2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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20 package jalview.datamodel;
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24 public class HiddenSequences
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26 Hashtable hiddenSequences;
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27 AlignmentI alignment;
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29 public HiddenSequences(AlignmentI al)
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34 public int getSize()
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36 return hiddenSequences == null ? 0 : hiddenSequences.size();
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39 public void hideSequence(SequenceI sequence)
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41 if(hiddenSequences==null)
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42 hiddenSequences = new Hashtable();
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44 int alignmentIndex = alignment.findIndex(sequence);
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45 alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
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47 hiddenSequences.put(new Integer(alignmentIndex), sequence);
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49 alignment.deleteSequence(sequence);
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52 public void showSequence(int alignmentIndex)
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54 SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
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55 if(repSequence.getHiddenSequences()==null && alignmentIndex>0)
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56 repSequence = alignment.getSequenceAt(alignmentIndex-1);
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57 if(repSequence.getHiddenSequences()==null)
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60 int start = adjustForHiddenSeqs(alignmentIndex-1);
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61 int end = adjustForHiddenSeqs(alignmentIndex);
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63 for(int index = end; index > start; index--)
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65 SequenceI seq = (SequenceI)hiddenSequences.remove(new Integer(
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70 alignment.getSequences().insertElementAt(seq, alignmentIndex);
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71 if(repSequence!=null)
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73 repSequence.showHiddenSequence(seq);
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79 public SequenceI getHiddenSequence(int alignmentIndex)
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81 return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
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84 public int findIndexWithoutHiddenSeqs(int alignmentIndex)
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88 while(index <= alignmentIndex)
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90 if(hiddenSequences.containsKey(new Integer(index)))
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97 return (alignmentIndex - hiddenSeqs) ;
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100 public int adjustForHiddenSeqs(int alignmentIndex)
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103 while(index <= alignmentIndex)
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105 if(hiddenSequences.containsKey(new Integer(index)))
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112 return alignmentIndex ;
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