2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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 public SequenceI [] 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 if(hiddenSequences==null)
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41 for(int i=0; i<hiddenSequences.length; i++)
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42 if(hiddenSequences[i] !=null )
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48 public int getWidth()
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51 for (int i = 0; i < hiddenSequences.length; i++)
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52 if (hiddenSequences[i] != null && hiddenSequences[i].getLength()>width)
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53 width = hiddenSequences[i].getLength();
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59 * Call this method if sequences are removed from the
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62 public void adjustHeightSequenceDeleted(int seqIndex)
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64 if(hiddenSequences==null)
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69 int alHeight = alignment.getHeight();
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71 SequenceI [] tmp = new SequenceI [alHeight + getSize()];
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72 int deletionIndex = adjustForHiddenSeqs(seqIndex);
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74 for (int i = 0; i < hiddenSequences.length; i++)
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76 if(hiddenSequences[i]==null)
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79 if (i > deletionIndex)
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80 tmp[i-1] = hiddenSequences[i];
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82 tmp[i] = hiddenSequences[i];
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85 hiddenSequences = tmp;
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90 * Call this method if sequences are added to or removed from the
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93 public void adjustHeightSequenceAdded()
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95 if(hiddenSequences==null)
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100 int alHeight = alignment.getHeight();
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102 SequenceI [] tmp = new SequenceI [alHeight + getSize()];
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103 System.arraycopy(hiddenSequences,0,tmp,0,hiddenSequences.length);
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104 hiddenSequences = tmp;
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108 public void hideSequence(SequenceI sequence)
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110 if(hiddenSequences==null)
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111 hiddenSequences = new SequenceI[alignment.getHeight()];
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113 int alignmentIndex = alignment.findIndex(sequence);
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114 alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
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116 if(hiddenSequences[alignmentIndex]!=null)
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117 System.out.println("ERROR!!!!!!!!!!!");
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119 hiddenSequences[alignmentIndex] = sequence;
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121 alignment.deleteSequence(sequence);
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124 public Vector showAll()
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126 Vector revealedSeqs = new Vector();
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127 for(int i=0; i<hiddenSequences.length; i++)
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129 if(hiddenSequences[i]!=null)
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131 Vector tmp = showSequence(i);
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132 for (int t = 0; t < tmp.size(); t++)
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133 revealedSeqs.addElement(tmp.elementAt(t));
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136 return revealedSeqs;
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139 public Vector showSequence(int alignmentIndex)
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141 Vector revealedSeqs = new Vector();
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142 SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
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143 if(repSequence!=null
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144 && repSequence.getHiddenSequences()==null
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145 && alignmentIndex>0)
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146 repSequence = alignment.getSequenceAt(alignmentIndex-1);
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148 if(repSequence!=null
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149 && repSequence.getHiddenSequences()==null)
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150 repSequence = null;
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152 int start = adjustForHiddenSeqs(alignmentIndex-1);
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153 int end = adjustForHiddenSeqs(alignmentIndex);
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154 if(end>=hiddenSequences.length)
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155 end = hiddenSequences.length-1;
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157 for(int index = end; index > start; index--)
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159 SequenceI seq = hiddenSequences[index];
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160 hiddenSequences[index] = null;
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164 if(seq.getLength()>0)
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166 revealedSeqs.addElement(seq);
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167 alignment.getSequences().insertElementAt(seq, alignmentIndex);
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170 System.out.println(seq.getName()+" has been deleted whilst hidden");
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172 if (repSequence != null)
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174 repSequence.showHiddenSequence(seq);
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180 return revealedSeqs;
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183 public SequenceI getHiddenSequence(int alignmentIndex)
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185 return hiddenSequences[alignmentIndex];
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188 public int findIndexWithoutHiddenSeqs(int alignmentIndex)
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191 int hiddenSeqs = 0;
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192 if(hiddenSequences.length<=alignmentIndex)
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193 alignmentIndex = hiddenSequences.length-1;
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195 while(index <= alignmentIndex)
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197 if(hiddenSequences[index]!=null)
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204 return (alignmentIndex - hiddenSeqs) ;
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207 public int adjustForHiddenSeqs(int alignmentIndex)
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210 int hSize = hiddenSequences.length;
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211 while(index <= alignmentIndex && index<hSize)
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213 if(hiddenSequences[index]!=null)
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220 return alignmentIndex ;
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224 public AlignmentI getFullAlignment()
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226 int isize = hiddenSequences.length;
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227 SequenceI [] seq = new Sequence[isize];
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230 for(int i=0; i<hiddenSequences.length; i++)
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232 if(hiddenSequences[i]!=null)
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233 seq[i] = hiddenSequences[i];
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236 seq[i] = alignment.getSequenceAt(index);
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241 return new Alignment(seq);
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244 public boolean isHidden(SequenceI seq)
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246 for(int i=0; i<hiddenSequences.length; i++)
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247 if(hiddenSequences[i] !=null && hiddenSequences[i]==seq)
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