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.datamodel;
23 import java.util.ArrayList;
24 import java.util.List;
27 public class HiddenSequences
30 * holds a list of hidden sequences associated with an alignment.
32 public SequenceI[] hiddenSequences;
37 * Constructor given a reference to an alignment (with no hidden sequences)
41 public HiddenSequences(AlignmentI al)
47 * Answers the number of hidden sequences
53 if (hiddenSequences == null)
58 for (SequenceI seq : hiddenSequences)
70 * Answers the length of the longest hidden sequence
76 if (hiddenSequences == null)
81 for (SequenceI seq : hiddenSequences)
83 if (seq != null && seq.getLength() > width)
85 width = seq.getLength();
93 * Call this method after a sequence is removed from the main alignment
95 public void adjustHeightSequenceDeleted(int seqIndex)
97 if (hiddenSequences == null)
102 int alHeight = alignment.getHeight();
104 SequenceI[] tmp = new SequenceI[alHeight + getSize()];
105 int deletionIndex = adjustForHiddenSeqs(seqIndex);
107 for (int i = 0; i < hiddenSequences.length; i++)
109 if (hiddenSequences[i] == null)
114 if (i > deletionIndex)
116 tmp[i - 1] = hiddenSequences[i];
120 tmp[i] = hiddenSequences[i];
124 hiddenSequences = tmp;
129 * Call this method after a sequence is added to the main alignment
131 public void adjustHeightSequenceAdded()
133 if (hiddenSequences == null)
138 int alHeight = alignment.getHeight();
140 SequenceI[] tmp = new SequenceI[alHeight + getSize()];
141 System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
142 hiddenSequences = tmp;
146 * Mark the specified sequence as hidden
150 public void hideSequence(SequenceI sequence)
152 if (hiddenSequences == null)
154 hiddenSequences = new SequenceI[alignment.getHeight()];
157 int absAlignmentIndex = alignment.findIndex(sequence);
158 int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
160 if (hiddenSequences[alignmentIndex] != null)
162 System.out.println("ERROR!!!!!!!!!!!");
165 hiddenSequences[alignmentIndex] = sequence;
167 alignment.deleteHiddenSequence(absAlignmentIndex);
170 public List<SequenceI> showAll(
171 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
173 List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
174 for (int i = 0; i < hiddenSequences.length; i++)
176 if (hiddenSequences[i] != null)
178 List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
179 for (SequenceI seq : tmp)
181 revealedSeqs.add(seq);
189 * Reveals (unhides) consecutive hidden sequences just above the given
190 * alignment index. The revealed sequences are selected (including their
191 * visible representative sequence if there was one and 'reveal' is being
194 * @param alignmentIndex
195 * @param hiddenRepSequences
196 * a map of representative sequences to the sequences they represent
199 public List<SequenceI> showSequence(int alignmentIndex,
200 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
202 List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
203 SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
204 if (repSequence != null && hiddenRepSequences != null
205 && hiddenRepSequences.containsKey(repSequence))
207 hiddenRepSequences.remove(repSequence);
208 revealedSeqs.add(repSequence);
211 int start = adjustForHiddenSeqs(alignmentIndex - 1);
212 int end = adjustForHiddenSeqs(alignmentIndex);
213 if (end >= hiddenSequences.length)
215 end = hiddenSequences.length - 1;
218 List<SequenceI> asequences;
219 synchronized (asequences = alignment.getSequences())
221 for (int index = end; index > start; index--)
223 SequenceI seq = hiddenSequences[index];
224 hiddenSequences[index] = null;
228 if (seq.getLength() > 0)
230 revealedSeqs.add(seq);
231 asequences.add(alignmentIndex, seq);
235 System.out.println(seq.getName()
236 + " has been deleted whilst hidden");
244 public SequenceI getHiddenSequence(int alignmentIndex)
246 return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
250 * Convert absolute alignment index to visible alignment index
252 * @param alignmentIndex
255 public int findIndexWithoutHiddenSeqs(int alignmentIndex)
257 if (hiddenSequences == null)
259 return alignmentIndex;
263 if (hiddenSequences.length <= alignmentIndex)
265 alignmentIndex = hiddenSequences.length - 1;
268 while (index <= alignmentIndex)
270 if (hiddenSequences[index] != null)
277 return (alignmentIndex - hiddenSeqs);
281 * Convert alignment index from visible alignment to absolute alignment
283 * @param alignmentIndex
286 public int adjustForHiddenSeqs(int alignmentIndex)
288 if (hiddenSequences == null)
290 return alignmentIndex;
293 int hSize = hiddenSequences.length;
294 while (index <= alignmentIndex && index < hSize)
296 if (hiddenSequences[index] != null)
304 return alignmentIndex;
308 * makes a copy of the alignment with hidden sequences included. Using the
309 * copy for anything other than simple output is not recommended. Note - this
310 * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
314 public AlignmentI getFullAlignment()
317 if (hiddenSequences == null)
319 seq = alignment.getSequencesArray();
323 int isize = hiddenSequences.length;
324 seq = new Sequence[isize];
327 for (int i = 0; i < hiddenSequences.length; i++)
329 if (hiddenSequences[i] != null)
331 seq[i] = hiddenSequences[i];
335 seq[i] = alignment.getSequenceAt(index);
340 Alignment fAlignmt = new Alignment(seq);
341 fAlignmt.annotations = alignment.getAlignmentAnnotation();
342 fAlignmt.alignmentProperties = alignment.getProperties();
343 fAlignmt.groups = alignment.getGroups();
344 fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
345 fAlignmt.setSeqrep(alignment.getSeqrep());
350 public boolean isHidden(SequenceI seq)
352 if (hiddenSequences != null)
354 for (int i = 0; i < hiddenSequences.length; i++)
356 if (hiddenSequences[i] != null && hiddenSequences[i] == seq)