortByFeatureAscending = true;
895    }
896    else
897    {
898  2 sortByFeatureAscending = !sortByFeatureAscending;
899    }
900  6 sortByFeatureCriteria = scoreCriteria;
901    }
902   
903    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 6 2024 14:54:51 GMT using coverage data from Wed Nov 6 2024 14:54:40 GMT.
  • OpenClover is free and open-source software.