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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19 package jalview.gui;
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24 * NOTE: Columns are zero based.
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26 public class ColumnSelection
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28 Vector selected = new Vector();
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30 //Vector of int [] {startCol, endCol}
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31 Vector hiddenColumns;
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36 * @param col DOCUMENT ME!
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38 public void addElement(int col)
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40 if (!selected.contains(new Integer(col)))
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42 selected.addElement(new Integer(col));
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51 selected.removeAllElements();
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57 * @param col DOCUMENT ME!
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59 public void removeElement(int col)
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61 Integer colInt = new Integer(col);
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63 if (selected.contains(colInt))
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65 selected.removeElement(colInt);
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69 public void removeElements(int start, int end)
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72 for(int i=start; i<end; i++)
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74 colInt = new Integer(i);
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75 if (selected.contains(colInt))
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77 selected.removeElement(colInt);
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85 * @param col DOCUMENT ME!
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87 * @return DOCUMENT ME!
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89 public boolean contains(int col)
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91 return selected.contains(new Integer(col));
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97 * @param i DOCUMENT ME!
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99 * @return DOCUMENT ME!
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101 public int columnAt(int i)
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103 return ((Integer) selected.elementAt(i)).intValue();
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109 * @return DOCUMENT ME!
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113 return selected.size();
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119 * @return DOCUMENT ME!
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121 public int getMax()
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125 for (int i = 0; i < selected.size(); i++)
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127 if (columnAt(i) > max)
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139 * @return DOCUMENT ME!
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141 public int getMin()
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143 int min = 1000000000;
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145 for (int i = 0; i < selected.size(); i++)
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147 if (columnAt(i) < min)
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160 * @param start DOCUMENT ME!
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161 * @param change DOCUMENT ME!
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163 public void compensateForEdit(int start, int change)
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165 for (int i = 0; i < size(); i++)
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167 int temp = columnAt(i);
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171 selected.setElementAt(new Integer(temp - change), i);
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177 * This Method is used to return all the HiddenColumn regions
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178 * less than the given index.
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182 public Vector getHiddenColumns()
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184 return hiddenColumns;
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187 public int adjustForHiddenColumns(int column)
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189 int result = column;
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190 if (hiddenColumns != null)
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192 for (int i = 0; i < hiddenColumns.size(); i++)
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194 int[] region = (int[]) hiddenColumns.elementAt(i);
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195 if (result >= region[0])
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197 result += region[1] - region[0] + 1;
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205 * Use this method to find out where a visible column is in the alignment
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206 * when hidden columns exist
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207 * @param hiddenColumn int
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210 public int findColumnPosition(int hiddenColumn)
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212 int result = hiddenColumn;
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213 if (hiddenColumns != null)
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219 int[] region = (int[]) hiddenColumns.elementAt(index);
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220 if (hiddenColumn > region[1])
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222 result -= region[1]+1-region[0];
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226 while (index < hiddenColumns.size());
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235 * Use this method to determine where the next hiddenRegion starts
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237 public int findHiddenRegionPosition(int hiddenRegion)
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240 if (hiddenColumns != null)
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246 int[] region = (int[]) hiddenColumns.elementAt(index);
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247 if(hiddenRegion==0)
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252 gaps += region[1] +1 - region[0];
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253 result = region[1] +1;
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256 while(index < hiddenRegion+1);
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265 * THis method returns the rightmost limit of a
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266 * region of an alignment with hidden columns.
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267 * In otherwords, the next hidden column.
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270 public int getHiddenBoundaryRight(int alPos)
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272 if (hiddenColumns != null)
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277 int[] region = (int[]) hiddenColumns.elementAt(index);
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278 if(alPos < region[0])
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283 while(index < hiddenColumns.size());
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290 * THis method returns the rightmost limit of a
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291 * region of an alignment with hidden columns.
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292 * In otherwords, the next hidden column.
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295 public int getHiddenBoundaryLeft(int alPos)
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297 if (hiddenColumns != null)
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299 int index = hiddenColumns.size()-1;
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302 int[] region = (int[]) hiddenColumns.elementAt(index);
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303 if(alPos > region[1])
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316 public void hideColumns(int res, AlignViewport av)
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318 if(hiddenColumns==null)
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319 hiddenColumns = new Vector();
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321 // First find out range of columns to hide
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322 int min = res, max = res+1;
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323 while( contains(min) )
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324 { removeElement(min); min --; }
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326 while( contains(max) )
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327 { removeElement(max); max ++; }
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331 boolean added = false;
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332 for(int i=0; i<hiddenColumns.size(); i++)
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334 int [] region = (int[])hiddenColumns.elementAt(i);
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335 if( max < region[0])
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337 hiddenColumns.insertElementAt(new int[]{min, max}, i);
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344 hiddenColumns.addElement(new int[]{min, max});
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347 av.setSelectionGroup(null);
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348 av.hasHiddenColumns = true;
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351 public void revealAllHiddenColumns(AlignViewport av)
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353 av.hasHiddenColumns = false;
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354 hiddenColumns = null;
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357 public void revealHiddenColumns(int res, AlignViewport av)
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359 for(int i=0; i<hiddenColumns.size(); i++)
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361 int [] region = (int[])hiddenColumns.elementAt(i);
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362 if( res == region[0])
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364 hiddenColumns.remove(region);
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370 if(hiddenColumns.size()<1)
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371 av.hasHiddenColumns = false;
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374 public boolean isVisible(int column)
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376 for(int i=0; i<hiddenColumns.size(); i++)
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378 int [] region = (int[])hiddenColumns.elementAt(i);
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379 if( column >= region[0] && column <= region[1])
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