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.BitSet;
25 import java.util.Iterator;
26 import java.util.List;
27 import java.util.concurrent.locks.ReentrantReadWriteLock;
30 * This class manages the collection of hidden columns associated with an
31 * alignment. To iterate over the collection, or over visible columns/regions,
32 * use an iterator obtained from one of:
34 * - getBoundedIterator: iterate over the hidden regions, within some bounds
36 * - getBoundedStartIterator: iterate over the start positions of hidden
37 * regions, within some bounds
39 * - getVisContigsIterator: iterate over visible regions in a range, returning
42 * - getVisibleBlocksIterator
44 * - getVisibleColsIterator: iterate over the visible *columns*
46 * For performance reasons, provide bounds where possible.
51 public class HiddenColumns
53 private static final int HASH_MULTIPLIER = 31;
55 private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
58 * Cursor which tracks the last used hidden columns region, and the number
59 * of hidden columns up to (but not including) that region.
61 private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
64 * cache of the number of hidden columns
66 private int numColumns = 0;
69 * list of hidden column [start, end] ranges; the list is maintained in
70 * ascending start column order
72 private ArrayList<int[]> hiddenColumns;
77 public HiddenColumns()
82 * Methods which change the hiddenColumns collection. These methods should
83 * use a writeLock to prevent other threads accessing the hiddenColumns
84 * collection while changes are being made. They should also reset the hidden
85 * columns cursor, and either update the hidden columns count, or set it to 0.
92 * the HiddenColumns object to copy from
94 public HiddenColumns(HiddenColumns copy)
98 LOCK.writeLock().lock();
102 if (copy.hiddenColumns != null)
104 hiddenColumns = new ArrayList<>();
105 Iterator<int[]> it = copy.iterator();
108 int[] region = it.next();
109 hiddenColumns.add(region);
110 numColumns += region[1] - region[0] + 1;
112 cursor.resetCursor(hiddenColumns);
117 LOCK.writeLock().unlock();
122 * Copy constructor within bounds and with offset. Copies hidden column
123 * regions fully contained between start and end, and offsets positions by
124 * subtracting offset.
127 * HiddenColumns instance to copy from
129 * lower bound to copy from
131 * upper bound to copy to
133 * offset to subtract from each region boundary position
136 public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
140 LOCK.writeLock().lock();
143 hiddenColumns = new ArrayList<>();
145 Iterator<int[]> it = copy.getBoundedIterator(start, end);
148 int[] region = it.next();
149 // still need to check boundaries because iterator returns
150 // all overlapping regions and we need contained regions
151 if (region[0] >= start && region[1] <= end)
155 { region[0] - offset, region[1] - offset });
156 numColumns += region[1] - region[0] + 1;
159 cursor.resetCursor(hiddenColumns);
163 LOCK.writeLock().unlock();
168 * Adds the specified column range to the hidden columns collection
171 * start of range to add (absolute position in alignment)
173 * end of range to add (absolute position in alignment)
175 public void hideColumns(int start, int end)
177 boolean wasAlreadyLocked = false;
180 // check if the write lock was already locked by this thread,
181 // as this method can be called internally in loops within HiddenColumns
182 if (!LOCK.isWriteLockedByCurrentThread())
184 LOCK.writeLock().lock();
188 wasAlreadyLocked = true;
191 if (hiddenColumns == null)
193 hiddenColumns = new ArrayList<>();
197 * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
199 if (hiddenColumns.isEmpty()
200 || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
202 hiddenColumns.add(new int[] { start, end });
207 * traverse existing hidden ranges and insert / amend / append as
210 boolean added = false;
211 for (int i = 0; !added && i < hiddenColumns.size(); i++)
213 added = insertRangeAtRegion(i, start, end);
216 if (!wasAlreadyLocked)
218 cursor.resetCursor(hiddenColumns);
220 // reset the number of columns so they will be recounted
225 if (!wasAlreadyLocked)
227 LOCK.writeLock().unlock();
233 * Insert [start, range] at the region at index i in hiddenColumns, if
239 * start of range to insert
241 * end of range to insert
242 * @return true if range was successfully inserted
244 private boolean insertRangeAtRegion(int i, int start, int end)
246 boolean added = false;
248 int[] region = hiddenColumns.get(i);
249 if (end < region[0] - 1)
252 * insert discontiguous preceding range
254 hiddenColumns.add(i, new int[] { start, end });
257 else if (end <= region[1])
260 * new range overlaps existing, or is contiguous preceding it - adjust
263 region[0] = Math.min(region[0], start);
266 else if (start <= region[1] + 1)
269 * new range overlaps existing, or is contiguous following it - adjust
270 * start and end columns
272 region[0] = Math.min(region[0], start);
273 region[1] = Math.max(region[1], end);
276 * also update or remove any subsequent ranges
277 * that are overlapped
279 while (i < hiddenColumns.size() - 1)
281 int[] nextRegion = hiddenColumns.get(i + 1);
282 if (nextRegion[0] > end + 1)
285 * gap to next hidden range - no more to update
289 region[1] = Math.max(nextRegion[1], end);
290 hiddenColumns.subList(i + 1, i + 2).clear();
298 * mark the columns corresponding to gap characters as hidden in the column
303 public void hideInsertionsFor(SequenceI sr)
307 LOCK.writeLock().lock();
308 List<int[]> inserts = sr.getInsertions();
309 for (int[] r : inserts)
311 hideColumns(r[0], r[1]);
313 cursor.resetCursor(hiddenColumns);
317 LOCK.writeLock().unlock();
322 * Unhides, and adds to the selection list, all hidden columns
324 public void revealAllHiddenColumns(ColumnSelection sel)
328 LOCK.writeLock().lock();
329 if (hiddenColumns != null)
331 Iterator<int[]> it = hiddenColumns.iterator();
334 int[] region = it.next();
335 for (int j = region[0]; j < region[1] + 1; j++)
340 hiddenColumns = null;
341 cursor.resetCursor(hiddenColumns);
346 LOCK.writeLock().unlock();
351 * Reveals, and marks as selected, the hidden column range with the given
355 * the start column to look for
357 * the column selection to add the hidden column range to
359 public void revealHiddenColumns(int start, ColumnSelection sel)
363 LOCK.writeLock().lock();
365 if (hiddenColumns != null)
367 int regionIndex = cursor.findRegionForColumn(start)
370 if (regionIndex != -1 && regionIndex != hiddenColumns.size())
372 // regionIndex is the region which either contains start
373 // or lies to the right of start
374 int[] region = hiddenColumns.get(regionIndex);
375 if (start == region[0])
377 for (int j = region[0]; j < region[1] + 1; j++)
381 int colsToRemove = region[1] - region[0] + 1;
382 hiddenColumns.remove(regionIndex);
384 if (hiddenColumns.isEmpty())
386 hiddenColumns = null;
391 numColumns -= colsToRemove;
393 cursor.updateForDeletedRegion(hiddenColumns);
399 LOCK.writeLock().unlock();
404 * Add gaps into the sequences aligned to profileseq under the given
408 * sequence in al which sequences are aligned to
410 * alignment to have gaps inserted into it
412 * alignment view where sequence corresponding to profileseq is first
414 * @return new HiddenColumns for new alignment view, with insertions into
415 * profileseq marked as hidden.
417 public static HiddenColumns propagateInsertions(SequenceI profileseq,
418 AlignmentI al, AlignmentView input)
422 char gc = al.getGapCharacter();
423 Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
424 HiddenColumns nview = (HiddenColumns) alandhidden[1];
425 SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
426 nview.propagateInsertions(profileseq, al, origseq);
433 * sequence in al which corresponds to origseq
435 * alignment which is to have gaps inserted into it
437 * sequence corresponding to profileseq which defines gap map for
440 private void propagateInsertions(SequenceI profileseq, AlignmentI al,
445 LOCK.writeLock().lock();
447 char gc = al.getGapCharacter();
449 // take the set of hidden columns, and the set of gaps in origseq,
450 // and remove all the hidden gaps from hiddenColumns
452 // first get the gaps as a Bitset
453 BitSet gaps = origseq.gapBitset();
455 // now calculate hidden ^ not(gap)
456 BitSet hidden = new BitSet();
457 markHiddenRegions(hidden);
459 hiddenColumns = null;
460 this.hideMarkedBits(hidden);
462 // for each sequence in the alignment, except the profile sequence,
463 // insert gaps corresponding to each hidden region but where each hidden
464 // column region is shifted backwards by the number of preceding visible
465 // gaps update hidden columns at the same time
466 Iterator<int[]> regions = hiddenColumns.iterator();
467 ArrayList<int[]> newhidden = new ArrayList<>();
469 int numGapsBefore = 0;
471 while (regions.hasNext())
473 // get region coordinates accounting for gaps
474 // we can rely on gaps not being *in* hidden regions because we already
476 int[] region = regions.next();
477 while (gapPosition < region[0])
480 if (gaps.get(gapPosition))
486 int left = region[0] - numGapsBefore;
487 int right = region[1] - numGapsBefore;
488 newhidden.add(new int[] { left, right });
490 // make a string with number of gaps = length of hidden region
491 StringBuffer sb = new StringBuffer();
492 for (int s = 0; s < right - left + 1; s++)
496 padGaps(sb, left, profileseq, al);
499 hiddenColumns = newhidden;
500 cursor.resetCursor(hiddenColumns);
504 LOCK.writeLock().unlock();
509 * Pad gaps in all sequences in alignment except profileseq
512 * gap string to insert
514 * position to insert at
516 * sequence not to pad
518 * alignment to pad sequences in
520 private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
523 // loop over the sequences and pad with gaps where required
524 for (int s = 0, ns = al.getHeight(); s < ns; s++)
526 SequenceI sqobj = al.getSequenceAt(s);
527 if (sqobj != profileseq)
529 String sq = al.getSequenceAt(s).getSequenceAsString();
530 if (sq.length() <= pos)
533 int diff = pos - sq.length() - 1;
538 while ((diff = pos - sq.length() - 1) > 0)
540 if (diff >= sb.length())
546 char[] buf = new char[diff];
547 sb.getChars(0, diff, buf, 0);
548 sq += buf.toString();
556 al.getSequenceAt(s).setSequence(
557 sq.substring(0, pos) + sb.toString() + sq.substring(pos));
564 * Methods which only need read access to the hidden columns collection.
565 * These methods should use a readLock to prevent other threads changing
566 * the hidden columns collection while it is in use.
570 * Output regions data as a string. String is in the format:
571 * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
574 * string to delimit regions
575 * @param betweenstring
576 * to put between start and end region values
577 * @return regions formatted according to delimiter and between strings
579 public String regionsToString(String delimiter, String between)
583 LOCK.readLock().lock();
584 StringBuilder regionBuilder = new StringBuilder();
585 if (hiddenColumns != null)
587 Iterator<int[]> it = hiddenColumns.iterator();
590 int[] range = it.next();
591 regionBuilder.append(delimiter).append(range[0]).append(between)
595 regionBuilder.deleteCharAt(0);
599 return regionBuilder.toString();
602 LOCK.readLock().unlock();
607 * Find the number of hidden columns
609 * @return number of hidden columns
615 LOCK.readLock().lock();
617 if (numColumns == 0 && hiddenColumns != null)
619 // numColumns is out of date, so recalculate
621 if (hiddenColumns != null)
623 Iterator<int[]> it = hiddenColumns.iterator();
626 int[] range = it.next();
627 size += range[1] - range[0] + 1;
636 LOCK.readLock().unlock();
641 * Get the number of distinct hidden regions
643 * @return number of regions
645 public int getNumberOfRegions()
649 LOCK.readLock().lock();
651 if (hasHiddenColumns())
653 num = hiddenColumns.size();
658 LOCK.readLock().unlock();
663 public boolean equals(Object obj)
667 LOCK.readLock().lock();
669 if (!(obj instanceof HiddenColumns))
673 HiddenColumns that = (HiddenColumns) obj;
676 * check hidden columns are either both null, or match
678 if (this.hiddenColumns == null)
680 return (that.hiddenColumns == null);
682 if (that.hiddenColumns == null
683 || that.hiddenColumns.size() != this.hiddenColumns.size())
688 Iterator<int[]> it = hiddenColumns.iterator();
689 Iterator<int[]> thatit = that.iterator();
692 int[] thisRange = it.next();
693 int[] thatRange = thatit.next();
694 if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
702 LOCK.readLock().unlock();
707 * Return absolute column index for a visible column index
710 * int column index in alignment view (count from zero)
711 * @return alignment column index for column
713 public int adjustForHiddenColumns(int column)
717 LOCK.readLock().lock();
720 if (hiddenColumns != null)
722 result += cursor.getHiddenOffset(column).getHiddenSoFar();
728 LOCK.readLock().unlock();
733 * Use this method to find out where a column will appear in the visible
734 * alignment when hidden columns exist. If the column is not visible, then the
735 * left-most visible column will always be returned.
737 * @param hiddenColumn
738 * the column index in the full alignment including hidden columns
739 * @return the position of the column in the visible alignment
741 public int findColumnPosition(int hiddenColumn)
745 LOCK.readLock().lock();
746 int result = hiddenColumn;
748 if (hiddenColumns != null)
750 HiddenCursorPosition cursorPos = cursor
751 .findRegionForColumn(hiddenColumn);
752 int index = cursorPos.getRegionIndex();
753 int hiddenBeforeCol = cursorPos.getHiddenSoFar();
755 // just subtract hidden cols count - this works fine if column is
757 result = hiddenColumn - hiddenBeforeCol;
759 // now check in case column is hidden - it will be in the returned
761 if (index < hiddenColumns.size())
763 int[] region = hiddenColumns.get(index);
764 if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
766 // actually col is hidden, return region[0]-1
767 // unless region[0]==0 in which case return 0
774 result = region[0] - 1 - hiddenBeforeCol;
780 return result; // return the shifted position after removing hidden
784 LOCK.readLock().unlock();
789 * Find the visible column which is a given visible number of columns to the
790 * left of another visible column. i.e. for a startColumn x, the column which
791 * is distance 1 away will be column x-1.
793 * @param visibleDistance
794 * the number of visible columns to offset by
796 * the column to start from
797 * @return the position of the column in the visible alignment
799 public int subtractVisibleColumns(int visibleDistance, int startColumn)
803 LOCK.readLock().lock();
804 int distance = visibleDistance;
806 // in case startColumn is in a hidden region, move it to the left
807 int start = adjustForHiddenColumns(findColumnPosition(startColumn));
809 Iterator<int[]> it = new ReverseRegionsIterator(0, start,
812 while (it.hasNext() && (distance > 0))
814 int[] region = it.next();
816 if (start > region[1])
818 // subtract the gap to right of region from distance
819 if (start - region[1] <= distance)
821 distance -= start - region[1];
822 start = region[0] - 1;
826 start = start - distance;
831 return start - distance;
835 LOCK.readLock().unlock();
840 * This method returns the rightmost limit of a region of an alignment with
841 * hidden columns. In otherwords, the next hidden column.
844 * the absolute (visible) alignmentPosition to find the next hidden
847 public int getHiddenBoundaryRight(int alPos)
851 LOCK.readLock().lock();
852 if (hiddenColumns != null)
854 int index = cursor.findRegionForColumn(alPos).getRegionIndex();
855 if (index < hiddenColumns.size())
857 int[] region = hiddenColumns.get(index);
858 if (alPos < region[0])
862 else if ((alPos <= region[1])
863 && (index + 1 < hiddenColumns.size()))
865 // alPos is within a hidden region, return the next one
867 region = hiddenColumns.get(index + 1);
875 LOCK.readLock().unlock();
880 * This method returns the leftmost limit of a region of an alignment with
881 * hidden columns. In otherwords, the previous hidden column.
884 * the absolute (visible) alignmentPosition to find the previous
887 public int getHiddenBoundaryLeft(int alPos)
891 LOCK.readLock().lock();
893 if (hiddenColumns != null)
895 int index = cursor.findRegionForColumn(alPos).getRegionIndex();
899 int[] region = hiddenColumns.get(index - 1);
906 LOCK.readLock().unlock();
912 * Answers if a column in the alignment is visible
915 * absolute position of column in the alignment
916 * @return true if column is visible
918 public boolean isVisible(int column)
922 LOCK.readLock().lock();
924 int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
925 if (regionindex > -1 && regionindex < hiddenColumns.size())
927 int[] region = hiddenColumns.get(regionindex);
928 if (column >= region[0] && column <= region[1])
937 LOCK.readLock().unlock();
942 * Get the visible sections of a set of sequences
945 * sequence position to start from
947 * sequence position to end at
949 * an array of sequences
950 * @return an array of strings encoding the visible parts of each sequence
952 public String[] getVisibleSequenceStrings(int start, int end,
957 LOCK.readLock().lock();
958 int iSize = seqs.length;
959 String[] selections = new String[iSize];
960 if (hiddenColumns != null && hiddenColumns.size() > 0)
962 for (int i = 0; i < iSize; i++)
964 StringBuffer visibleSeq = new StringBuffer();
966 Iterator<int[]> blocks = new VisibleContigsIterator(start,
967 end + 1, hiddenColumns);
969 while (blocks.hasNext())
971 int[] block = blocks.next();
972 if (blocks.hasNext())
975 .append(seqs[i].getSequence(block[0], block[1] + 1));
980 .append(seqs[i].getSequence(block[0], block[1]));
984 selections[i] = visibleSeq.toString();
989 for (int i = 0; i < iSize; i++)
991 selections[i] = seqs[i].getSequenceAsString(start, end);
998 LOCK.readLock().unlock();
1003 * Locate the first position visible for this sequence. If seq isn't visible
1004 * then return the position of the left side of the hidden boundary region.
1007 * sequence to find position for
1008 * @return visible start position
1010 public int locateVisibleStartOfSequence(SequenceI seq)
1014 LOCK.readLock().lock();
1017 if (hiddenColumns == null || hiddenColumns.size() == 0)
1019 return seq.findIndex(seq.getStart()) - 1;
1022 // Simply walk along the sequence whilst watching for hidden column
1024 Iterator<int[]> regions = hiddenColumns.iterator();
1025 int hideStart = seq.getLength();
1029 boolean foundStart = false;
1031 // step through the non-gapped positions of the sequence
1032 for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
1034 // get alignment position of this residue in the sequence
1035 int p = seq.findIndex(i) - 1;
1037 // update hidden region start/end
1038 while (hideEnd < p && regions.hasNext())
1040 int[] region = regions.next();
1042 visNext += region[0] - visPrev;
1043 hideStart = region[0];
1044 hideEnd = region[1];
1048 hideStart = seq.getLength();
1050 // update visible boundary for sequence
1060 return findColumnPosition(start);
1062 // otherwise, sequence was completely hidden
1066 LOCK.readLock().unlock();
1071 * delete any columns in alignmentAnnotation that are hidden (including
1072 * sequence associated annotation).
1074 * @param alignmentAnnotation
1076 public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
1078 makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
1079 alignmentAnnotation);
1083 * delete any columns in alignmentAnnotation that are hidden (including
1084 * sequence associated annotation).
1087 * remove any annotation to the right of this column
1089 * remove any annotation to the left of this column
1090 * @param alignmentAnnotation
1091 * the annotation to operate on
1093 public void makeVisibleAnnotation(int start, int end,
1094 AlignmentAnnotation alignmentAnnotation)
1098 LOCK.readLock().lock();
1100 int startFrom = start;
1103 if (alignmentAnnotation.annotations != null)
1105 if (hiddenColumns != null && hiddenColumns.size() > 0)
1107 removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
1111 alignmentAnnotation.restrict(startFrom, endAt);
1116 LOCK.readLock().unlock();
1120 private void removeHiddenAnnotation(int start, int end,
1121 AlignmentAnnotation alignmentAnnotation)
1123 // mangle the alignmentAnnotation annotation array
1124 ArrayList<Annotation[]> annels = new ArrayList<>();
1125 Annotation[] els = null;
1129 Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
1133 int annotationLength;
1134 while (blocks.hasNext())
1136 int[] block = blocks.next();
1137 annotationLength = block[1] - block[0] + 1;
1139 if (blocks.hasNext())
1141 // copy just the visible segment of the annotation row
1142 copylength = annotationLength;
1146 if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
1148 // copy just the visible segment of the annotation row
1149 copylength = annotationLength;
1153 // copy to the end of the annotation row
1154 copylength = alignmentAnnotation.annotations.length - block[0];
1158 els = new Annotation[annotationLength];
1160 System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
1162 w += annotationLength;
1167 alignmentAnnotation.annotations = new Annotation[w];
1170 for (Annotation[] chnk : annels)
1172 System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
1181 * @return true if there are columns hidden
1183 public boolean hasHiddenColumns()
1187 LOCK.readLock().lock();
1188 return hiddenColumns != null && hiddenColumns.size() > 0;
1191 LOCK.readLock().unlock();
1197 * @return true if there are more than one set of columns hidden
1199 public boolean hasManyHiddenColumns()
1203 LOCK.readLock().lock();
1204 return hiddenColumns != null && hiddenColumns.size() > 1;
1207 LOCK.readLock().unlock();
1213 * Returns a hashCode built from hidden column ranges
1216 public int hashCode()
1220 LOCK.readLock().lock();
1222 Iterator<int[]> it = hiddenColumns.iterator();
1223 while (it.hasNext())
1225 int[] hidden = it.next();
1226 hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
1227 hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
1232 LOCK.readLock().unlock();
1237 * Hide columns corresponding to the marked bits
1240 * - columns map to bits starting from zero
1242 public void hideMarkedBits(BitSet inserts)
1246 LOCK.writeLock().lock();
1247 for (int firstSet = inserts
1248 .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
1249 .nextSetBit(lastSet))
1251 lastSet = inserts.nextClearBit(firstSet);
1252 hideColumns(firstSet, lastSet - 1);
1254 cursor.resetCursor(hiddenColumns);
1258 LOCK.writeLock().unlock();
1265 * BitSet where hidden columns will be marked
1267 public void markHiddenRegions(BitSet inserts)
1271 LOCK.readLock().lock();
1272 if (hiddenColumns == null)
1276 Iterator<int[]> it = hiddenColumns.iterator();
1277 while (it.hasNext())
1279 int[] range = it.next();
1280 inserts.set(range[0], range[1] + 1);
1284 LOCK.readLock().unlock();
1289 * Calculate the visible start and end index of an alignment.
1292 * full alignment width
1293 * @return integer array where: int[0] = startIndex, and int[1] = endIndex
1295 public int[] getVisibleStartAndEndIndex(int width)
1299 LOCK.readLock().lock();
1300 int[] alignmentStartEnd = new int[] { 0, width - 1 };
1301 int startPos = alignmentStartEnd[0];
1302 int endPos = alignmentStartEnd[1];
1304 int[] lowestRange = new int[] { -1, -1 };
1305 int[] higestRange = new int[] { -1, -1 };
1307 if (hiddenColumns == null)
1309 return new int[] { startPos, endPos };
1312 Iterator<int[]> it = hiddenColumns.iterator();
1313 while (it.hasNext())
1315 int[] range = it.next();
1316 lowestRange = (range[0] <= startPos) ? range : lowestRange;
1317 higestRange = (range[1] >= endPos) ? range : higestRange;
1320 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1322 startPos = alignmentStartEnd[0];
1326 startPos = lowestRange[1] + 1;
1329 if (higestRange[0] == -1 && higestRange[1] == -1)
1331 endPos = alignmentStartEnd[1];
1335 endPos = higestRange[0] - 1;
1337 return new int[] { startPos, endPos };
1340 LOCK.readLock().unlock();
1345 * Finds the hidden region (if any) which starts or ends at res
1348 * visible residue position, unadjusted for hidden columns
1349 * @return region as [start,end] or null if no matching region is found
1351 public int[] getRegionWithEdgeAtRes(int res)
1355 LOCK.readLock().lock();
1356 int adjres = adjustForHiddenColumns(res);
1358 int[] reveal = null;
1360 if (hiddenColumns != null)
1362 // look for a region ending just before adjres
1363 int regionindex = cursor.findRegionForColumn(adjres - 1)
1365 if (regionindex < hiddenColumns.size()
1366 && hiddenColumns.get(regionindex)[1] == adjres - 1)
1368 reveal = hiddenColumns.get(regionindex);
1370 // check if the region ends just after adjres
1371 else if (regionindex < hiddenColumns.size()
1372 && hiddenColumns.get(regionindex)[0] == adjres + 1)
1374 reveal = hiddenColumns.get(regionindex);
1376 // or try the next region
1380 if (regionindex < hiddenColumns.size()
1381 && hiddenColumns.get(regionindex)[0] == adjres + 1)
1383 reveal = hiddenColumns.get(regionindex);
1391 LOCK.readLock().unlock();
1396 * Return an iterator over the hidden regions
1398 public Iterator<int[]> iterator()
1402 LOCK.readLock().lock();
1403 return new BoundedHiddenColsIterator(hiddenColumns);
1406 LOCK.readLock().unlock();
1411 * Return a bounded iterator over the hidden regions
1414 * position to start from (inclusive, absolute column position)
1416 * position to end at (inclusive, absolute column position)
1419 public Iterator<int[]> getBoundedIterator(int start, int end)
1423 LOCK.readLock().lock();
1424 return new BoundedHiddenColsIterator(start, end, hiddenColumns);
1427 LOCK.readLock().unlock();
1432 * Return a bounded iterator over the *visible* start positions of hidden
1436 * position to start from (inclusive, visible column position)
1438 * position to end at (inclusive, visible column position)
1440 public Iterator<Integer> getBoundedStartIterator(int start, int end)
1444 LOCK.readLock().lock();
1446 // get absolute position of column in alignment
1447 int absoluteStart = adjustForHiddenColumns(start);
1449 // Get cursor position and supply it to the iterator:
1450 // Since we want visible region start, we look for a cursor for the
1451 // (absoluteStart-1), then if absoluteStart is the start of a visible
1452 // region we'll get the cursor pointing to the region before, which is
1454 HiddenCursorPosition pos = cursor
1455 .findRegionForColumn(absoluteStart - 1);
1457 return new BoundedStartRegionIterator(pos, start, end,
1461 LOCK.readLock().unlock();
1466 * Return an iterator over visible *columns* (not regions) between the given
1467 * start and end boundaries
1470 * first column (inclusive)
1472 * last column (inclusive)
1474 public Iterator<Integer> getVisibleColsIterator(int start, int end)
1478 LOCK.readLock().lock();
1479 return new VisibleColsIterator(start, end, hiddenColumns);
1482 LOCK.readLock().unlock();
1487 * return an iterator over visible segments between the given start and end
1491 * first column, inclusive from 0
1493 * last column - not inclusive
1494 * @param useVisibleCoords
1495 * if true, start and end are visible column positions, not absolute
1498 public Iterator<int[]> getVisContigsIterator(int start, int end,
1499 boolean useVisibleCoords)
1501 int adjstart = start;
1503 if (useVisibleCoords)
1505 adjstart = adjustForHiddenColumns(start);
1506 adjend = adjustForHiddenColumns(end);
1511 LOCK.readLock().lock();
1512 return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
1515 LOCK.readLock().unlock();