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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19 package jalview.datamodel;
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21 import jalview.util.ShiftList;
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26 * NOTE: Columns are zero based.
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28 public class ColumnSelection
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30 Vector selected = new Vector();
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32 //Vector of int [] {startCol, endCol}
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33 Vector hiddenColumns;
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36 * Add a column to the selection
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38 * @param col index of column
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40 public void addElement(int col)
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42 Integer column = new Integer(col);
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43 if (!selected.contains(column))
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45 selected.addElement(column);
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50 * clears column selection
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54 selected.removeAllElements();
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58 * removes col from selection
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60 * @param col index of column to be removed
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62 public void removeElement(int col)
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64 Integer colInt = new Integer(col);
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66 if (selected.contains(colInt))
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68 selected.removeElement(colInt);
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73 * removes a range of columns from the selection
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74 * @param start int - first column in range to be removed
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75 * @param end int - last col
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77 public void removeElements(int start, int end)
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80 for(int i=start; i<end; i++)
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82 colInt = new Integer(i);
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83 if (selected.contains(colInt))
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85 selected.removeElement(colInt);
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91 * @return Vector containing selected columns as Integers
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93 public Vector getSelected()
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100 * @param col index to search for in column selection
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102 * @return true if Integer(col) is in selection.
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104 public boolean contains(int col)
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106 return selected.contains(new Integer(col));
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112 * @param i DOCUMENT ME!
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114 * @return DOCUMENT ME!
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116 public int columnAt(int i)
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118 return ((Integer) selected.elementAt(i)).intValue();
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124 * @return DOCUMENT ME!
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128 return selected.size();
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134 * @return DOCUMENT ME!
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136 public int getMax()
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140 for (int i = 0; i < selected.size(); i++)
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142 if (columnAt(i) > max)
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154 * @return DOCUMENT ME!
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156 public int getMin()
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158 int min = 1000000000;
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160 for (int i = 0; i < selected.size(); i++)
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162 if (columnAt(i) < min)
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173 * propagate shift in alignment columns to column selection
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175 * @param start beginning of edit
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176 * @param left shift in edit (+ve for removal, or -ve for inserts)
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178 public Vector compensateForEdit(int start, int change)
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180 Vector deletedHiddenColumns = null;
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181 for (int i = 0; i < size(); i++)
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183 int temp = columnAt(i);
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187 selected.setElementAt(new Integer(temp - change), i);
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191 if(hiddenColumns!=null)
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193 deletedHiddenColumns = new Vector();
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194 int hSize = hiddenColumns.size();
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195 for(int i=0; i<hSize; i++)
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197 int[] region = (int[]) hiddenColumns.elementAt(i);
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198 if ( region[0]>start && start+change>region[1] )
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200 deletedHiddenColumns.addElement(
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201 hiddenColumns.elementAt(i));
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203 hiddenColumns.removeElementAt(i);
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209 if(region[0]>start)
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211 region[0] -= change;
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212 region[1] -= change;
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220 this.revealHiddenColumns(0);
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223 return deletedHiddenColumns;
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226 * propagate shift in alignment columns to column selection
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227 * special version of compensateForEdit - allowing for edits within hidden regions
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228 * @param start beginning of edit
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229 * @param left shift in edit (+ve for removal, or -ve for inserts)
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231 private void compensateForDelEdits(int start, int change)
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233 for (int i = 0; i < size(); i++)
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235 int temp = columnAt(i);
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239 selected.setElementAt(new Integer(temp - change), i);
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243 if(hiddenColumns!=null)
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245 for(int i=0; i<hiddenColumns.size(); i++)
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247 int[] region = (int[]) hiddenColumns.elementAt(i);
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248 if(region[0] >= start)
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250 region[0] -= change;
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252 if (region[1]>= start) {
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253 region[1] -=change;
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255 if (region[1]<region[0]) {
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256 hiddenColumns.removeElementAt(i--);
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267 * Adjust hidden column boundaries based on a series of column
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268 * additions or deletions in visible regions.
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269 * @param shiftrecord
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272 public ShiftList compensateForEdits(ShiftList shiftrecord) {
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273 if (shiftrecord!=null) {
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274 Vector shifts = shiftrecord.shifts;
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275 if (shifts!=null && shifts.size()>0) {
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277 for (int i=0,j=shifts.size(); i<j; i++) {
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278 int[] sh = (int[]) shifts.elementAt(i);
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279 //compensateForEdit(shifted+sh[0], sh[1]);
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280 compensateForDelEdits(shifted+sh[0], sh[1]);
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284 return shiftrecord.getInverse();
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289 * removes intersection of position,length ranges in deletions
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290 * from the start,end regions marked in intervals.
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295 private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
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296 boolean pruned=false;
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297 int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
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298 int hr[]=(int[]) intervals.elementAt(i);
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299 int sr[]=(int[]) deletions.elementAt(s);
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300 while (i<=j && s<=t) {
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301 boolean trailinghn=hr[1]>=sr[0];
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304 hr=(int[]) intervals.elementAt(++i);
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309 int endshift=sr[0]+sr[1]; // deletion ranges - -ve means an insert
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310 if (endshift<hr[0] || endshift<sr[0]) { // leadinghc disjoint or not a deletion
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312 sr=(int[]) deletions.elementAt(++s);
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317 boolean leadinghn=hr[0]>=sr[0];
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318 boolean leadinghc=hr[0]<endshift;
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319 boolean trailinghc=hr[1]<endshift;
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321 if (trailinghc) {// deleted hidden region.
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322 intervals.removeElementAt(i);
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326 hr=(int[]) intervals.elementAt(i);
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330 hr[0]=endshift; // clip c terminal region
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331 leadinghn=!leadinghn;
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342 // sr contained in hr
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344 sr=(int[]) deletions.elementAt(++s);
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351 return pruned; // true if any interval was removed or modified by operations.
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353 private boolean pruneColumnList(Vector deletion, Vector list) {
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354 int s=0,t=deletion.size();
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355 int[] sr=(int[])list.elementAt(s++);
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356 boolean pruned=false;
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357 int i=0, j=list.size();
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358 while (i<j && s<=t) {
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359 int c=((Integer)list.elementAt(i++)).intValue();
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361 if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
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362 list.removeElementAt(--i);
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366 sr = (int[])deletion.elementAt(s);
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374 * remove any hiddenColumns or selected columns and shift remaining
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375 * based on a series of position, range deletions.
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378 public void pruneDeletions(ShiftList deletions) {
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379 if (deletions!=null) {
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380 Vector shifts=deletions.shifts;
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381 if (shifts!=null && shifts.size()>0) {
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382 // delete any intervals intersecting.
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383 if (hiddenColumns!=null) {
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384 pruneIntervalVector(shifts, hiddenColumns);
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385 if (hiddenColumns!=null && hiddenColumns.size()==0) {
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386 hiddenColumns=null;
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389 if (selected!=null && selected.size()>0) {
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390 pruneColumnList(shifts, selected);
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391 if (selected!=null && selected.size()==0)
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394 // and shift the rest.
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395 this.compensateForEdits(deletions);
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400 * This Method is used to return all the HiddenColumn regions
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401 * less than the given index.
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405 public Vector getHiddenColumns()
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407 return hiddenColumns;
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410 * Return absolute column index for a visible column index
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411 * @param column int column index in alignment view
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412 * @return alignment column index for column
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414 public int adjustForHiddenColumns(int column)
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416 int result = column;
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417 if (hiddenColumns != null)
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419 for (int i = 0; i < hiddenColumns.size(); i++)
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421 int[] region = (int[]) hiddenColumns.elementAt(i);
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422 if (result >= region[0])
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424 result += region[1] - region[0] + 1;
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432 * Use this method to find out where a visible column is in the alignment
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433 * when hidden columns exist
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434 * @param hiddenColumn int
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437 public int findColumnPosition(int hiddenColumn)
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439 int result = hiddenColumn;
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440 if (hiddenColumns != null)
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446 int[] region = (int[]) hiddenColumns.elementAt(index);
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447 if (hiddenColumn > region[1])
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449 result -= region[1]+1-region[0];
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453 while (index < hiddenColumns.size());
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462 * Use this method to determine where the next hiddenRegion starts
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464 public int findHiddenRegionPosition(int hiddenRegion)
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467 if (hiddenColumns != null)
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473 int[] region = (int[]) hiddenColumns.elementAt(index);
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474 if(hiddenRegion==0)
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479 gaps += region[1] +1 - region[0];
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480 result = region[1] +1;
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483 while(index < hiddenRegion+1);
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492 * THis method returns the rightmost limit of a
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493 * region of an alignment with hidden columns.
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494 * In otherwords, the next hidden column.
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497 public int getHiddenBoundaryRight(int alPos)
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499 if (hiddenColumns != null)
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504 int[] region = (int[]) hiddenColumns.elementAt(index);
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505 if(alPos < region[0])
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510 while(index < hiddenColumns.size());
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517 * THis method returns the rightmost limit of a
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518 * region of an alignment with hidden columns.
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519 * In otherwords, the next hidden column.
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522 public int getHiddenBoundaryLeft(int alPos)
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524 if (hiddenColumns != null)
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526 int index = hiddenColumns.size()-1;
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529 int[] region = (int[]) hiddenColumns.elementAt(index);
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530 if(alPos > region[1])
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542 public void hideSelectedColumns()
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546 int column = ( (Integer) getSelected().firstElement()).intValue();
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547 hideColumns(column);
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552 public void hideColumns(int start, int end)
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554 if(hiddenColumns==null)
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555 hiddenColumns = new Vector();
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557 boolean added = false;
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558 boolean overlap = false;
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560 for (int i = 0; i < hiddenColumns.size(); i++)
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562 int[] region = (int[]) hiddenColumns.elementAt(i);
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563 if ( start<=region[1] && end>=region[0])
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565 hiddenColumns.removeElementAt(i);
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569 else if (end < region[0] && start < region[0])
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571 hiddenColumns.insertElementAt(new int[]
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580 hideColumns(start, end);
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583 hiddenColumns.addElement(new int[] {start, end});
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588 * This method will find a range of selected columns
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589 * around the column specified
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592 public void hideColumns(int col)
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594 // First find out range of columns to hide
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595 int min = col, max = col+1;
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596 while( contains(min) )
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597 { removeElement(min); min --; }
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599 while( contains(max) )
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600 { removeElement(max); max ++; }
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606 hideColumns(min, max);
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609 public void revealAllHiddenColumns()
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611 if(hiddenColumns!=null)
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613 for (int i = 0; i < hiddenColumns.size(); i++)
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615 int[] region = (int[]) hiddenColumns.elementAt(i);
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616 for (int j = region[0]; j < region[1]+1; j++)
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623 hiddenColumns = null;
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626 public void revealHiddenColumns(int res)
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628 for(int i=0; i<hiddenColumns.size(); i++)
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630 int [] region = (int[])hiddenColumns.elementAt(i);
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631 if( res == region[0])
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633 for (int j = region[0]; j < region[1]+1; j++)
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638 hiddenColumns.removeElement(region);
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642 if(hiddenColumns.size()==0)
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643 hiddenColumns = null;
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646 public boolean isVisible(int column)
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648 for(int i=0; i<hiddenColumns.size(); i++)
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650 int [] region = (int[])hiddenColumns.elementAt(i);
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651 if( column >= region[0] && column <= region[1])
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662 public ColumnSelection(ColumnSelection copy) {
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664 if (copy.selected!=null) {
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665 selected = new Vector();
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666 for (int i=0,j=copy.selected.size(); i<j; i++) {
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667 selected.addElement(copy.selected.elementAt(i));
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670 if (copy.hiddenColumns!=null) {
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671 hiddenColumns=new Vector(copy.hiddenColumns.size());
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672 for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
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674 rh = (int[])copy.hiddenColumns.elementAt(i);
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676 cp = new int[rh.length];
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677 System.arraycopy(rh, 0, cp, 0, rh.length);
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678 hiddenColumns.addElement(cp);
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687 public ColumnSelection()
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691 public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
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692 int i,iSize=seqs.length;
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693 String selection[] = new String[iSize];
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694 if (hiddenColumns!=null && hiddenColumns.size()>0)
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696 for (i=0; i<iSize; i++) {
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697 StringBuffer visibleSeq = new StringBuffer();
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698 Vector regions = getHiddenColumns();
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700 int blockStart = start, blockEnd=end;
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702 int hideStart, hideEnd;
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704 for (int j = 0; j < regions.size(); j++)
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706 region = (int[]) regions.elementAt(j);
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707 hideStart = region[0];
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708 hideEnd = region[1];
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710 if(hideStart < start)
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715 blockStart = Math.min(blockStart, hideEnd+1);
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716 blockEnd = Math.min(blockEnd, hideStart);
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718 if(blockStart>blockEnd)
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724 visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
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726 blockStart = hideEnd+1;
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731 visibleSeq.append(seqs[i].getSequence(blockStart, end));
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733 selection[i] = visibleSeq.toString();
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738 for(i=0; i<iSize; i++)
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740 selection[i] = seqs[i].getSequence(start, end);
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747 * return all visible segments between the given start and end boundaries
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749 * @param start (first column inclusive from 0)
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750 * @param end (last column - not inclusive)
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751 * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end
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753 public int[] getVisibleContigs(int start, int end) {
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754 if (hiddenColumns!=null && hiddenColumns.size()>0)
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756 Vector visiblecontigs=new Vector();
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757 Vector regions = getHiddenColumns();
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759 int vstart = start;
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761 int hideStart, hideEnd;
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763 for (int j = 0; vstart<end && j < regions.size(); j++)
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765 region = (int[]) regions.elementAt(j);
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766 hideStart = region[0];
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767 hideEnd = region[1];
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769 if(hideEnd < vstart)
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773 if (hideStart>vstart) {
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774 visiblecontigs.addElement(new int[] {vstart, hideStart-1});
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780 visiblecontigs.addElement(new int[] { vstart, end-1});
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781 int[] vcontigs = new int[visiblecontigs.size()*2];
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782 for (int i=0,j=visiblecontigs.size(); i<j; i++) {
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783 int [] vc = (int[]) visiblecontigs.elementAt(i);
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784 visiblecontigs.setElementAt(null, i);
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785 vcontigs[i*2] = vc[0];
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786 vcontigs[i*2+1] = vc[1];
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788 visiblecontigs.removeAllElements();
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793 return new int[] { start, end-1 };
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