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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38 System.out.println("H is null");
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42 for(int i=0; i<hiddenSequences.length; i++)
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43 if(hiddenSequences[i] !=null )
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49 public int getWidth()
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52 for (int i = 0; i < hiddenSequences.length; i++)
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53 if (hiddenSequences[i] != null && hiddenSequences[i].getLength()>width)
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54 width = hiddenSequences[i].getLength();
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60 * Call this method if sequences are removed from the
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63 public void adjustHeightSequenceDeleted(int seqIndex)
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65 if(hiddenSequences==null)
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70 int alHeight = alignment.getHeight();
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72 SequenceI [] tmp = new SequenceI [alHeight + getSize()];
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73 int deletionIndex = adjustForHiddenSeqs(seqIndex);
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75 for (int i = 0; i < hiddenSequences.length; i++)
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77 if (i > deletionIndex)
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78 tmp[i-1] = hiddenSequences[i];
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80 tmp[i] = hiddenSequences[i];
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83 hiddenSequences = tmp;
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88 * Call this method if sequences are added to or removed from the
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91 public void adjustHeightSequenceAdded()
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93 if(hiddenSequences==null)
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98 int alHeight = alignment.getHeight();
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100 SequenceI [] tmp = new SequenceI [alHeight + getSize()];
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101 System.arraycopy(hiddenSequences,0,tmp,0,hiddenSequences.length);
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102 hiddenSequences = tmp;
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106 public void hideSequence(SequenceI sequence)
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108 if(hiddenSequences==null)
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109 hiddenSequences = new SequenceI[alignment.getHeight()];
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111 int alignmentIndex = alignment.findIndex(sequence);
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112 alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
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114 if(hiddenSequences[alignmentIndex]!=null)
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115 System.out.println("ERROR!!!!!!!!!!!");
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117 hiddenSequences[alignmentIndex] = sequence;
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119 alignment.deleteSequence(sequence);
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122 public Vector showAll()
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124 Vector revealedSeqs = new Vector();
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125 for(int i=0; i<hiddenSequences.length; i++)
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127 if(hiddenSequences[i]!=null)
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129 Vector tmp = showSequence(i);
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130 for (int t = 0; t < tmp.size(); t++)
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131 revealedSeqs.addElement(tmp.elementAt(t));
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134 return revealedSeqs;
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137 public Vector showSequence(int alignmentIndex)
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139 Vector revealedSeqs = new Vector();
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140 SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
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141 if(repSequence!=null
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142 && repSequence.getHiddenSequences()==null
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143 && alignmentIndex>0)
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144 repSequence = alignment.getSequenceAt(alignmentIndex-1);
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146 if(repSequence!=null
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147 && repSequence.getHiddenSequences()==null)
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148 repSequence = null;
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150 int start = adjustForHiddenSeqs(alignmentIndex-1);
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151 int end = adjustForHiddenSeqs(alignmentIndex);
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152 if(end>=hiddenSequences.length)
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153 end = hiddenSequences.length-1;
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155 for(int index = end; index > start; index--)
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157 SequenceI seq = hiddenSequences[index];
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158 hiddenSequences[index] = null;
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162 revealedSeqs.addElement(seq);
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163 alignment.getSequences().insertElementAt(seq, alignmentIndex);
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164 if(repSequence!=null)
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166 repSequence.showHiddenSequence(seq);
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172 return revealedSeqs;
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175 public SequenceI getHiddenSequence(int alignmentIndex)
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177 return hiddenSequences[alignmentIndex];
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180 public int findIndexWithoutHiddenSeqs(int alignmentIndex)
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183 int hiddenSeqs = 0;
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184 if(hiddenSequences.length<=alignmentIndex)
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185 System.out.println(alignmentIndex+" "+hiddenSequences.length);
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187 while(index <= alignmentIndex)
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189 if(hiddenSequences[index]!=null)
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196 return (alignmentIndex - hiddenSeqs) ;
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199 public int adjustForHiddenSeqs(int alignmentIndex)
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202 int hSize = hiddenSequences.length;
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203 while(index <= alignmentIndex && index<hSize)
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205 if(hiddenSequences[index]!=null)
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212 return alignmentIndex ;
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216 public AlignmentI getFullAlignment()
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218 int isize = hiddenSequences.length;
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219 SequenceI [] seq = new Sequence[isize];
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222 for(int i=0; i<hiddenSequences.length; i++)
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224 if(hiddenSequences[i]!=null)
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225 seq[i] = hiddenSequences[i];
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228 seq[i] = alignment.getSequenceAt(index);
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233 return new Alignment(seq);
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236 public boolean isHidden(SequenceI seq)
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238 for(int i=0; i<hiddenSequences.length; i++)
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239 if(hiddenSequences[i] !=null && hiddenSequences[i]==seq)
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