2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.datamodel;
\r
21 import jalview.util.ShiftList;
\r
26 * NOTE: Columns are zero based.
\r
28 public class ColumnSelection
\r
30 Vector selected = new Vector();
\r
32 //Vector of int [] {startCol, endCol}
\r
33 Vector hiddenColumns;
\r
36 * Add a column to the selection
\r
38 * @param col index of column
\r
40 public void addElement(int col)
\r
42 Integer column = new Integer(col);
\r
43 if (!selected.contains(column))
\r
45 selected.addElement(column);
\r
50 * clears column selection
\r
54 selected.removeAllElements();
\r
58 * removes col from selection
\r
60 * @param col index of column to be removed
\r
62 public void removeElement(int col)
\r
64 Integer colInt = new Integer(col);
\r
66 if (selected.contains(colInt))
\r
68 selected.removeElement(colInt);
\r
73 * removes a range of columns from the selection
\r
74 * @param start int - first column in range to be removed
\r
75 * @param end int - last col
\r
77 public void removeElements(int start, int end)
\r
80 for(int i=start; i<end; i++)
\r
82 colInt = new Integer(i);
\r
83 if (selected.contains(colInt))
\r
85 selected.removeElement(colInt);
\r
91 * @return Vector containing selected columns as Integers
\r
93 public Vector getSelected()
\r
100 * @param col index to search for in column selection
\r
102 * @return true if Integer(col) is in selection.
\r
104 public boolean contains(int col)
\r
106 return selected.contains(new Integer(col));
\r
112 * @param i DOCUMENT ME!
\r
114 * @return DOCUMENT ME!
\r
116 public int columnAt(int i)
\r
118 return ((Integer) selected.elementAt(i)).intValue();
\r
124 * @return DOCUMENT ME!
\r
128 return selected.size();
\r
134 * @return DOCUMENT ME!
\r
136 public int getMax()
\r
140 for (int i = 0; i < selected.size(); i++)
\r
142 if (columnAt(i) > max)
\r
154 * @return DOCUMENT ME!
\r
156 public int getMin()
\r
158 int min = 1000000000;
\r
160 for (int i = 0; i < selected.size(); i++)
\r
162 if (columnAt(i) < min)
\r
173 * propagate shift in alignment columns to column selection
\r
175 * @param start beginning of edit
\r
176 * @param change shift in edit (-ve or +ve number of columns)
\r
178 public void compensateForEdit(int start, int change)
\r
180 for (int i = 0; i < size(); i++)
\r
182 int temp = columnAt(i);
\r
186 selected.setElementAt(new Integer(temp - change), i);
\r
190 if(hiddenColumns!=null)
\r
192 for(int i=0; i<hiddenColumns.size(); i++)
\r
194 int[] region = (int[]) hiddenColumns.elementAt(i);
\r
195 if(region[0] > start)
\r
197 region[0] -= change;
\r
198 region[1] -= change;
\r
207 public ShiftList compensateForEdits(ShiftList shiftrecord) {
\r
208 if (shiftrecord!=null) {
\r
209 Vector shifts = shiftrecord.shifts;
\r
210 if (shifts!=null && shifts.size()>0) {
\r
211 for (int i=0,j=shifts.size(); i<j; i++) {
\r
212 int[] sh = (int[]) shifts.elementAt(i);
\r
213 compensateForEdit(sh[0], sh[1]);
\r
216 return shiftrecord.getInverse();
\r
221 * This Method is used to return all the HiddenColumn regions
\r
222 * less than the given index.
\r
226 public Vector getHiddenColumns()
\r
228 return hiddenColumns;
\r
231 * Return absolute column index for a visible column index
\r
232 * @param column int column index in alignment view
\r
233 * @return alignment column index for column
\r
235 public int adjustForHiddenColumns(int column)
\r
237 int result = column;
\r
238 if (hiddenColumns != null)
\r
240 for (int i = 0; i < hiddenColumns.size(); i++)
\r
242 int[] region = (int[]) hiddenColumns.elementAt(i);
\r
243 if (result >= region[0])
\r
245 result += region[1] - region[0] + 1;
\r
253 * Use this method to find out where a visible column is in the alignment
\r
254 * when hidden columns exist
\r
255 * @param hiddenColumn int
\r
258 public int findColumnPosition(int hiddenColumn)
\r
260 int result = hiddenColumn;
\r
261 if (hiddenColumns != null)
\r
267 int[] region = (int[]) hiddenColumns.elementAt(index);
\r
268 if (hiddenColumn > region[1])
\r
270 result -= region[1]+1-region[0];
\r
274 while (index < hiddenColumns.size());
\r
283 * Use this method to determine where the next hiddenRegion starts
\r
285 public int findHiddenRegionPosition(int hiddenRegion)
\r
288 if (hiddenColumns != null)
\r
294 int[] region = (int[]) hiddenColumns.elementAt(index);
\r
295 if(hiddenRegion==0)
\r
300 gaps += region[1] +1 - region[0];
\r
301 result = region[1] +1;
\r
304 while(index < hiddenRegion+1);
\r
313 * THis method returns the rightmost limit of a
\r
314 * region of an alignment with hidden columns.
\r
315 * In otherwords, the next hidden column.
\r
318 public int getHiddenBoundaryRight(int alPos)
\r
320 if (hiddenColumns != null)
\r
325 int[] region = (int[]) hiddenColumns.elementAt(index);
\r
326 if(alPos < region[0])
\r
331 while(index < hiddenColumns.size());
\r
338 * THis method returns the rightmost limit of a
\r
339 * region of an alignment with hidden columns.
\r
340 * In otherwords, the next hidden column.
\r
343 public int getHiddenBoundaryLeft(int alPos)
\r
345 if (hiddenColumns != null)
\r
347 int index = hiddenColumns.size()-1;
\r
350 int[] region = (int[]) hiddenColumns.elementAt(index);
\r
351 if(alPos > region[1])
\r
363 public void hideSelectedColumns()
\r
367 int column = ( (Integer) getSelected().firstElement()).intValue();
\r
368 hideColumns(column);
\r
373 public void hideColumns(int start, int end)
\r
375 if(hiddenColumns==null)
\r
376 hiddenColumns = new Vector();
\r
378 boolean added = false;
\r
379 boolean overlap = false;
\r
381 for (int i = 0; i < hiddenColumns.size(); i++)
\r
383 int[] region = (int[]) hiddenColumns.elementAt(i);
\r
384 if ( start<=region[1] && end>=region[0])
\r
386 hiddenColumns.removeElementAt(i);
\r
390 else if (end < region[0] && start < region[0])
\r
392 hiddenColumns.insertElementAt(new int[]
\r
401 hideColumns(start, end);
\r
404 hiddenColumns.addElement(new int[] {start, end});
\r
409 * This method will find a range of selected columns
\r
410 * around the column specified
\r
413 public void hideColumns(int col)
\r
415 // First find out range of columns to hide
\r
416 int min = col, max = col+1;
\r
417 while( contains(min) )
\r
418 { removeElement(min); min --; }
\r
420 while( contains(max) )
\r
421 { removeElement(max); max ++; }
\r
425 hideColumns(min, max);
\r
428 public void revealAllHiddenColumns()
\r
430 if(hiddenColumns!=null)
\r
432 for (int i = 0; i < hiddenColumns.size(); i++)
\r
434 int[] region = (int[]) hiddenColumns.elementAt(i);
\r
435 for (int j = region[0]; j < region[1]+1; j++)
\r
442 hiddenColumns = null;
\r
445 public void revealHiddenColumns(int res)
\r
447 for(int i=0; i<hiddenColumns.size(); i++)
\r
449 int [] region = (int[])hiddenColumns.elementAt(i);
\r
450 if( res == region[0])
\r
452 for (int j = region[0]; j < region[1]+1; j++)
\r
457 hiddenColumns.removeElement(region);
\r
461 if(hiddenColumns.size()==0)
\r
462 hiddenColumns = null;
\r
465 public boolean isVisible(int column)
\r
467 for(int i=0; i<hiddenColumns.size(); i++)
\r
469 int [] region = (int[])hiddenColumns.elementAt(i);
\r
470 if( column >= region[0] && column <= region[1])
\r
481 public ColumnSelection(ColumnSelection copy) {
\r
483 if (copy.selected!=null) {
\r
484 selected = new Vector();
\r
485 for (int i=0,j=copy.selected.size(); i<j; i++) {
\r
486 selected.setElementAt(((Integer) copy.selected.elementAt(i)), i);
\r
489 if (copy.hiddenColumns!=null) {
\r
490 hiddenColumns=new Vector();
\r
491 for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
\r
493 rh = (int[])copy.hiddenColumns.elementAt(i);
\r
495 cp = new int[rh.length];
\r
496 System.arraycopy(rh, 0, cp, 0, rh.length);
\r
497 hiddenColumns.setElementAt(cp, i);
\r
507 public ColumnSelection()
\r