2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.analysis;
23 import java.util.Locale;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.SequenceI;
29 import java.util.Arrays;
30 import java.util.Comparator;
31 import java.util.HashMap;
35 * A helper class to sort all annotations associated with an alignment in
41 public class AnnotationSorter
45 * enum for annotation sort options. The text description is used in the
46 * Preferences drop-down options. The enum name is saved in the preferences
52 public enum SequenceAnnotationOrder
54 // Text descriptions surface in the Preferences Sort by... options
55 SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"),
58 private String description;
60 private SequenceAnnotationOrder(String s)
66 public String toString()
71 public static SequenceAnnotationOrder forDescription(String d)
73 for (SequenceAnnotationOrder order : values())
75 if (order.toString().equals(d))
84 // the alignment with respect to which annotations are sorted
85 private final AlignmentI alignment;
87 // user preference for placement of non-sequence annotations
88 private boolean showAutocalcAbove;
90 // working map of sequence index in alignment
91 private final Map<SequenceI, Integer> sequenceIndices = new HashMap<SequenceI, Integer>();
94 * Constructor given an alignment and the location (top or bottom) of
95 * Consensus and similar.
98 * @param showAutocalculatedAbove
100 public AnnotationSorter(AlignmentI alignmentI,
101 boolean showAutocalculatedAbove)
103 this.alignment = alignmentI;
104 this.showAutocalcAbove = showAutocalculatedAbove;
108 * Default comparator sorts as follows by annotation type within sequence
111 * <li>annotations with a reference to a sequence in the alignment are sorted
112 * on sequence ordering</li>
113 * <li>other annotations go 'at the end', with their mutual order
115 * <li>within the same sequence ref, sort by label (non-case-sensitive)</li>
118 private final Comparator<? super AlignmentAnnotation> bySequenceAndLabel = new Comparator<AlignmentAnnotation>()
121 public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
123 if (o1 == null && o2 == null)
136 // TODO how to treat sequence-related autocalculated annotation
137 boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
138 boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
140 * Ignore label (keep existing ordering) for
141 * Conservation/Quality/Consensus etc
143 if (o1auto && o2auto)
149 * Sort autocalculated before or after sequence-related.
153 return showAutocalcAbove ? -1 : 1;
157 return showAutocalcAbove ? 1 : -1;
159 int computedOrder = compareSequences(o1, o2);
160 if (computedOrder==0) {
161 computedOrder = compareLabels(o1, o2);
163 if (computedOrder==0)
165 computedOrder = compareDescriptions(o1,o2);
167 return computedOrder;
171 public String toString()
173 return "Sort by sequence and label";
178 * This comparator sorts as follows by sequence order within annotation type
180 * <li>annotations with a reference to a sequence in the alignment are sorted
181 * on label (non-case-sensitive)</li>
182 * <li>other annotations go 'at the end', with their mutual order
184 * <li>within the same label, sort by order of the related sequences</li>
187 private final Comparator<? super AlignmentAnnotation> byLabelAndSequence = new Comparator<AlignmentAnnotation>()
190 public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
192 if (o1 == null && o2 == null)
205 // TODO how to treat sequence-related autocalculated annotation
206 boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
207 boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
209 * Ignore label (keep existing ordering) for
210 * Conservation/Quality/Consensus etc
212 if (o1auto && o2auto)
218 * Sort autocalculated before or after sequence-related.
222 return showAutocalcAbove ? -1 : 1;
226 return showAutocalcAbove ? 1 : -1;
228 int labelOrder = compareLabels(o1, o2);
229 return labelOrder == 0 ? compareSequences(o1, o2) : labelOrder;
233 public String toString()
235 return "Sort by label and sequence";
240 * noSort leaves sort order unchanged, within sequence- and autocalculated
241 * annotations, but may switch the ordering of these groups. Note this is
242 * guaranteed (at least in Java 7) as Arrays.sort() is guaranteed to be
243 * 'stable' (not change ordering of equal items).
245 private Comparator<? super AlignmentAnnotation> noSort = new Comparator<AlignmentAnnotation>()
248 public int compare(AlignmentAnnotation o1, AlignmentAnnotation o2)
250 // TODO how to treat sequence-related autocalculated annotation
251 boolean o1auto = o1.autoCalculated && o1.sequenceRef == null;
252 boolean o2auto = o2.autoCalculated && o2.sequenceRef == null;
253 // TODO skip this test to allow customised ordering of all annotations
254 // - needs a third option: place autocalculated first / last / none
255 if (o1 != null && o2 != null)
257 if (o1auto && !o2auto)
259 return showAutocalcAbove ? -1 : 1;
261 if (!o1auto && o2auto)
263 return showAutocalcAbove ? 1 : -1;
270 public String toString()
277 * Sort by the specified ordering of sequence-specific annotations.
279 * @param alignmentAnnotations
282 public void sort(AlignmentAnnotation[] alignmentAnnotations,
283 SequenceAnnotationOrder order)
285 if (alignmentAnnotations == null)
289 // cache 'alignment sequence position' for the annotations
290 saveSequenceIndices(alignmentAnnotations);
292 Comparator<? super AlignmentAnnotation> comparator = getComparator(
295 if (alignmentAnnotations != null)
297 synchronized (alignmentAnnotations)
299 Arrays.sort(alignmentAnnotations, comparator);
305 * Calculate and save in a temporary map the position of each annotation's
306 * sequence (if it has one) in the alignment. Faster to do this once than for
307 * every annotation comparison.
309 * @param alignmentAnnotations
311 private void saveSequenceIndices(
312 AlignmentAnnotation[] alignmentAnnotations)
314 sequenceIndices.clear();
315 for (AlignmentAnnotation ann : alignmentAnnotations)
317 SequenceI seq = ann.sequenceRef;
320 int index = AlignmentUtils.getSequenceIndex(alignment, seq);
321 sequenceIndices.put(seq, index);
327 * Get the comparator for the specified sort order.
332 private Comparator<? super AlignmentAnnotation> getComparator(
333 SequenceAnnotationOrder order)
343 case SEQUENCE_AND_LABEL:
344 return this.bySequenceAndLabel;
345 case LABEL_AND_SEQUENCE:
346 return this.byLabelAndSequence;
348 throw new UnsupportedOperationException(order.toString());
353 * Non-case-sensitive comparison of annotation labels. Returns zero if either
360 private int compareLabels(AlignmentAnnotation o1, AlignmentAnnotation o2)
362 if (o1 == null || o2 == null)
366 String label1 = o1.label;
367 String label2 = o2.label;
368 return compareString(label1,label2);
372 * Non-case-sensitive comparison of annotation descriptions. Returns zero if either
379 private int compareDescriptions(AlignmentAnnotation o1, AlignmentAnnotation o2)
381 if (o1 == null || o2 == null)
385 String label1 = o1.description;
386 String label2 = o2.description;
387 return compareString(label1,label2);
389 private int compareString(String label1, String label2)
391 if (label1 == null && label2 == null)
403 return label1.toUpperCase(Locale.ROOT)
404 .compareTo(label2.toUpperCase(Locale.ROOT));
408 * Comparison based on position of associated sequence (if any) in the
409 * alignment. Returns zero if either argument is null.
415 private int compareSequences(AlignmentAnnotation o1,
416 AlignmentAnnotation o2)
418 SequenceI seq1 = o1.sequenceRef;
419 SequenceI seq2 = o2.sequenceRef;
420 if (seq1 == null && seq2 == null)
425 * Sort non-sequence-related before or after sequence-related.
429 return showAutocalcAbove ? -1 : 1;
433 return showAutocalcAbove ? 1 : -1;
435 // get sequence index - but note -1 means 'at end' so needs special handling
436 int index1 = sequenceIndices.get(seq1);
437 int index2 = sequenceIndices.get(seq2);
438 if (index1 == index2)
450 return Integer.compare(index1, index2);