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;
25 import java.util.ArrayList;
26 import java.util.BitSet;
27 import java.util.Iterator;
28 import java.util.List;
29 import java.util.NoSuchElementException;
30 import java.util.Vector;
31 import java.util.concurrent.locks.ReentrantReadWriteLock;
33 public class HiddenColumns
35 private static final int HASH_MULTIPLIER = 31;
37 private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
40 * list of hidden column [start, end] ranges; the list is maintained in
41 * ascending start column order
43 private ArrayList<int[]> hiddenColumns;
48 public HiddenColumns()
57 public HiddenColumns(HiddenColumns copy)
61 LOCK.writeLock().lock();
64 if (copy.hiddenColumns != null)
66 hiddenColumns = copy.copyHiddenRegionsToArrayList(0);
71 LOCK.writeLock().unlock();
76 * Copy constructor within bounds and with offset. Copies hidden column
77 * regions fully contained between start and end, and offsets positions by
81 * HiddenColumns instance to copy from
83 * lower bound to copy from
85 * upper bound to copy to
87 * offset to subtract from each region boundary position
90 public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
94 LOCK.writeLock().lock();
97 hiddenColumns = new ArrayList<>();
98 Iterator<int[]> it = copy.getBoundedIterator(start, end);
101 int[] region = it.next();
102 // still need to check boundaries because iterator returns
103 // all overlapping regions and we need contained regions
104 if (region[0] >= start && region[1] <= end)
108 { region[0] - offset, region[1] - offset });
114 LOCK.writeLock().unlock();
119 * Output regions data as a string. String is in the format:
120 * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
123 * string to delimit regions
124 * @param betweenstring
125 * to put between start and end region values
126 * @return regions formatted according to delimiter and between strings
128 public String regionsToString(String delimiter, String between)
132 LOCK.readLock().lock();
133 StringBuilder regionBuilder = new StringBuilder();
134 if (hiddenColumns != null)
136 for (int[] range : hiddenColumns)
138 regionBuilder.append(delimiter).append(range[0]).append(between)
142 regionBuilder.deleteCharAt(0);
144 return regionBuilder.toString();
147 LOCK.readLock().unlock();
152 * Find the number of hidden columns
154 * @return number of hidden columns
160 LOCK.readLock().lock();
162 if (hasHiddenColumns())
164 for (int[] range : hiddenColumns)
166 size += range[1] - range[0] + 1;
172 LOCK.readLock().unlock();
177 * Get the number of distinct hidden regions
179 * @return number of regions
181 public int getNumberOfRegions()
185 LOCK.readLock().lock();
187 if (hasHiddenColumns())
189 num = hiddenColumns.size();
194 LOCK.readLock().unlock();
199 public boolean equals(Object obj)
203 LOCK.readLock().lock();
205 if (!(obj instanceof HiddenColumns))
209 HiddenColumns that = (HiddenColumns) obj;
212 * check hidden columns are either both null, or match
214 if (this.hiddenColumns == null)
216 return (that.hiddenColumns == null);
218 if (that.hiddenColumns == null
219 || that.hiddenColumns.size() != this.hiddenColumns.size())
224 for (int[] thisRange : hiddenColumns)
226 int[] thatRange = that.hiddenColumns.get(i++);
227 if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
235 LOCK.readLock().unlock();
240 * Return absolute column index for a visible column index
243 * int column index in alignment view (count from zero)
244 * @return alignment column index for column
246 public int adjustForHiddenColumns(int column)
250 LOCK.readLock().lock();
252 if (hiddenColumns != null)
254 for (int i = 0; i < hiddenColumns.size(); i++)
256 int[] region = hiddenColumns.get(i);
257 if (result >= region[0])
259 result += region[1] - region[0] + 1;
266 LOCK.readLock().unlock();
271 * Use this method to find out where a column will appear in the visible
272 * alignment when hidden columns exist. If the column is not visible, then the
273 * left-most visible column will always be returned.
275 * @param hiddenColumn
276 * the column index in the full alignment including hidden columns
277 * @return the position of the column in the visible alignment
279 public int findColumnPosition(int hiddenColumn)
283 LOCK.readLock().lock();
284 int result = hiddenColumn;
285 if (hiddenColumns != null)
291 region = hiddenColumns.get(index++);
292 if (hiddenColumn > region[1])
294 result -= region[1] + 1 - region[0];
296 } while ((hiddenColumn > region[1])
297 && (index < hiddenColumns.size()));
299 if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
301 // Here the hidden column is within a region, so
302 // we want to return the position of region[0]-1, adjusted for any
303 // earlier hidden columns.
304 // Calculate the difference between the actual hidden col position
305 // and region[0]-1, and then subtract from result to convert result
307 // the adjusted hiddenColumn value to the adjusted region[0]-1 value
309 // However, if the region begins at 0 we cannot return region[0]-1
317 return result - (hiddenColumn - region[0] + 1);
321 return result; // return the shifted position after removing hidden
325 LOCK.readLock().unlock();
330 * Find the visible column which is a given visible number of columns to the
331 * left of another visible column. i.e. for a startColumn x, the column which
332 * is distance 1 away will be column x-1.
334 * @param visibleDistance
335 * the number of visible columns to offset by
337 * the column to start from
338 * @return the position of the column in the visible alignment
340 public int subtractVisibleColumns(int visibleDistance, int startColumn)
345 LOCK.readLock().lock();
346 int distance = visibleDistance;
348 // in case startColumn is in a hidden region, move it to the left
349 int start = adjustForHiddenColumns(findColumnPosition(startColumn));
351 // get index of hidden region to left of start
352 int index = getHiddenIndexLeft(start);
355 // no hidden regions to left of startColumn
356 return start - distance;
359 // walk backwards through the alignment subtracting the counts of visible
360 // columns from distance
363 int nextstart = start;
365 while ((index > -1) && (distance - gap > 0))
367 // subtract the gap to right of region from distance
371 // calculate the next gap
372 region = hiddenColumns.get(index);
373 gap = start - region[1];
375 // set start to just to left of current region
376 nextstart = region[0] - 1;
380 if (distance - gap > 0)
382 // fell out of loop because there are no more hidden regions
384 return nextstart - distance;
386 return start - distance;
389 LOCK.readLock().unlock();
397 * This method returns the rightmost limit of a region of an alignment with
398 * hidden columns. In otherwords, the next hidden column.
403 public int getHiddenBoundaryRight(int alPos)
407 LOCK.readLock().lock();
408 if (hiddenColumns != null)
413 int[] region = hiddenColumns.get(index);
414 if (alPos < region[0])
420 } while (index < hiddenColumns.size());
426 LOCK.readLock().unlock();
432 * This method returns the leftmost limit of a region of an alignment with
433 * hidden columns. In otherwords, the previous hidden column.
438 public int getHiddenBoundaryLeft(int alPos)
442 LOCK.readLock().lock();
444 if (hiddenColumns != null)
446 int index = hiddenColumns.size() - 1;
449 int[] region = hiddenColumns.get(index);
450 if (alPos > region[1])
456 } while (index > -1);
462 LOCK.readLock().unlock();
467 * This method returns the index of the hidden region to the left of a column
468 * position. If the column is in a hidden region it returns the index of the
469 * region to the left. If there is no hidden region to the left it returns -1.
474 private int getHiddenIndexLeft(int pos)
479 LOCK.readLock().lock();
480 if (hiddenColumns != null)
482 int index = hiddenColumns.size() - 1;
485 int[] region = hiddenColumns.get(index);
492 } while (index > -1);
498 LOCK.readLock().unlock();
504 * Adds the specified column range to the hidden columns
509 public void hideColumns(int start, int end)
511 boolean wasAlreadyLocked = false;
514 // check if the write lock was already locked by this thread,
515 // as this method can be called internally in loops within HiddenColumns
516 if (!LOCK.isWriteLockedByCurrentThread())
518 LOCK.writeLock().lock();
522 wasAlreadyLocked = true;
525 if (hiddenColumns == null)
527 hiddenColumns = new ArrayList<>();
531 * traverse existing hidden ranges and insert / amend / append as
534 for (int i = 0; i < hiddenColumns.size(); i++)
536 int[] region = hiddenColumns.get(i);
538 if (end < region[0] - 1)
541 * insert discontiguous preceding range
543 hiddenColumns.add(i, new int[] { start, end });
547 if (end <= region[1])
550 * new range overlaps existing, or is contiguous preceding it - adjust
553 region[0] = Math.min(region[0], start);
557 if (start <= region[1] + 1)
560 * new range overlaps existing, or is contiguous following it - adjust
561 * start and end columns
563 region[0] = Math.min(region[0], start);
564 region[1] = Math.max(region[1], end);
567 * also update or remove any subsequent ranges
568 * that are overlapped
570 while (i < hiddenColumns.size() - 1)
572 int[] nextRegion = hiddenColumns.get(i + 1);
573 if (nextRegion[0] > end + 1)
576 * gap to next hidden range - no more to update
580 region[1] = Math.max(nextRegion[1], end);
581 hiddenColumns.remove(i + 1);
588 * remaining case is that the new range follows everything else
590 hiddenColumns.add(new int[] { start, end });
593 if (!wasAlreadyLocked)
595 LOCK.writeLock().unlock();
600 public boolean isVisible(int column)
604 LOCK.readLock().lock();
606 if (hiddenColumns != null)
608 for (int[] region : hiddenColumns)
610 if (column >= region[0] && column <= region[1])
620 LOCK.readLock().unlock();
624 private ArrayList<int[]> copyHiddenRegionsToArrayList(int startIndex)
627 if (hiddenColumns != null)
629 size = hiddenColumns.size();
631 ArrayList<int[]> copy = new ArrayList<>(size);
633 for (int i = startIndex, j = size; i < j; i++)
637 rh = hiddenColumns.get(i);
640 cp = new int[rh.length];
641 System.arraycopy(rh, 0, cp, 0, rh.length);
649 public String[] getVisibleSequenceStrings(int start, int end,
654 LOCK.readLock().lock();
655 int iSize = seqs.length;
656 String[] selections = new String[iSize];
657 if (hiddenColumns != null && hiddenColumns.size() > 0)
659 for (int i = 0; i < iSize; i++)
661 StringBuffer visibleSeq = new StringBuffer();
663 Iterator<int[]> blocks = new VisibleBlocksIterator(start,
665 while (blocks.hasNext())
667 int[] block = blocks.next();
668 visibleSeq.append(seqs[i].getSequence(block[0], block[1]));
671 selections[i] = visibleSeq.toString();
676 for (int i = 0; i < iSize; i++)
678 selections[i] = seqs[i].getSequenceAsString(start, end);
685 LOCK.readLock().unlock();
690 * Locate the first and last position visible for this sequence. if seq isn't
691 * visible then return the position of the left and right of the hidden
692 * boundary region, and the corresponding alignment column indices for the
693 * extent of the sequence
696 * @return int[] { visible start, first seqpos, last seqpos }
698 public int locateVisibleBoundsOfSequence(SequenceI seq)
702 LOCK.readLock().lock();
705 if (hiddenColumns == null || hiddenColumns.size() == 0)
707 return seq.findIndex(seq.getStart()) - 1;
710 // Simply walk along the sequence whilst watching for hidden column
712 Iterator<int[]> regions = iterator();
713 int spos = seq.getStart();
714 int hideStart = seq.getLength();
719 boolean foundStart = false;
720 for (int p = 0; spos <= seq.getEnd() && p < seq.getLength(); p++)
722 if (!Comparison.isGap(seq.getCharAt(p)))
724 // update hidden region start/end
725 while (hideEnd < p && regions.hasNext())
727 int[] region = regions.next();
729 visNext += region[0] - visPrev;
730 hideStart = region[0];
735 hideStart = seq.getLength();
737 // update visible boundary for sequence
738 if ((p < hideStart) && (!foundStart))
743 // look for next sequence position
749 return findColumnPosition(start);
751 // otherwise, sequence was completely hidden
755 LOCK.readLock().unlock();
760 * delete any columns in alignmentAnnotation that are hidden (including
761 * sequence associated annotation).
763 * @param alignmentAnnotation
765 public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
767 makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
768 alignmentAnnotation);
772 * delete any columns in alignmentAnnotation that are hidden (including
773 * sequence associated annotation).
776 * remove any annotation to the right of this column
778 * remove any annotation to the left of this column
779 * @param alignmentAnnotation
780 * the annotation to operate on
782 public void makeVisibleAnnotation(int start, int end,
783 AlignmentAnnotation alignmentAnnotation)
787 LOCK.readLock().lock();
789 int startFrom = start;
792 if (alignmentAnnotation.annotations != null)
794 if (hiddenColumns != null && hiddenColumns.size() > 0)
796 removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
800 alignmentAnnotation.restrict(startFrom, endAt);
805 LOCK.readLock().unlock();
809 private void removeHiddenAnnotation(int start, int end,
810 AlignmentAnnotation alignmentAnnotation)
812 // mangle the alignmentAnnotation annotation array
813 Vector<Annotation[]> annels = new Vector<>();
814 Annotation[] els = null;
818 Iterator<int[]> blocks = new VisibleBlocksIterator(start, end,
821 int annotationLength;
822 while (blocks.hasNext())
824 int[] block = blocks.next();
826 if (blocks.hasNext())
828 annotationLength = block[1] - block[0];
829 // copy just the visible segment of the annotation row
830 copylength = annotationLength;
834 annotationLength = block[1] - block[0] + 1;
835 if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
837 // copy just the visible segment of the annotation row
838 copylength = annotationLength;
842 // copy to the end of the annotation row
843 copylength = alignmentAnnotation.annotations.length - block[0];
847 els = new Annotation[annotationLength];
848 annels.addElement(els);
849 System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
851 w += annotationLength;
856 alignmentAnnotation.annotations = new Annotation[w];
859 for (Annotation[] chnk : annels)
861 System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
870 * @return true if there are columns hidden
872 public boolean hasHiddenColumns()
876 LOCK.readLock().lock();
877 return hiddenColumns != null && hiddenColumns.size() > 0;
880 LOCK.readLock().unlock();
886 * @return true if there are more than one set of columns hidden
888 public boolean hasManyHiddenColumns()
892 LOCK.readLock().lock();
893 return hiddenColumns != null && hiddenColumns.size() > 1;
896 LOCK.readLock().unlock();
901 * mark the columns corresponding to gap characters as hidden in the column
906 public void hideInsertionsFor(SequenceI sr)
910 LOCK.writeLock().lock();
911 List<int[]> inserts = sr.getInsertions();
912 for (int[] r : inserts)
914 hideColumns(r[0], r[1]);
918 LOCK.writeLock().unlock();
923 * Unhides, and adds to the selection list, all hidden columns
925 public void revealAllHiddenColumns(ColumnSelection sel)
929 LOCK.writeLock().lock();
930 if (hiddenColumns != null)
932 for (int i = 0; i < hiddenColumns.size(); i++)
934 int[] region = hiddenColumns.get(i);
935 for (int j = region[0]; j < region[1] + 1; j++)
942 hiddenColumns = null;
945 LOCK.writeLock().unlock();
950 * Reveals, and marks as selected, the hidden column range with the given
955 public void revealHiddenColumns(int start, ColumnSelection sel)
959 LOCK.writeLock().lock();
960 for (int i = 0; i < hiddenColumns.size(); i++)
962 int[] region = hiddenColumns.get(i);
963 if (start == region[0])
965 for (int j = region[0]; j < region[1] + 1; j++)
970 hiddenColumns.remove(region);
974 if (hiddenColumns.size() == 0)
976 hiddenColumns = null;
980 LOCK.writeLock().unlock();
985 * Add gaps into the sequences aligned to profileseq under the given
990 * - alignment to have gaps inserted into it
992 * - alignment view where sequence corresponding to profileseq is
994 * @return new HiddenColumns for new alignment view, with insertions into
995 * profileseq marked as hidden.
997 public static HiddenColumns propagateInsertions(SequenceI profileseq,
998 AlignmentI al, AlignmentView input)
1002 char gc = al.getGapCharacter();
1003 Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
1004 HiddenColumns nview = (HiddenColumns) alandhidden[1];
1005 SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
1006 nview.propagateInsertions(profileseq, al, origseq);
1013 * - sequence in al which corresponds to origseq
1015 * - alignment which is to have gaps inserted into it
1017 * - sequence corresponding to profileseq which defines gap map for
1020 private void propagateInsertions(SequenceI profileseq, AlignmentI al,
1025 LOCK.writeLock().lock();
1027 char gc = al.getGapCharacter();
1029 // take the set of hidden columns, and the set of gaps in origseq,
1030 // and remove all the hidden gaps from hiddenColumns
1032 // first get the gaps as a Bitset
1033 BitSet gaps = origseq.gapBitset();
1035 // now calculate hidden ^ not(gap)
1036 BitSet hidden = new BitSet();
1037 markHiddenRegions(hidden);
1038 hidden.andNot(gaps);
1039 hiddenColumns = null;
1040 this.hideMarkedBits(hidden);
1042 // for each sequence in the alignment, except the profile sequence,
1043 // insert gaps corresponding to each hidden region
1044 // but where each hidden column region is shifted backwards by the number
1046 // preceding visible gaps
1047 // update hidden columns at the same time
1048 Iterator<int[]> regions = iterator();
1049 ArrayList<int[]> newhidden = new ArrayList<>();
1051 int numGapsBefore = 0;
1052 int gapPosition = 0;
1053 while (regions.hasNext())
1055 // get region coordinates accounting for gaps
1056 // we can rely on gaps not being *in* hidden regions because we already
1058 int[] region = regions.next();
1059 while (gapPosition < region[0])
1062 if (gaps.get(gapPosition))
1068 int left = region[0] - numGapsBefore;
1069 int right = region[1] - numGapsBefore;
1070 newhidden.add(new int[] { left, right });
1072 // make a string with number of gaps = length of hidden region
1073 StringBuffer sb = new StringBuffer();
1074 for (int s = 0; s < right - left + 1; s++)
1078 padGaps(sb, left, profileseq, al);
1081 hiddenColumns = newhidden;
1084 LOCK.writeLock().unlock();
1089 * Pad gaps in all sequences in alignment except profileseq
1092 * gap string to insert
1094 * position to insert at
1096 * sequence not to pad
1098 * alignment to pad sequences in
1100 private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
1103 // loop over the sequences and pad with gaps where required
1104 for (int s = 0, ns = al.getHeight(); s < ns; s++)
1106 SequenceI sqobj = al.getSequenceAt(s);
1107 if (sqobj != profileseq)
1109 String sq = al.getSequenceAt(s).getSequenceAsString();
1110 if (sq.length() <= pos)
1113 int diff = pos - sq.length() - 1;
1118 while ((diff = pos - sq.length() - 1) > 0)
1120 if (diff >= sb.length())
1122 sq += sb.toString();
1126 char[] buf = new char[diff];
1127 sb.getChars(0, diff, buf, 0);
1128 sq += buf.toString();
1132 sq += sb.toString();
1136 al.getSequenceAt(s).setSequence(
1137 sq.substring(0, pos) + sb.toString() + sq.substring(pos));
1144 * Returns a hashCode built from hidden column ranges
1147 public int hashCode()
1151 LOCK.readLock().lock();
1153 if (hiddenColumns != null)
1155 for (int[] hidden : hiddenColumns)
1157 hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
1158 hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
1164 LOCK.readLock().unlock();
1169 * Hide columns corresponding to the marked bits
1172 * - columns map to bits starting from zero
1174 public void hideMarkedBits(BitSet inserts)
1178 LOCK.writeLock().lock();
1179 for (int firstSet = inserts
1180 .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
1181 .nextSetBit(lastSet))
1183 lastSet = inserts.nextClearBit(firstSet);
1184 hideColumns(firstSet, lastSet - 1);
1188 LOCK.writeLock().unlock();
1195 * BitSet where hidden columns will be marked
1197 public void markHiddenRegions(BitSet inserts)
1201 LOCK.readLock().lock();
1202 if (hiddenColumns == null)
1206 for (int[] range : hiddenColumns)
1208 inserts.set(range[0], range[1] + 1);
1212 LOCK.readLock().unlock();
1217 * Calculate the visible start and end index of an alignment.
1220 * full alignment width
1221 * @return integer array where: int[0] = startIndex, and int[1] = endIndex
1223 public int[] getVisibleStartAndEndIndex(int width)
1227 LOCK.readLock().lock();
1228 int[] alignmentStartEnd = new int[] { 0, width - 1 };
1229 int startPos = alignmentStartEnd[0];
1230 int endPos = alignmentStartEnd[1];
1232 int[] lowestRange = new int[] { -1, -1 };
1233 int[] higestRange = new int[] { -1, -1 };
1235 if (hiddenColumns == null)
1237 return new int[] { startPos, endPos };
1240 for (int[] hiddenCol : hiddenColumns)
1242 lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
1243 higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
1246 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1248 startPos = alignmentStartEnd[0];
1252 startPos = lowestRange[1] + 1;
1255 if (higestRange[0] == -1 && higestRange[1] == -1)
1257 endPos = alignmentStartEnd[1];
1261 endPos = higestRange[0] - 1;
1263 return new int[] { startPos, endPos };
1266 LOCK.readLock().unlock();
1272 * Finds the hidden region (if any) which starts or ends at res
1275 * visible residue position, unadjusted for hidden columns
1276 * @return region as [start,end] or null if no matching region is found
1278 public int[] getRegionWithEdgeAtRes(int res)
1282 LOCK.readLock().lock();
1283 int adjres = adjustForHiddenColumns(res);
1285 int[] reveal = null;
1286 if (hiddenColumns != null)
1288 for (int[] region : hiddenColumns)
1290 if (adjres + 1 == region[0] || adjres - 1 == region[1])
1300 LOCK.readLock().unlock();
1305 * Return an iterator over the hidden regions
1307 public Iterator<int[]> iterator()
1309 if (hiddenColumns != null)
1311 int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
1312 return new BoundedHiddenColsIterator(0, last, true);
1316 return new BoundedHiddenColsIterator(0, 0, true);
1321 * Return a bounded iterator over the hidden regions
1324 * position to start from (inclusive, absolute column position)
1326 * position to end at (inclusive, absolute column position)
1329 public Iterator<int[]> getBoundedIterator(int start, int end)
1331 return new BoundedHiddenColsIterator(start, end, true);
1335 * Return a bounded iterator over the *visible* start positions of hidden
1339 * position to start from (inclusive, visible column position)
1341 * position to end at (inclusive, visible column position)
1343 public Iterator<Integer> getBoundedStartIterator(int start, int end)
1345 return new BoundedStartRegionIterator(start, end, true);
1349 * Return an iterator over visible columns between the given start and end
1353 * first column (inclusive)
1355 * last column (inclusive)
1357 public Iterator<Integer> getVisibleColsIterator(int start, int end)
1359 return new VisibleColsIterator(start, end, true);
1363 * return an iterator over visible segments between the given start and end
1367 * (first column inclusive from 0)
1369 * (last column - not inclusive)
1371 public Iterator<int[]> getVisContigsIterator(int start, int end)
1373 return new VisibleContigsIterator(start, end, true);
1377 * return an iterator over visible segments between the given start and end
1381 * (first column - inclusive from 0)
1383 * (last column - inclusive)
1384 * @param useVisibleCoords
1385 * if true, start and end are visible column positions, not absolute
1388 public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
1389 boolean useVisibleCoords)
1391 if (useVisibleCoords)
1394 // we should really just convert start and end here with
1395 // adjustForHiddenColumns
1396 // and then create a VisibleBlocksIterator
1397 // but without a cursor this will be horribly slow in some situations
1398 // ... so until then...
1399 return new VisibleBlocksVisBoundsIterator(start, end, true);
1403 return new VisibleBlocksIterator(start, end, true);
1408 * An iterator which iterates over hidden column regions in a range.
1410 private class BoundedHiddenColsIterator implements Iterator<int[]>
1412 private int start; // start position to iterate from
1414 private int end; // end position to iterate to
1416 // current index in hiddenColumns
1417 private int currentPosition = 0;
1419 // current column in hiddenColumns
1420 private int[] currentRegion;
1422 // whether to make a local copy of hiddenColumns
1423 private final boolean useCopy;
1425 // local copy or reference to hiddenColumns
1426 private List<int[]> localHidden;
1429 * Construct an iterator over hiddenColums bounded at
1430 * [lowerBound,upperBound]
1433 * lower bound to iterate from
1435 * upper bound to iterate to
1436 * @param useCopyCols
1437 * whether to make a local copy of hiddenColumns for iteration (set
1438 * to true if calling from outwith the HiddenColumns class)
1440 BoundedHiddenColsIterator(int lowerBound, int upperBound,
1441 boolean useCopyCols)
1445 useCopy = useCopyCols;
1451 // assume that if useCopy is false the calling code has locked
1453 LOCK.readLock().lock();
1456 if (hiddenColumns != null)
1458 localHidden = new ArrayList<>();
1460 // iterate until a region overlaps with [start,end]
1462 while ((i < hiddenColumns.size())
1463 && (hiddenColumns.get(i)[1] < start))
1468 // iterate from start to end, adding each hidden region. Positions are
1469 // absolute, and all regions which *overlap* [start,end] are added.
1470 while (i < hiddenColumns.size()
1471 && (hiddenColumns.get(i)[0] <= end))
1475 rh = hiddenColumns.get(i);
1478 cp = new int[rh.length];
1479 System.arraycopy(rh, 0, cp, 0, rh.length);
1480 localHidden.add(cp);
1490 LOCK.readLock().unlock();
1496 public boolean hasNext()
1498 return (localHidden != null)
1499 && (currentPosition < localHidden.size());
1505 currentRegion = localHidden.get(currentPosition);
1507 return currentRegion;
1512 * An iterator which iterates over visible start positions of hidden column
1513 * regions in a range.
1515 private class BoundedStartRegionIterator implements Iterator<Integer>
1517 // start position to iterate from
1520 // end position to iterate to
1523 // current index in hiddenColumns
1524 private int currentPosition = 0;
1526 // local copy or reference to hiddenColumns
1527 private List<Integer> positions = null;
1530 * Construct an iterator over hiddenColums bounded at
1531 * [lowerBound,upperBound]
1534 * lower bound to iterate from
1536 * upper bound to iterate to
1537 * @param useCopyCols
1538 * whether to make a local copy of hiddenColumns for iteration (set
1539 * to true if calling from outwith the HiddenColumns class)
1541 BoundedStartRegionIterator(int lowerBound, int upperBound,
1551 // assume that if useCopy is false the calling code has locked
1553 LOCK.readLock().lock();
1556 if (hiddenColumns != null)
1558 positions = new ArrayList<>(hiddenColumns.size());
1560 // navigate to start, keeping count of hidden columns
1562 int hiddenSoFar = 0;
1563 while ((i < hiddenColumns.size())
1564 && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
1566 int[] region = hiddenColumns.get(i);
1567 hiddenSoFar += region[1] - region[0] + 1;
1571 // iterate from start to end, adding start positions of each
1572 // hidden region. Positions are visible columns count, not absolute
1573 while (i < hiddenColumns.size()
1574 && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
1576 int[] region = hiddenColumns.get(i);
1577 positions.add(region[0] - hiddenSoFar);
1578 hiddenSoFar += region[1] - region[0] + 1;
1584 positions = new ArrayList<>();
1590 LOCK.readLock().unlock();
1596 public boolean hasNext()
1598 return (currentPosition < positions.size());
1602 * Get next hidden region start position
1604 * @return the start position in *visible* coordinates
1607 public Integer next()
1609 int result = positions.get(currentPosition);
1615 private class VisibleColsIterator implements Iterator<Integer>
1619 private int current;
1623 private List<int[]> localHidden = new ArrayList<>();
1625 private int nexthiddenregion;
1627 VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
1632 nexthiddenregion = 0;
1638 // assume that if useCopy is false the calling code has locked
1640 LOCK.readLock().lock();
1643 if (hiddenColumns != null)
1646 for (i = 0; i < hiddenColumns.size()
1647 && (current <= hiddenColumns.get(i)[0]); ++i)
1649 if (current >= hiddenColumns.get(i)[0]
1650 && current <= hiddenColumns.get(i)[1])
1652 // current is hidden, move to right
1653 current = hiddenColumns.get(i)[1] + 1;
1655 nexthiddenregion = i + 1;
1659 for (i = hiddenColumns.size() - 1; i >= 0
1660 && (last >= hiddenColumns.get(i)[1]); --i)
1662 if (last >= hiddenColumns.get(i)[0]
1663 && last <= hiddenColumns.get(i)[1])
1665 // last is hidden, move to left
1666 last = hiddenColumns.get(i)[0] - 1;
1670 // make a local copy of the bit we need
1671 i = nexthiddenregion;
1672 while (i < hiddenColumns.size()
1673 && hiddenColumns.get(i)[0] <= last)
1675 int[] region = new int[] { hiddenColumns.get(i)[0],
1676 hiddenColumns.get(i)[1] };
1677 localHidden.add(region);
1685 LOCK.readLock().unlock();
1691 public boolean hasNext()
1693 return next <= last;
1697 public Integer next()
1701 throw new NoSuchElementException();
1704 if ((localHidden != null)
1705 && (nexthiddenregion < localHidden.size()))
1707 // still some more hidden regions
1708 if (next + 1 < localHidden.get(nexthiddenregion)[0])
1710 // next+1 is still before the next hidden region
1713 else if ((next + 1 >= localHidden.get(nexthiddenregion)[0])
1714 && (next + 1 <= localHidden.get(nexthiddenregion)[1]))
1716 // next + 1 is in the next hidden region
1717 next = localHidden.get(nexthiddenregion)[1] + 1;
1723 // finished with hidden regions, just increment normally
1730 public void remove()
1732 throw new UnsupportedOperationException();
1737 * An iterator which iterates over visible regions in a range.
1739 private class VisibleContigsIterator implements Iterator<int[]>
1741 private List<int[]> vcontigs = new ArrayList<>();
1743 private int currentPosition = 0;
1745 VisibleContigsIterator(int start, int end, boolean usecopy)
1751 LOCK.readLock().lock();
1754 if (hiddenColumns != null && hiddenColumns.size() > 0)
1760 for (int[] region : hiddenColumns)
1762 hideStart = region[0];
1763 hideEnd = region[1];
1765 // navigate to start
1766 if (hideEnd < vstart)
1770 if (hideStart > vstart)
1772 int[] contig = new int[] { vstart, hideStart - 1 };
1773 vcontigs.add(contig);
1775 vstart = hideEnd + 1;
1777 // exit if we're past the end
1786 int[] contig = new int[] { vstart, end - 1 };
1787 vcontigs.add(contig);
1792 int[] contig = new int[] { start, end - 1 };
1793 vcontigs.add(contig);
1799 LOCK.readLock().unlock();
1805 public boolean hasNext()
1807 return (currentPosition < vcontigs.size());
1813 int[] result = vcontigs.get(currentPosition);
1820 * An iterator which iterates over visible regions in a range.
1822 private class VisibleBlocksIterator implements Iterator<int[]>
1824 private List<int[]> vcontigs = new ArrayList<>();
1826 private int currentPosition = 0;
1828 VisibleBlocksIterator(int start, int end, boolean usecopy)
1834 LOCK.readLock().lock();
1837 if (hiddenColumns != null && hiddenColumns.size() > 0)
1839 int blockStart = start;
1842 // iterate until a region overlaps with [start,end]
1844 while ((i < hiddenColumns.size())
1845 && (hiddenColumns.get(i)[1] < start))
1850 // iterate from start to end, adding each hidden region. Positions are
1851 // absolute, and all regions which *overlap* [start,end] are used.
1852 while (i < hiddenColumns.size()
1853 && (hiddenColumns.get(i)[0] <= end))
1855 int[] region = hiddenColumns.get(i);
1857 blockStart = Math.min(blockStart, region[1] + 1);
1858 blockEnd = Math.min(blockEnd, region[0]);
1860 int[] contig = new int[] { blockStart, blockEnd };
1861 vcontigs.add(contig);
1863 blockStart = region[1] + 1;
1869 if (end > blockStart)
1871 int[] contig = new int[] { blockStart, end };
1872 vcontigs.add(contig);
1877 int[] contig = new int[] { start, end };
1878 vcontigs.add(contig);
1884 LOCK.readLock().unlock();
1890 public boolean hasNext()
1892 return (currentPosition < vcontigs.size());
1898 int[] result = vcontigs.get(currentPosition);
1905 * An iterator which iterates over visible regions in a range. The range is
1906 * specified in terms of visible column positions. Provides a special
1907 * "endsAtHidden" indicator to allow callers to determine if the final visible
1908 * column is adjacent to a hidden region.
1910 public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
1912 private List<int[]> vcontigs = new ArrayList<>();
1914 private int currentPosition = 0;
1916 private boolean endsAtHidden = false;
1919 * Constructor for iterator over visible regions in a range.
1922 * start position in terms of visible column position
1924 * end position in terms of visible column position
1926 * whether to use a local copy of hidden columns
1928 VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
1930 /* actually this implementation always uses a local copy but this may change in future */
1935 LOCK.readLock().lock();
1938 if (hiddenColumns != null && hiddenColumns.size() > 0)
1940 int blockStart = start;
1942 int hiddenSoFar = 0;
1945 // iterate until a region begins within (start,end]
1947 while ((i < hiddenColumns.size())
1948 && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar))
1950 hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0]
1955 blockStart += hiddenSoFar; // convert start to absolute position
1956 blockEnd += hiddenSoFar; // convert end to absolute position
1958 // iterate from start to end, adding each visible region. Positions
1960 // absolute, and all hidden regions which overlap [start,end] are
1962 while (i < hiddenColumns.size()
1963 && (hiddenColumns.get(i)[0] <= blockEnd))
1965 int[] region = hiddenColumns.get(i);
1967 // end position of this visible region is either just before the
1968 // start of the next hidden region, or the absolute position of
1969 // 'end', whichever is lowest
1970 blockEnd = Math.min(blockEnd, region[0] - 1);
1972 vcontigs.add(new int[] { blockStart, blockEnd });
1974 visSoFar += blockEnd - blockStart + 1;
1976 // next visible region starts after this hidden region
1977 blockStart = region[1] + 1;
1979 hiddenSoFar += region[1] - region[0] + 1;
1981 // reset blockEnd to absolute position of 'end', assuming we've now
1982 // passed all hidden regions before end
1983 blockEnd = end + hiddenSoFar;
1987 if (visSoFar < end - start)
1989 // the number of visible columns we've accounted for is less than
1990 // the number specified by end-start; work out the end position of
1991 // the last visible region
1992 blockEnd = blockStart + end - start - visSoFar;
1993 vcontigs.add(new int[] { blockStart, blockEnd });
1995 // if the last visible region ends at the next hidden region, set
1996 // endsAtHidden=true
1997 if (i < hiddenColumns.size()
1998 && hiddenColumns.get(i)[0] - 1 == blockEnd)
2000 endsAtHidden = true;
2006 // there are no hidden columns, return a single visible contig
2007 vcontigs.add(new int[] { start, end });
2008 endsAtHidden = false;
2014 LOCK.readLock().unlock();
2020 public boolean hasNext()
2022 return (currentPosition < vcontigs.size());
2028 int[] result = vcontigs.get(currentPosition);
2033 public boolean endsAtHidden()
2035 return endsAtHidden;