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 java.util.ArrayList;
24 import java.util.Arrays;
25 import java.util.BitSet;
26 import java.util.Iterator;
27 import java.util.List;
28 import java.util.concurrent.locks.ReentrantReadWriteLock;
31 * This class manages the collection of hidden columns associated with an
32 * alignment. To iterate over the collection, or over visible columns/regions,
33 * use an iterator obtained from one of:
35 * - getBoundedIterator: iterates over the hidden regions, within some bounds,
36 * returning *absolute* positions
38 * - getBoundedStartIterator: iterates over the start positions of hidden
39 * regions, within some bounds, returning *visible* positions
41 * - getVisContigsIterator: iterates over visible regions in a range, returning
42 * *absolute* positions
44 * - getVisibleColsIterator: iterates over the visible *columns*
46 * For performance reasons, provide bounds where possible. Note that column
47 * numbering begins at 0 throughout this class.
52 /* Implementation notes:
54 * Methods which change the hiddenColumns collection should use a writeLock to
55 * prevent other threads accessing the hiddenColumns collection while changes
56 * are being made. They should also reset the hidden columns cursor, and either
57 * update the hidden columns count, or set it to 0 (so that it will later be
58 * updated when needed).
61 * Methods which only need read access to the hidden columns collection should
62 * use a readLock to prevent other threads changing the hidden columns
63 * collection while it is in use.
65 public class HiddenColumns
67 private static final int HASH_MULTIPLIER = 31;
69 private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
72 * Cursor which tracks the last used hidden columns region, and the number
73 * of hidden columns up to (but not including) that region.
75 private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
78 * cache of the number of hidden columns
80 private int numColumns = 0;
83 * list of hidden column [start, end] ranges; the list is maintained in
84 * ascending start column order
86 private List<int[]> hiddenColumns = new ArrayList<>();
91 public HiddenColumns()
99 * the HiddenColumns object to copy from
101 public HiddenColumns(HiddenColumns copy)
103 this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
107 * Copy constructor within bounds and with offset. Copies hidden column
108 * regions fully contained between start and end, and offsets positions by
109 * subtracting offset.
112 * HiddenColumns instance to copy from
114 * lower bound to copy from
116 * upper bound to copy to
118 * offset to subtract from each region boundary position
121 public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
125 LOCK.writeLock().lock();
129 Iterator<int[]> it = copy.getBoundedIterator(start, end);
132 int[] region = it.next();
133 // still need to check boundaries because iterator returns
134 // all overlapping regions and we need contained regions
135 if (region[0] >= start && region[1] <= end)
139 { region[0] - offset, region[1] - offset });
140 numColumns += region[1] - region[0] + 1;
143 cursor = new HiddenColumnsCursor(hiddenColumns);
147 LOCK.writeLock().unlock();
152 * Adds the specified column range to the hidden columns collection
155 * start of range to add (absolute position in alignment)
157 * end of range to add (absolute position in alignment)
159 public void hideColumns(int start, int end)
163 LOCK.writeLock().lock();
166 int prevHiddenCount = 0;
168 if (!hiddenColumns.isEmpty())
170 // set up cursor reset values
171 HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start, false);
172 regionindex = cursorPos.getRegionIndex();
176 // get previous index and hidden count for updating the cursor later
177 previndex = regionindex - 1;
178 int[] prevRegion = hiddenColumns.get(previndex);
179 prevHiddenCount = cursorPos.getHiddenSoFar()
180 - (prevRegion[1] - prevRegion[0] + 1);
184 // new range follows everything else; check first to avoid looping over
185 // whole hiddenColumns collection
186 if (hiddenColumns.isEmpty()
187 || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
189 hiddenColumns.add(new int[] { start, end });
190 numColumns += end - start + 1;
195 * traverse existing hidden ranges and insert / amend / append as
198 boolean added = false;
201 added = insertRangeAtRegion(regionindex - 1, start, end);
203 if (!added && regionindex < hiddenColumns.size())
205 insertRangeAtRegion(regionindex, start, end);
209 // reset the cursor to just before our insertion point: this saves
210 // a lot of reprocessing in large alignments
211 cursor = new HiddenColumnsCursor(hiddenColumns, previndex,
215 LOCK.writeLock().unlock();
220 * Insert [start, range] at the region at index i in hiddenColumns, if
226 * start of range to insert
228 * end of range to insert
229 * @return true if range was successfully inserted
231 private boolean insertRangeAtRegion(int i, int start, int end)
233 boolean added = false;
235 int[] region = hiddenColumns.get(i);
236 if (end < region[0] - 1)
239 * insert discontiguous preceding range
241 hiddenColumns.add(i, new int[] { start, end });
242 numColumns += end - start + 1;
245 else if (end <= region[1])
248 * new range overlaps existing, or is contiguous preceding it - adjust
251 int oldstart = region[0];
252 region[0] = Math.min(region[0], start);
253 numColumns += oldstart - region[0]; // new columns are between old and
257 else if (start <= region[1] + 1)
260 * new range overlaps existing, or is contiguous following it - adjust
261 * start and end columns
263 insertRangeAtOverlap(i, start, end, region);
270 * Insert a range whose start position overlaps an existing region and/or is
271 * contiguous to the right of the region
276 * start of range to insert
278 * end of range to insert
280 * the overlapped/continued region
282 private void insertRangeAtOverlap(int i, int start, int end, int[] region)
284 int oldstart = region[0];
285 int oldend = region[1];
286 region[0] = Math.min(region[0], start);
287 region[1] = Math.max(region[1], end);
289 numColumns += oldstart - region[0];
290 numColumns += region[1] - oldend;
293 * also update or remove any subsequent ranges
294 * that are overlapped
297 while (endi < hiddenColumns.size() - 1)
299 int[] nextRegion = hiddenColumns.get(endi + 1);
300 if (nextRegion[0] > end + 1)
303 * gap to next hidden range - no more to update
307 numColumns -= nextRegion[1] - nextRegion[0] + 1;
308 oldend = nextRegion[1];
309 region[1] = Math.max(nextRegion[1], end);
310 numColumns += region[1] - oldend + 1;
313 hiddenColumns.subList(i + 1, endi + 1).clear();
317 * hide a list of ranges
321 public void hideList(List<int[]> ranges)
325 LOCK.writeLock().lock();
326 for (int[] r : ranges)
328 hideColumns(r[0], r[1]);
330 cursor = new HiddenColumnsCursor(hiddenColumns);
334 LOCK.writeLock().unlock();
339 * Unhides, and adds to the selection list, all hidden columns
341 public void revealAllHiddenColumns(ColumnSelection sel)
345 LOCK.writeLock().lock();
347 for (int[] region : hiddenColumns)
349 for (int j = region[0]; j < region[1] + 1; j++)
354 hiddenColumns.clear();
355 cursor = new HiddenColumnsCursor(hiddenColumns);
360 LOCK.writeLock().unlock();
365 * Reveals, and marks as selected, the hidden column range with the given
369 * the start column to look for
371 * the column selection to add the hidden column range to
373 public void revealHiddenColumns(int start, ColumnSelection sel)
377 LOCK.writeLock().lock();
379 if (!hiddenColumns.isEmpty())
381 int regionIndex = cursor.findRegionForColumn(start, false)
384 if (regionIndex != -1 && regionIndex != hiddenColumns.size())
386 // regionIndex is the region which either contains start
387 // or lies to the right of start
388 int[] region = hiddenColumns.get(regionIndex);
389 if (start == region[0])
391 for (int j = region[0]; j < region[1] + 1; j++)
395 int colsToRemove = region[1] - region[0] + 1;
396 hiddenColumns.remove(regionIndex);
397 numColumns -= colsToRemove;
399 cursor.updateForDeletedRegion(hiddenColumns);
405 LOCK.writeLock().unlock();
410 * Output regions data as a string. String is in the format:
411 * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
414 * string to delimit regions
415 * @param betweenstring
416 * to put between start and end region values
417 * @return regions formatted according to delimiter and between strings
419 public String regionsToString(String delimiter, String between)
423 LOCK.readLock().lock();
424 StringBuilder regionBuilder = new StringBuilder();
426 boolean first = true;
427 for (int[] range : hiddenColumns)
431 regionBuilder.append(delimiter);
437 regionBuilder.append(range[0]).append(between).append(range[1]);
441 return regionBuilder.toString();
444 LOCK.readLock().unlock();
449 * Find the number of hidden columns
451 * @return number of hidden columns
459 * Get the number of distinct hidden regions
461 * @return number of regions
463 public int getNumberOfRegions()
467 LOCK.readLock().lock();
468 return hiddenColumns.size();
471 LOCK.readLock().unlock();
476 public boolean equals(Object obj)
480 LOCK.readLock().lock();
482 if (!(obj instanceof HiddenColumns))
486 HiddenColumns that = (HiddenColumns) obj;
489 * check hidden columns are either both null, or match
492 if (that.hiddenColumns.size() != this.hiddenColumns.size())
497 Iterator<int[]> it = this.iterator();
498 Iterator<int[]> thatit = that.iterator();
501 if (!(Arrays.equals(it.next(), thatit.next())))
510 LOCK.readLock().unlock();
515 * Return absolute column index for a visible column index
518 * int column index in alignment view (count from zero)
519 * @return alignment column index for column
521 public int visibleToAbsoluteColumn(int column)
525 LOCK.readLock().lock();
528 if (!hiddenColumns.isEmpty())
530 result += cursor.findRegionForColumn(column, true)
537 LOCK.readLock().unlock();
542 * Use this method to find out where a column will appear in the visible
543 * alignment when hidden columns exist. If the column is not visible, then the
544 * index of the next visible column on the left will be returned (or 0 if
545 * there is no visible column on the left)
547 * @param hiddenColumn
548 * the column index in the full alignment including hidden columns
549 * @return the position of the column in the visible alignment
551 public int absoluteToVisibleColumn(int hiddenColumn)
555 LOCK.readLock().lock();
556 int result = hiddenColumn;
558 if (!hiddenColumns.isEmpty())
560 HiddenCursorPosition cursorPos = cursor
561 .findRegionForColumn(hiddenColumn, false);
562 int index = cursorPos.getRegionIndex();
563 int hiddenBeforeCol = cursorPos.getHiddenSoFar();
565 // just subtract hidden cols count - this works fine if column is
567 result = hiddenColumn - hiddenBeforeCol;
569 // now check in case column is hidden - it will be in the returned
571 if (index < hiddenColumns.size())
573 int[] region = hiddenColumns.get(index);
574 if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
576 // actually col is hidden, return region[0]-1
577 // unless region[0]==0 in which case return 0
584 result = region[0] - 1 - hiddenBeforeCol;
590 return result; // return the shifted position after removing hidden
594 LOCK.readLock().unlock();
599 * Find the visible column which is a given visible number of columns to the
600 * left (negative visibleDistance) or right (positive visibleDistance) of
601 * startColumn. If startColumn is not visible, we use the visible column at
602 * the left boundary of the hidden region containing startColumn.
604 * @param visibleDistance
605 * the number of visible columns to offset by (left offset = negative
606 * value; right offset = positive value)
608 * the position of the column to start from (absolute position)
609 * @return the position of the column which is <visibleDistance> away
610 * (absolute position)
612 public int offsetByVisibleColumns(int visibleDistance, int startColumn)
616 LOCK.readLock().lock();
617 int start = absoluteToVisibleColumn(startColumn);
618 return visibleToAbsoluteColumn(start + visibleDistance);
622 LOCK.readLock().unlock();
627 * This method returns the rightmost limit of a region of an alignment with
628 * hidden columns. In otherwords, the next hidden column.
631 * the absolute (visible) alignmentPosition to find the next hidden
633 * @return the index of the next hidden column, or alPos if there is no next
636 public int getNextHiddenBoundary(boolean left, int alPos)
640 LOCK.readLock().lock();
641 if (!hiddenColumns.isEmpty())
643 int index = cursor.findRegionForColumn(alPos, false)
646 if (left && index > 0)
648 int[] region = hiddenColumns.get(index - 1);
651 else if (!left && index < hiddenColumns.size())
653 int[] region = hiddenColumns.get(index);
654 if (alPos < region[0])
658 else if ((alPos <= region[1])
659 && (index + 1 < hiddenColumns.size()))
661 // alPos is within a hidden region, return the next one
663 region = hiddenColumns.get(index + 1);
671 LOCK.readLock().unlock();
676 * Answers if a column in the alignment is visible
679 * absolute position of column in the alignment
680 * @return true if column is visible
682 public boolean isVisible(int column)
686 LOCK.readLock().lock();
688 int regionindex = cursor.findRegionForColumn(column, false)
690 if (regionindex > -1 && regionindex < hiddenColumns.size())
692 int[] region = hiddenColumns.get(regionindex);
693 // already know that column <= region[1] as cursor returns containing
694 // region or region to right
695 if (column >= region[0])
704 LOCK.readLock().unlock();
710 * @return true if there are columns hidden
712 public boolean hasHiddenColumns()
716 LOCK.readLock().lock();
718 // we don't use getSize()>0 here because it has to iterate over
719 // the full hiddenColumns collection and so will be much slower
720 return (!hiddenColumns.isEmpty());
723 LOCK.readLock().unlock();
729 * @return true if there is more than one hidden column region
731 public boolean hasMultiHiddenColumnRegions()
735 LOCK.readLock().lock();
736 return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1;
739 LOCK.readLock().unlock();
745 * Returns a hashCode built from hidden column ranges
748 public int hashCode()
752 LOCK.readLock().lock();
755 for (int[] hidden : hiddenColumns)
757 hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
758 hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
763 LOCK.readLock().unlock();
768 * Hide columns corresponding to the marked bits
771 * - columns mapped to bits starting from zero
773 public void hideColumns(BitSet inserts)
777 LOCK.writeLock().lock();
778 for (int firstSet = inserts
779 .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
780 .nextSetBit(lastSet))
782 lastSet = inserts.nextClearBit(firstSet);
783 hideColumns(firstSet, lastSet - 1);
785 cursor = new HiddenColumnsCursor(hiddenColumns);
788 LOCK.writeLock().unlock();
793 * Hide columns corresponding to the marked bits, within the range
794 * [start,end]. Entries in tohide which are outside [start,end] are ignored.
797 * columns mapped to bits starting from zero
799 * start of range to hide columns within
801 * end of range to hide columns within
803 public void hideColumns(BitSet tohide, int start, int end)
805 clearHiddenColumnsInRange(start, end);
807 // make sure only bits between start and end are set
808 if (!tohide.isEmpty())
810 tohide.clear(0, start);
811 tohide.clear(Math.min(end + 1, tohide.length() + 1),
812 tohide.length() + 1);
819 * Make all columns in the range [start,end] visible
822 * start of range to show columns
824 * end of range to show columns
826 private void clearHiddenColumnsInRange(int start, int end)
830 LOCK.writeLock().lock();
832 if (!hiddenColumns.isEmpty())
834 HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
835 int index = pos.getRegionIndex();
837 if (index != -1 && index != hiddenColumns.size())
839 // regionIndex is the region which either contains start
840 // or lies to the right of start
841 int[] region = hiddenColumns.get(index);
842 if (region[0] < start && region[1] >= start)
844 // region contains start, truncate so that it ends just before start
845 numColumns -= region[1] - start + 1;
846 region[1] = start - 1;
851 while (endi < hiddenColumns.size())
853 region = hiddenColumns.get(endi);
857 if (region[0] <= end)
859 // region contains end, truncate so it starts just after end
860 numColumns -= end - region[0] + 1;
866 numColumns -= region[1] - region[0] + 1;
869 hiddenColumns.subList(index, endi).clear();
873 cursor = new HiddenColumnsCursor(hiddenColumns);
877 LOCK.writeLock().unlock();
884 * BitSet where hidden columns will be marked
886 protected void andNot(BitSet updates)
890 LOCK.writeLock().lock();
892 BitSet hiddenBitSet = new BitSet();
893 for (int[] range : hiddenColumns)
895 hiddenBitSet.set(range[0], range[1] + 1);
897 hiddenBitSet.andNot(updates);
898 hiddenColumns.clear();
899 hideColumns(hiddenBitSet);
902 LOCK.writeLock().unlock();
907 * Calculate the visible start and end index of an alignment.
910 * full alignment width
911 * @return integer array where: int[0] = startIndex, and int[1] = endIndex
913 public int[] getVisibleStartAndEndIndex(int width)
917 LOCK.readLock().lock();
919 int firstVisible = 0;
920 int lastVisible = width - 1;
922 if (!hiddenColumns.isEmpty())
924 // first visible col with index 0, convert to absolute index
925 firstVisible = visibleToAbsoluteColumn(0);
927 // last visible column is either immediately to left of
928 // last hidden region, or is just the last column in the alignment
929 int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1);
930 if (lastregion[1] == width - 1)
932 // last region is at very end of alignment
933 // last visible column immediately precedes it
934 lastVisible = lastregion[0] - 1;
937 return new int[] { firstVisible, lastVisible };
941 LOCK.readLock().unlock();
946 * Finds the hidden region (if any) which starts or ends at res
949 * visible residue position, unadjusted for hidden columns
950 * @return region as [start,end] or null if no matching region is found. If
951 * res is adjacent to two regions, returns the left region.
953 public int[] getRegionWithEdgeAtRes(int res)
957 LOCK.readLock().lock();
958 int adjres = visibleToAbsoluteColumn(res);
962 if (!hiddenColumns.isEmpty())
964 // look for a region ending just before adjres
965 int regionindex = cursor.findRegionForColumn(adjres - 1, false)
967 if (regionindex < hiddenColumns.size()
968 && hiddenColumns.get(regionindex)[1] == adjres - 1)
970 reveal = hiddenColumns.get(regionindex);
972 // check if the region ends just after adjres
973 else if (regionindex < hiddenColumns.size()
974 && hiddenColumns.get(regionindex)[0] == adjres + 1)
976 reveal = hiddenColumns.get(regionindex);
983 LOCK.readLock().unlock();
988 * Return an iterator over the hidden regions
990 public Iterator<int[]> iterator()
994 LOCK.readLock().lock();
995 return new HiddenColsIterator(hiddenColumns);
998 LOCK.readLock().unlock();
1003 * Return a bounded iterator over the hidden regions
1006 * position to start from (inclusive, absolute column position)
1008 * position to end at (inclusive, absolute column position)
1011 public Iterator<int[]> getBoundedIterator(int start, int end)
1015 LOCK.readLock().lock();
1016 return new HiddenColsIterator(start, end, hiddenColumns);
1019 LOCK.readLock().unlock();
1024 * Return a bounded iterator over the *visible* start positions of hidden
1028 * position to start from (inclusive, visible column position)
1030 * position to end at (inclusive, visible column position)
1032 public Iterator<Integer> getBoundedStartIterator(int start, int end)
1036 LOCK.readLock().lock();
1038 // get absolute position of column in alignment
1039 int absoluteStart = visibleToAbsoluteColumn(start);
1041 // Get cursor position and supply it to the iterator:
1042 // Since we want visible region start, we look for a cursor for the
1043 // (absoluteStart-1), then if absoluteStart is the start of a visible
1044 // region we'll get the cursor pointing to the region before, which is
1046 HiddenCursorPosition pos = cursor
1047 .findRegionForColumn(absoluteStart - 1, false);
1049 return new BoundedStartRegionIterator(pos, start, end,
1053 LOCK.readLock().unlock();
1058 * Return an iterator over visible *columns* (not regions) between the given
1059 * start and end boundaries
1062 * first column (inclusive)
1064 * last column (inclusive)
1066 public Iterator<Integer> getVisibleColsIterator(int start, int end)
1070 LOCK.readLock().lock();
1071 return new VisibleColsIterator(start, end, hiddenColumns);
1074 LOCK.readLock().unlock();
1079 * return an iterator over visible segments between the given start and end
1083 * first column, inclusive from 0
1085 * last column - not inclusive
1086 * @param useVisibleCoords
1087 * if true, start and end are visible column positions, not absolute
1090 public VisibleContigsIterator getVisContigsIterator(int start,
1092 boolean useVisibleCoords)
1094 int adjstart = start;
1096 if (useVisibleCoords)
1098 adjstart = visibleToAbsoluteColumn(start);
1099 adjend = visibleToAbsoluteColumn(end);
1104 LOCK.readLock().lock();
1105 return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
1108 LOCK.readLock().unlock();