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.datamodel;
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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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82 public Vector getSelected()
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90 * @param col DOCUMENT ME!
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92 * @return DOCUMENT ME!
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94 public boolean contains(int col)
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96 return selected.contains(new Integer(col));
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102 * @param i DOCUMENT ME!
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104 * @return DOCUMENT ME!
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106 public int columnAt(int i)
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108 return ((Integer) selected.elementAt(i)).intValue();
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114 * @return DOCUMENT ME!
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118 return selected.size();
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124 * @return DOCUMENT ME!
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126 public int getMax()
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130 for (int i = 0; i < selected.size(); i++)
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132 if (columnAt(i) > max)
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144 * @return DOCUMENT ME!
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146 public int getMin()
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148 int min = 1000000000;
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150 for (int i = 0; i < selected.size(); i++)
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152 if (columnAt(i) < min)
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165 * @param start DOCUMENT ME!
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166 * @param change DOCUMENT ME!
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168 public void compensateForEdit(int start, int change)
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170 for (int i = 0; i < size(); i++)
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172 int temp = columnAt(i);
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176 selected.setElementAt(new Integer(temp - change), i);
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180 if(hiddenColumns!=null)
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182 for(int i=0; i<hiddenColumns.size(); i++)
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184 int[] region = (int[]) hiddenColumns.elementAt(i);
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185 if(region[0] > start)
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187 region[0] -= change;
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188 region[1] -= change;
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199 * This Method is used to return all the HiddenColumn regions
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200 * less than the given index.
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204 public Vector getHiddenColumns()
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206 return hiddenColumns;
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209 public int adjustForHiddenColumns(int column)
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211 int result = column;
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212 if (hiddenColumns != null)
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214 for (int i = 0; i < hiddenColumns.size(); i++)
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216 int[] region = (int[]) hiddenColumns.elementAt(i);
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217 if (result >= region[0])
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219 result += region[1] - region[0] + 1;
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227 * Use this method to find out where a visible column is in the alignment
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228 * when hidden columns exist
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229 * @param hiddenColumn int
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232 public int findColumnPosition(int hiddenColumn)
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234 int result = hiddenColumn;
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235 if (hiddenColumns != null)
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241 int[] region = (int[]) hiddenColumns.elementAt(index);
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242 if (hiddenColumn > region[1])
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244 result -= region[1]+1-region[0];
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248 while (index < hiddenColumns.size());
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257 * Use this method to determine where the next hiddenRegion starts
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259 public int findHiddenRegionPosition(int hiddenRegion)
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262 if (hiddenColumns != null)
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268 int[] region = (int[]) hiddenColumns.elementAt(index);
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269 if(hiddenRegion==0)
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274 gaps += region[1] +1 - region[0];
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275 result = region[1] +1;
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278 while(index < hiddenRegion+1);
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287 * THis method returns the rightmost limit of a
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288 * region of an alignment with hidden columns.
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289 * In otherwords, the next hidden column.
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292 public int getHiddenBoundaryRight(int alPos)
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294 if (hiddenColumns != null)
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299 int[] region = (int[]) hiddenColumns.elementAt(index);
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300 if(alPos < region[0])
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305 while(index < hiddenColumns.size());
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312 * THis method returns the rightmost limit of a
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313 * region of an alignment with hidden columns.
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314 * In otherwords, the next hidden column.
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317 public int getHiddenBoundaryLeft(int alPos)
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319 if (hiddenColumns != null)
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321 int index = hiddenColumns.size()-1;
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324 int[] region = (int[]) hiddenColumns.elementAt(index);
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325 if(alPos > region[1])
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336 public void hideSelectedColumns()
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340 int column = ( (Integer) getSelected().firstElement()).intValue();
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341 hideColumns(column);
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346 public void hideColumns(int start, int end)
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348 if(hiddenColumns==null)
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349 hiddenColumns = new Vector();
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351 boolean added = false;
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352 boolean overlap = false;
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354 for (int i = 0; i < hiddenColumns.size(); i++)
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356 int[] region = (int[]) hiddenColumns.elementAt(i);
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357 if ( start<=region[1] && end>=region[0])
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359 hiddenColumns.removeElementAt(i);
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363 else if (end < region[0] && start < region[0])
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365 hiddenColumns.insertElementAt(new int[]
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374 hideColumns(start, end);
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377 hiddenColumns.addElement(new int[] {start, end});
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382 * This method will find a range of selected columns
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383 * around the column specified
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386 public void hideColumns(int col)
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388 // First find out range of columns to hide
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389 int min = col, max = col+1;
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390 while( contains(min) )
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391 { removeElement(min); min --; }
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393 while( contains(max) )
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394 { removeElement(max); max ++; }
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398 hideColumns(min, max);
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401 public void revealAllHiddenColumns()
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403 if(hiddenColumns!=null)
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405 for (int i = 0; i < hiddenColumns.size(); i++)
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407 int[] region = (int[]) hiddenColumns.elementAt(i);
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408 for (int j = region[0]; j < region[1]; j++)
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415 hiddenColumns = null;
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418 public void revealHiddenColumns(int res)
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420 for(int i=0; i<hiddenColumns.size(); i++)
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422 int [] region = (int[])hiddenColumns.elementAt(i);
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423 if( res == region[0])
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425 for (int j = region[0]; j < region[1]; j++)
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430 hiddenColumns.removeElement(region);
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434 if(hiddenColumns.size()==0)
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435 hiddenColumns = null;
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438 public boolean isVisible(int column)
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440 for(int i=0; i<hiddenColumns.size(); i++)
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442 int [] region = (int[])hiddenColumns.elementAt(i);
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443 if( column >= region[0] && column <= region[1])
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