2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import jalview.util.Comparison;
24 import jalview.util.ShiftList;
25 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
26 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
28 import java.util.ArrayList;
29 import java.util.BitSet;
30 import java.util.Collections;
31 import java.util.List;
32 import java.util.Vector;
35 * Data class holding the selected columns and hidden column ranges for a view.
38 public class ColumnSelection
41 * A class to hold an efficient representation of selected columns
46 * list of selected columns (ordered by selection order, not column order)
48 private List<Integer> order;
51 * an unmodifiable view of the selected columns list
53 private List<Integer> _uorder;
56 * bitfield for column selection - allows quick lookup
58 private BitSet selected;
65 order = new ArrayList<Integer>();
66 _uorder = Collections.unmodifiableList(order);
67 selected = new BitSet();
75 IntList(IntList other)
81 for (int i = 0; i < j; i++)
83 add(other.elementAt(i));
89 * adds a new column i to the selection - only if i is not already selected
97 order.add(Integer.valueOf(i));
111 Integer colInt = new Integer(col);
113 if (selected.get(col))
115 // if this ever changes to List.remove(), ensure Integer not int
117 // as List.remove(int i) removes the i'th item which is wrong
118 order.remove(colInt);
123 boolean contains(Integer colInt)
125 return selected.get(colInt);
130 return order.isEmpty();
134 * Returns a read-only view of the selected columns list
138 List<Integer> getList()
149 * gets the column that was selected first, second or i'th
159 protected boolean pruneColumnList(final List<int[]> shifts)
161 int s = 0, t = shifts.size();
162 int[] sr = shifts.get(s++);
163 boolean pruned = false;
164 int i = 0, j = order.size();
165 while (i < j && s <= t)
167 int c = order.get(i++).intValue();
170 if (sr[1] + sr[0] >= c)
171 { // sr[1] -ve means inseriton.
190 * shift every selected column at or above start by change
193 * - leftmost column to be shifted
197 void compensateForEdits(int start, int change)
199 BitSet mask = new BitSet();
200 for (int i = 0; i < order.size(); i++)
202 int temp = order.get(i);
206 // clear shifted bits and update List of selected columns
207 selected.clear(temp);
208 mask.set(temp - change);
209 order.set(i, new Integer(temp - change));
212 // lastly update the bitfield all at once
216 boolean isSelected(int column)
218 return selected.get(column);
223 return selected.length() - 1;
228 return selected.get(0) ? 0 : selected.nextSetBit(0);
232 * @return a series of selection intervals along the range
234 List<int[]> getRanges()
236 List<int[]> rlist = new ArrayList<int[]>();
237 if (selected.isEmpty())
241 int next = selected.nextSetBit(0), clear = -1;
244 clear = selected.nextClearBit(next);
245 rlist.add(new int[] { next, clear - 1 });
246 next = selected.nextSetBit(clear);
252 public int hashCode()
254 // TODO Auto-generated method stub
255 return selected.hashCode();
259 public boolean equals(Object obj)
261 if (obj instanceof IntList)
263 return ((IntList) obj).selected.equals(selected);
269 IntList selection = new IntList();
272 * list of hidden column [start, end] ranges; the list is maintained in
273 * ascending start column order
275 Vector<int[]> hiddenColumns;
278 * Add a column to the selection
283 public void addElement(int col)
289 * clears column selection
297 * Removes value 'col' from the selection (not the col'th item)
300 * index of column to be removed
302 public void removeElement(int col)
304 selection.remove(col);
308 * removes a range of columns from the selection
311 * int - first column in range to be removed
315 public void removeElements(int start, int end)
318 for (int i = start; i < end; i++)
320 colInt = new Integer(i);
321 if (selection.contains(colInt))
323 selection.remove(colInt);
329 * Returns a read-only view of the (possibly empty) list of selected columns
331 * The list contains no duplicates but is not necessarily ordered. It also may
332 * include columns hidden from the current view. To modify (for example sort)
333 * the list, you should first make a copy.
335 * The list is not thread-safe: iterating over it could result in
336 * ConcurrentModificationException if it is modified by another thread.
338 public List<Integer> getSelected()
340 return selection.getList();
344 * @return list of int arrays containing start and end column position for
345 * runs of selected columns ordered from right to left.
347 public List<int[]> getSelectedRanges()
349 return selection.getRanges();
355 * index to search for in column selection
357 * @return true if col is selected
359 public boolean contains(int col)
361 return (col > -1) ? selection.isSelected(col) : false;
365 * Answers true if no columns are selected, else false
367 public boolean isEmpty()
369 return selection == null || selection.isEmpty();
373 * rightmost selected column
375 * @return rightmost column in alignment that is selected
379 if (selection.isEmpty())
383 return selection.getMaxColumn();
387 * Leftmost column in selection
389 * @return column index of leftmost column in selection
393 if (selection.isEmpty())
397 return selection.getMinColumn();
401 * propagate shift in alignment columns to column selection
406 * shift in edit (+ve for removal, or -ve for inserts)
408 public List<int[]> compensateForEdit(int start, int change)
410 List<int[]> deletedHiddenColumns = null;
411 selection.compensateForEdits(start, change);
413 if (hiddenColumns != null)
415 deletedHiddenColumns = new ArrayList<int[]>();
416 int hSize = hiddenColumns.size();
417 for (int i = 0; i < hSize; i++)
419 int[] region = hiddenColumns.elementAt(i);
420 if (region[0] > start && start + change > region[1])
422 deletedHiddenColumns.add(region);
424 hiddenColumns.removeElementAt(i);
430 if (region[0] > start)
443 this.revealHiddenColumns(0);
446 return deletedHiddenColumns;
450 * propagate shift in alignment columns to column selection special version of
451 * compensateForEdit - allowing for edits within hidden regions
456 * shift in edit (+ve for removal, or -ve for inserts)
458 private void compensateForDelEdits(int start, int change)
461 selection.compensateForEdits(start, change);
463 if (hiddenColumns != null)
465 for (int i = 0; i < hiddenColumns.size(); i++)
467 int[] region = hiddenColumns.elementAt(i);
468 if (region[0] >= start)
472 if (region[1] >= start)
476 if (region[1] < region[0])
478 hiddenColumns.removeElementAt(i--);
494 * Adjust hidden column boundaries based on a series of column additions or
495 * deletions in visible regions.
500 public ShiftList compensateForEdits(ShiftList shiftrecord)
502 if (shiftrecord != null)
504 final List<int[]> shifts = shiftrecord.getShifts();
505 if (shifts != null && shifts.size() > 0)
508 for (int i = 0, j = shifts.size(); i < j; i++)
510 int[] sh = shifts.get(i);
511 // compensateForEdit(shifted+sh[0], sh[1]);
512 compensateForDelEdits(shifted + sh[0], sh[1]);
516 return shiftrecord.getInverse();
522 * removes intersection of position,length ranges in deletions from the
523 * start,end regions marked in intervals.
529 private boolean pruneIntervalVector(final List<int[]> shifts,
530 Vector<int[]> intervals)
532 boolean pruned = false;
533 int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
534 int hr[] = intervals.elementAt(i);
535 int sr[] = shifts.get(s);
536 while (i <= j && s <= t)
538 boolean trailinghn = hr[1] >= sr[0];
543 hr = intervals.elementAt(++i);
551 int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
552 if (endshift < hr[0] || endshift < sr[0])
553 { // leadinghc disjoint or not a deletion
556 sr = shifts.get(++s);
564 boolean leadinghn = hr[0] >= sr[0];
565 boolean leadinghc = hr[0] < endshift;
566 boolean trailinghc = hr[1] < endshift;
570 { // deleted hidden region.
571 intervals.removeElementAt(i);
576 hr = intervals.elementAt(i);
582 hr[0] = endshift; // clip c terminal region
583 leadinghn = !leadinghn;
599 // sr contained in hr
602 sr = shifts.get(++s);
612 return pruned; // true if any interval was removed or modified by
617 * remove any hiddenColumns or selected columns and shift remaining based on a
618 * series of position, range deletions.
622 public void pruneDeletions(ShiftList deletions)
624 if (deletions != null)
626 final List<int[]> shifts = deletions.getShifts();
627 if (shifts != null && shifts.size() > 0)
629 // delete any intervals intersecting.
630 if (hiddenColumns != null)
632 pruneIntervalVector(shifts, hiddenColumns);
633 if (hiddenColumns != null && hiddenColumns.size() == 0)
635 hiddenColumns = null;
638 if (selection != null && selection.size() > 0)
640 selection.pruneColumnList(shifts);
641 if (selection != null && selection.size() == 0)
646 // and shift the rest.
647 this.compensateForEdits(deletions);
653 * This Method is used to return all the HiddenColumn regions
655 * @return empty list or List of hidden column intervals
657 public List<int[]> getHiddenColumns()
659 return hiddenColumns == null ? Collections.<int[]> emptyList()
664 * Return absolute column index for a visible column index
667 * int column index in alignment view (count from zero)
668 * @return alignment column index for column
670 public int adjustForHiddenColumns(int column)
673 if (hiddenColumns != null)
675 for (int i = 0; i < hiddenColumns.size(); i++)
677 int[] region = hiddenColumns.elementAt(i);
678 if (result >= region[0])
680 result += region[1] - region[0] + 1;
688 * Use this method to find out where a column will appear in the visible
689 * alignment when hidden columns exist. If the column is not visible, then the
690 * left-most visible column will always be returned.
692 * @param hiddenColumn
696 public int findColumnPosition(int hiddenColumn)
698 int result = hiddenColumn;
699 if (hiddenColumns != null)
705 region = hiddenColumns.elementAt(index++);
706 if (hiddenColumn > region[1])
708 result -= region[1] + 1 - region[0];
710 } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
711 if (hiddenColumn > region[0] && hiddenColumn < region[1])
713 return region[0] + hiddenColumn - result;
716 return result; // return the shifted position after removing hidden columns.
720 * Use this method to determine where the next hiddenRegion starts
722 * @param hiddenRegion
723 * index of hidden region (counts from 0)
724 * @return column number in visible view
726 public int findHiddenRegionPosition(int hiddenRegion)
729 if (hiddenColumns != null)
735 int[] region = hiddenColumns.elementAt(index);
736 if (hiddenRegion == 0)
741 gaps += region[1] + 1 - region[0];
742 result = region[1] + 1;
744 } while (index <= hiddenRegion);
753 * THis method returns the rightmost limit of a region of an alignment with
754 * hidden columns. In otherwords, the next hidden column.
759 public int getHiddenBoundaryRight(int alPos)
761 if (hiddenColumns != null)
766 int[] region = hiddenColumns.elementAt(index);
767 if (alPos < region[0])
773 } while (index < hiddenColumns.size());
781 * This method returns the leftmost limit of a region of an alignment with
782 * hidden columns. In otherwords, the previous hidden column.
787 public int getHiddenBoundaryLeft(int alPos)
789 if (hiddenColumns != null)
791 int index = hiddenColumns.size() - 1;
794 int[] region = hiddenColumns.elementAt(index);
795 if (alPos > region[1])
801 } while (index > -1);
808 public void hideSelectedColumns()
810 synchronized (selection)
812 for (int[] selregions : selection.getRanges())
814 hideColumns(selregions[0], selregions[1]);
822 * Adds the specified column range to the hidden columns
827 public void hideColumns(int start, int end)
829 if (hiddenColumns == null)
831 hiddenColumns = new Vector<int[]>();
835 * traverse existing hidden ranges and insert / amend / append as
838 for (int i = 0; i < hiddenColumns.size(); i++)
840 int[] region = hiddenColumns.elementAt(i);
842 if (end < region[0] - 1)
845 * insert discontiguous preceding range
847 hiddenColumns.insertElementAt(new int[] { start, end }, i);
851 if (end <= region[1])
854 * new range overlaps existing, or is contiguous preceding it - adjust
857 region[0] = Math.min(region[0], start);
861 if (start <= region[1] + 1)
864 * new range overlaps existing, or is contiguous following it - adjust
865 * start and end columns
867 region[0] = Math.min(region[0], start);
868 region[1] = Math.max(region[1], end);
874 * remaining case is that the new range follows everything else
876 hiddenColumns.addElement(new int[] { start, end });
880 * Hides the specified column and any adjacent selected columns
885 public void hideColumns(int col)
888 * deselect column (whether selected or not!)
893 * find adjacent selected columns
895 int min = col - 1, max = col + 1;
896 while (contains(min))
902 while (contains(max))
909 * min, max are now the closest unselected columns
918 hideColumns(min, max);
922 * Unhides, and adds to the selection list, all hidden columns
924 public void revealAllHiddenColumns()
926 if (hiddenColumns != null)
928 for (int i = 0; i < hiddenColumns.size(); i++)
930 int[] region = hiddenColumns.elementAt(i);
931 for (int j = region[0]; j < region[1] + 1; j++)
938 hiddenColumns = null;
942 * Reveals, and marks as selected, the hidden column range with the given
947 public void revealHiddenColumns(int start)
949 for (int i = 0; i < hiddenColumns.size(); i++)
951 int[] region = hiddenColumns.elementAt(i);
952 if (start == region[0])
954 for (int j = region[0]; j < region[1] + 1; j++)
959 hiddenColumns.removeElement(region);
963 if (hiddenColumns.size() == 0)
965 hiddenColumns = null;
969 public boolean isVisible(int column)
971 if (hiddenColumns != null)
973 for (int[] region : hiddenColumns)
975 if (column >= region[0] && column <= region[1])
990 public ColumnSelection(ColumnSelection copy)
994 selection = new IntList(copy.selection);
995 if (copy.hiddenColumns != null)
997 hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
998 for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
1001 rh = copy.hiddenColumns.elementAt(i);
1004 cp = new int[rh.length];
1005 System.arraycopy(rh, 0, cp, 0, rh.length);
1006 hiddenColumns.addElement(cp);
1016 public ColumnSelection()
1020 public String[] getVisibleSequenceStrings(int start, int end,
1023 int i, iSize = seqs.length;
1024 String selections[] = new String[iSize];
1025 if (hiddenColumns != null && hiddenColumns.size() > 0)
1027 for (i = 0; i < iSize; i++)
1029 StringBuffer visibleSeq = new StringBuffer();
1030 List<int[]> regions = getHiddenColumns();
1032 int blockStart = start, blockEnd = end;
1034 int hideStart, hideEnd;
1036 for (int j = 0; j < regions.size(); j++)
1038 region = regions.get(j);
1039 hideStart = region[0];
1040 hideEnd = region[1];
1042 if (hideStart < start)
1047 blockStart = Math.min(blockStart, hideEnd + 1);
1048 blockEnd = Math.min(blockEnd, hideStart);
1050 if (blockStart > blockEnd)
1055 visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
1057 blockStart = hideEnd + 1;
1061 if (end > blockStart)
1063 visibleSeq.append(seqs[i].getSequence(blockStart, end));
1066 selections[i] = visibleSeq.toString();
1071 for (i = 0; i < iSize; i++)
1073 selections[i] = seqs[i].getSequenceAsString(start, end);
1081 * return all visible segments between the given start and end boundaries
1084 * (first column inclusive from 0)
1086 * (last column - not inclusive)
1087 * @return int[] {i_start, i_end, ..} where intervals lie in
1088 * start<=i_start<=i_end<end
1090 public int[] getVisibleContigs(int start, int end)
1092 if (hiddenColumns != null && hiddenColumns.size() > 0)
1094 List<int[]> visiblecontigs = new ArrayList<int[]>();
1095 List<int[]> regions = getHiddenColumns();
1099 int hideStart, hideEnd;
1101 for (int j = 0; vstart < end && j < regions.size(); j++)
1103 region = regions.get(j);
1104 hideStart = region[0];
1105 hideEnd = region[1];
1107 if (hideEnd < vstart)
1111 if (hideStart > vstart)
1113 visiblecontigs.add(new int[] { vstart, hideStart - 1 });
1115 vstart = hideEnd + 1;
1120 visiblecontigs.add(new int[] { vstart, end - 1 });
1122 int[] vcontigs = new int[visiblecontigs.size() * 2];
1123 for (int i = 0, j = visiblecontigs.size(); i < j; i++)
1125 int[] vc = visiblecontigs.get(i);
1126 visiblecontigs.set(i, null);
1127 vcontigs[i * 2] = vc[0];
1128 vcontigs[i * 2 + 1] = vc[1];
1130 visiblecontigs.clear();
1135 return new int[] { start, end - 1 };
1140 * Locate the first and last position visible for this sequence. if seq isn't
1141 * visible then return the position of the left and right of the hidden
1142 * boundary region, and the corresponding alignment column indices for the
1143 * extent of the sequence
1146 * @return int[] { visible start, visible end, first seqpos, last seqpos,
1147 * alignment index for seq start, alignment index for seq end }
1149 public int[] locateVisibleBoundsOfSequence(SequenceI seq)
1151 int fpos = seq.getStart(), lpos = seq.getEnd();
1154 if (hiddenColumns == null || hiddenColumns.size() == 0)
1156 int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
1157 return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
1160 // Simply walk along the sequence whilst watching for hidden column
1162 List<int[]> regions = getHiddenColumns();
1163 int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
1164 .getLength(), hideEnd = -1;
1165 int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
1166 boolean foundStart = false;
1167 for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
1170 if (!Comparison.isGap(seq.getCharAt(p)))
1172 // keep track of first/last column
1173 // containing sequence data regardless of visibility
1179 // update hidden region start/end
1180 while (hideEnd < p && rcount < regions.size())
1182 int[] region = regions.get(rcount++);
1184 visNext += region[0] - visPrev;
1185 hideStart = region[0];
1186 hideEnd = region[1];
1190 hideStart = seq.getLength();
1192 // update visible boundary for sequence
1204 // look for next sequence position
1210 return new int[] { findColumnPosition(start),
1211 findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
1213 // otherwise, sequence was completely hidden
1214 return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
1218 * delete any columns in alignmentAnnotation that are hidden (including
1219 * sequence associated annotation).
1221 * @param alignmentAnnotation
1223 public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
1225 makeVisibleAnnotation(-1, -1, alignmentAnnotation);
1229 * delete any columns in alignmentAnnotation that are hidden (including
1230 * sequence associated annotation).
1233 * remove any annotation to the right of this column
1235 * remove any annotation to the left of this column
1236 * @param alignmentAnnotation
1237 * the annotation to operate on
1239 public void makeVisibleAnnotation(int start, int end,
1240 AlignmentAnnotation alignmentAnnotation)
1242 if (alignmentAnnotation.annotations == null)
1246 if (start == end && end == -1)
1249 end = alignmentAnnotation.annotations.length;
1251 if (hiddenColumns != null && hiddenColumns.size() > 0)
1253 // then mangle the alignmentAnnotation annotation array
1254 Vector<Annotation[]> annels = new Vector<Annotation[]>();
1255 Annotation[] els = null;
1256 List<int[]> regions = getHiddenColumns();
1257 int blockStart = start, blockEnd = end;
1259 int hideStart, hideEnd, w = 0;
1261 for (int j = 0; j < regions.size(); j++)
1263 region = regions.get(j);
1264 hideStart = region[0];
1265 hideEnd = region[1];
1267 if (hideStart < start)
1272 blockStart = Math.min(blockStart, hideEnd + 1);
1273 blockEnd = Math.min(blockEnd, hideStart);
1275 if (blockStart > blockEnd)
1280 annels.addElement(els = new Annotation[blockEnd - blockStart]);
1281 System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
1284 blockStart = hideEnd + 1;
1288 if (end > blockStart)
1290 annels.addElement(els = new Annotation[end - blockStart + 1]);
1291 if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
1293 // copy just the visible segment of the annotation row
1294 System.arraycopy(alignmentAnnotation.annotations, blockStart,
1295 els, 0, els.length);
1299 // copy to the end of the annotation row
1300 System.arraycopy(alignmentAnnotation.annotations, blockStart,
1302 (alignmentAnnotation.annotations.length - blockStart));
1311 alignmentAnnotation.annotations = new Annotation[w];
1314 for (Annotation[] chnk : annels)
1316 System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
1323 alignmentAnnotation.restrict(start, end);
1328 * Invert the column selection from first to end-1. leaves hiddenColumns
1329 * untouched (and unselected)
1334 public void invertColumnSelection(int first, int width)
1336 boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
1337 for (int i = first; i < width; i++)
1345 if (!hasHidden || isVisible(i))
1354 * add in any unselected columns from the given column selection, excluding
1355 * any that are hidden.
1359 public void addElementsFrom(ColumnSelection colsel)
1361 if (colsel != null && !colsel.isEmpty())
1363 for (Integer col : colsel.getSelected())
1365 if (hiddenColumns != null && isVisible(col.intValue()))
1374 * set the selected columns the given column selection, excluding any columns
1379 public void setElementsFrom(ColumnSelection colsel)
1381 selection = new IntList();
1382 if (colsel.selection != null && colsel.selection.size() > 0)
1384 if (hiddenColumns != null && hiddenColumns.size() > 0)
1386 // only select visible columns in this columns selection
1387 addElementsFrom(colsel);
1391 // add everything regardless
1392 for (Integer col : colsel.getSelected())
1401 * Add gaps into the sequences aligned to profileseq under the given
1406 * - alignment to have gaps inserted into it
1408 * - alignment view where sequence corresponding to profileseq is
1410 * @return new Column selection for new alignment view, with insertions into
1411 * profileseq marked as hidden.
1413 public static ColumnSelection propagateInsertions(SequenceI profileseq,
1414 AlignmentI al, AlignmentView input)
1418 // return propagateInsertions(profileseq, al, )
1419 char gc = al.getGapCharacter();
1420 Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
1421 ColumnSelection nview = (ColumnSelection) alandcolsel[1];
1422 SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
1423 nview.propagateInsertions(profileseq, al, origseq);
1430 * - sequence in al which corresponds to origseq
1432 * - alignment which is to have gaps inserted into it
1434 * - sequence corresponding to profileseq which defines gap map for
1437 public void propagateInsertions(SequenceI profileseq, AlignmentI al,
1440 char gc = al.getGapCharacter();
1441 // recover mapping between sequence's non-gap positions and positions
1443 pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
1444 int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
1447 // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
1448 // alandcolsel[0])[0].gapMap()))
1449 // add profile to visible contigs
1450 for (int v = 0; v < viscontigs.length; v += 2)
1452 if (viscontigs[v] > spos)
1454 StringBuffer sb = new StringBuffer();
1455 for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
1459 for (int s = 0, ns = al.getHeight(); s < ns; s++)
1461 SequenceI sqobj = al.getSequenceAt(s);
1462 if (sqobj != profileseq)
1464 String sq = al.getSequenceAt(s).getSequenceAsString();
1465 if (sq.length() <= spos + offset)
1468 int diff = spos + offset - sq.length() - 1;
1473 while ((diff = spos + offset - sq.length() - 1) > 0)
1476 // + ((diff >= sb.length()) ? sb.toString() : sb
1477 // .substring(0, diff));
1478 if (diff >= sb.length())
1480 sq += sb.toString();
1484 char[] buf = new char[diff];
1485 sb.getChars(0, diff, buf, 0);
1486 sq += buf.toString();
1490 sq += sb.toString();
1494 al.getSequenceAt(s).setSequence(
1495 sq.substring(0, spos + offset) + sb.toString()
1496 + sq.substring(spos + offset));
1500 // offset+=sb.length();
1502 spos = viscontigs[v + 1] + 1;
1504 if ((offset + spos) < profileseq.getLength())
1506 // pad the final region with gaps.
1507 StringBuffer sb = new StringBuffer();
1508 for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
1512 for (int s = 0, ns = al.getHeight(); s < ns; s++)
1514 SequenceI sqobj = al.getSequenceAt(s);
1515 if (sqobj == profileseq)
1519 String sq = sqobj.getSequenceAsString();
1521 int diff = origseq.getLength() - sq.length();
1525 // + ((diff >= sb.length()) ? sb.toString() : sb
1526 // .substring(0, diff));
1527 if (diff >= sb.length())
1529 sq += sb.toString();
1533 char[] buf = new char[diff];
1534 sb.getChars(0, diff, buf, 0);
1535 sq += buf.toString();
1537 diff = origseq.getLength() - sq.length();
1545 * @return true if there are columns marked
1547 public boolean hasSelectedColumns()
1549 return (selection != null && selection.size() > 0);
1554 * @return true if there are columns hidden
1556 public boolean hasHiddenColumns()
1558 return hiddenColumns != null && hiddenColumns.size() > 0;
1563 * @return true if there are more than one set of columns hidden
1565 public boolean hasManyHiddenColumns()
1567 return hiddenColumns != null && hiddenColumns.size() > 1;
1571 * mark the columns corresponding to gap characters as hidden in the column
1576 public void hideInsertionsFor(SequenceI sr)
1578 List<int[]> inserts = sr.getInsertions();
1579 for (int[] r : inserts)
1581 hideColumns(r[0], r[1]);
1585 public boolean filterAnnotations(Annotation[] annotations,
1586 AnnotationFilterParameter filterParams)
1588 // JBPNote - this method needs to be refactored to become independent of
1589 // viewmodel package
1590 this.revealAllHiddenColumns();
1595 if (annotations[count] != null)
1598 boolean itemMatched = false;
1600 if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
1601 && annotations[count].value >= filterParams
1602 .getThresholdValue())
1606 if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
1607 && annotations[count].value <= filterParams
1608 .getThresholdValue())
1613 if (filterParams.isFilterAlphaHelix()
1614 && annotations[count].secondaryStructure == 'H')
1619 if (filterParams.isFilterBetaSheet()
1620 && annotations[count].secondaryStructure == 'E')
1625 if (filterParams.isFilterTurn()
1626 && annotations[count].secondaryStructure == 'S')
1631 String regexSearchString = filterParams.getRegexString();
1632 if (regexSearchString != null
1633 && !filterParams.getRegexSearchFields().isEmpty())
1635 List<SearchableAnnotationField> fields = filterParams
1636 .getRegexSearchFields();
1639 if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
1640 && annotations[count].displayCharacter
1641 .matches(regexSearchString))
1645 } catch (java.util.regex.PatternSyntaxException pse)
1647 if (annotations[count].displayCharacter
1648 .equals(regexSearchString))
1653 if (fields.contains(SearchableAnnotationField.DESCRIPTION)
1654 && annotations[count].description != null
1655 && annotations[count].description
1656 .matches(regexSearchString))
1664 this.addElement(count);
1668 } while (count < annotations.length);
1673 * Returns a hashCode built from selected columns and hidden column ranges
1676 public int hashCode()
1678 int hashCode = selection.hashCode();
1679 if (hiddenColumns != null)
1681 for (int[] hidden : hiddenColumns)
1683 hashCode = 31 * hashCode + hidden[0];
1684 hashCode = 31 * hashCode + hidden[1];
1691 * Answers true if comparing to a ColumnSelection with the same selected
1692 * columns and hidden columns, else false
1695 public boolean equals(Object obj)
1697 if (!(obj instanceof ColumnSelection))
1701 ColumnSelection that = (ColumnSelection) obj;
1704 * check columns selected are either both null, or match
1706 if (this.selection == null)
1708 if (that.selection != null)
1713 if (!this.selection.equals(that.selection))
1719 * check hidden columns are either both null, or match
1721 if (this.hiddenColumns == null)
1723 return (that.hiddenColumns == null);
1725 if (that.hiddenColumns == null
1726 || that.hiddenColumns.size() != this.hiddenColumns.size())
1731 for (int[] thisRange : hiddenColumns)
1733 int[] thatRange = that.hiddenColumns.get(i++);
1734 if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
1743 * Updates the column selection depending on the parameters, and returns true
1744 * if any change was made to the selection
1746 * @param markedColumns
1747 * a set identifying marked columns (base 0)
1749 * the first column of the range to operate over (base 0)
1751 * the last column of the range to operate over (base 0)
1753 * if true, deselect marked columns and select unmarked
1754 * @param extendCurrent
1755 * if true, extend rather than replacing the current column selection
1757 * if true, toggle the selection state of marked columns
1761 public boolean markColumns(BitSet markedColumns, int startCol,
1762 int endCol, boolean invert, boolean extendCurrent, boolean toggle)
1764 boolean changed = false;
1765 if (!extendCurrent && !toggle)
1767 changed = !this.isEmpty();
1772 // invert only in the currently selected sequence region
1773 int i = markedColumns.nextClearBit(startCol);
1774 int ibs = markedColumns.nextSetBit(startCol);
1775 while (i >= startCol && i <= endCol)
1777 if (ibs < 0 || i < ibs)
1780 if (toggle && contains(i))
1791 i = markedColumns.nextClearBit(ibs);
1792 ibs = markedColumns.nextSetBit(i);
1798 int i = markedColumns.nextSetBit(startCol);
1799 while (i >= startCol && i <= endCol)
1802 if (toggle && contains(i))
1810 i = markedColumns.nextSetBit(i + 1);