2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.datamodel;
23 public class HiddenSequences
26 * holds a list of hidden sequences associated with an alignment.
28 public SequenceI[] hiddenSequences;
31 public HiddenSequences(AlignmentI al)
38 if (hiddenSequences == null)
43 for (int i = 0; i < hiddenSequences.length; i++)
45 if (hiddenSequences[i] != null)
57 for (int i = 0; i < hiddenSequences.length; i++)
59 if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
61 width = hiddenSequences[i].getLength();
69 * Call this method if sequences are removed from the
72 public void adjustHeightSequenceDeleted(int seqIndex)
74 if (hiddenSequences == null)
79 int alHeight = alignment.getHeight();
81 SequenceI[] tmp = new SequenceI[alHeight + getSize()];
82 int deletionIndex = adjustForHiddenSeqs(seqIndex);
84 for (int i = 0; i < hiddenSequences.length; i++)
86 if (hiddenSequences[i] == null)
91 if (i > deletionIndex)
93 tmp[i - 1] = hiddenSequences[i];
97 tmp[i] = hiddenSequences[i];
101 hiddenSequences = tmp;
106 * Call this method if sequences are added to or removed from the
109 public void adjustHeightSequenceAdded()
111 if (hiddenSequences == null)
116 int alHeight = alignment.getHeight();
118 SequenceI[] tmp = new SequenceI[alHeight + getSize()];
119 System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
120 hiddenSequences = tmp;
123 public void hideSequence(SequenceI sequence)
125 if (hiddenSequences == null)
127 hiddenSequences = new SequenceI[alignment.getHeight()];
130 int alignmentIndex = alignment.findIndex(sequence);
131 alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
133 if (hiddenSequences[alignmentIndex] != null)
135 System.out.println("ERROR!!!!!!!!!!!");
138 hiddenSequences[alignmentIndex] = sequence;
140 alignment.deleteSequence(sequence);
143 public Vector showAll(Hashtable hiddenReps)
145 Vector revealedSeqs = new Vector();
146 for (int i = 0; i < hiddenSequences.length; i++)
148 if (hiddenSequences[i] != null)
150 Vector tmp = showSequence(i, hiddenReps);
151 for (int t = 0; t < tmp.size(); t++)
153 revealedSeqs.addElement(tmp.elementAt(t));
160 public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
162 Vector revealedSeqs = new Vector();
163 SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
164 if (repSequence != null &&
166 && hiddenReps.containsKey(repSequence))
168 hiddenReps.remove(repSequence);
169 revealedSeqs.addElement(repSequence);
172 int start = adjustForHiddenSeqs(alignmentIndex - 1);
173 int end = adjustForHiddenSeqs(alignmentIndex);
174 if (end >= hiddenSequences.length)
176 end = hiddenSequences.length - 1;
179 for (int index = end; index > start; index--)
181 SequenceI seq = hiddenSequences[index];
182 hiddenSequences[index] = null;
186 if (seq.getLength() > 0)
188 revealedSeqs.addElement(seq);
189 alignment.getSequences().insertElementAt(seq, alignmentIndex);
193 System.out.println(seq.getName() + " has been deleted whilst hidden");
202 public SequenceI getHiddenSequence(int alignmentIndex)
204 return hiddenSequences[alignmentIndex];
207 public int findIndexWithoutHiddenSeqs(int alignmentIndex)
211 if (hiddenSequences.length <= alignmentIndex)
213 alignmentIndex = hiddenSequences.length - 1;
216 while (index <= alignmentIndex)
218 if (hiddenSequences[index] != null)
226 return (alignmentIndex - hiddenSeqs);
229 public int adjustForHiddenSeqs(int alignmentIndex)
232 int hSize = hiddenSequences.length;
233 while (index <= alignmentIndex && index < hSize)
235 if (hiddenSequences[index] != null)
243 return alignmentIndex;
246 public AlignmentI getFullAlignment()
248 int isize = hiddenSequences.length;
249 SequenceI[] seq = new Sequence[isize];
252 for (int i = 0; i < hiddenSequences.length; i++)
254 if (hiddenSequences[i] != null)
256 seq[i] = hiddenSequences[i];
260 seq[i] = alignment.getSequenceAt(index);
265 return new Alignment(seq);
268 public boolean isHidden(SequenceI seq)
270 for (int i = 0; i < hiddenSequences.length; i++)
272 if (hiddenSequences[i] != null && hiddenSequences[i] == seq)