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;
29 public class HiddenColumns
31 private static final int HASH_MULTIPLIER = 31;
33 private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
35 private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
38 * list of hidden column [start, end] ranges; the list is maintained in
39 * ascending start column order
41 private ArrayList<int[]> hiddenColumns;
46 public HiddenColumns()
55 public HiddenColumns(HiddenColumns copy)
59 LOCK.writeLock().lock();
62 if (copy.hiddenColumns != null)
64 hiddenColumns = new ArrayList<>();
65 Iterator<int[]> it = copy.iterator();
68 hiddenColumns.add(it.next());
70 cursor.resetCursor(hiddenColumns);
75 LOCK.writeLock().unlock();
80 * Copy constructor within bounds and with offset. Copies hidden column
81 * regions fully contained between start and end, and offsets positions by
85 * HiddenColumns instance to copy from
87 * lower bound to copy from
89 * upper bound to copy to
91 * offset to subtract from each region boundary position
94 public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
98 LOCK.writeLock().lock();
101 hiddenColumns = new ArrayList<>();
102 Iterator<int[]> it = copy.getBoundedIterator(start, end);
105 int[] region = it.next();
106 // still need to check boundaries because iterator returns
107 // all overlapping regions and we need contained regions
108 if (region[0] >= start && region[1] <= end)
112 { region[0] - offset, region[1] - offset });
115 cursor.resetCursor(hiddenColumns);
119 LOCK.writeLock().unlock();
124 * Output regions data as a string. String is in the format:
125 * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
128 * string to delimit regions
129 * @param betweenstring
130 * to put between start and end region values
131 * @return regions formatted according to delimiter and between strings
133 public String regionsToString(String delimiter, String between)
137 LOCK.readLock().lock();
138 StringBuilder regionBuilder = new StringBuilder();
139 if (hiddenColumns != null)
141 Iterator<int[]> it = hiddenColumns.iterator();
144 int[] range = it.next();
145 regionBuilder.append(delimiter).append(range[0]).append(between)
149 regionBuilder.deleteCharAt(0);
153 return regionBuilder.toString();
156 LOCK.readLock().unlock();
161 * Find the number of hidden columns
163 * @return number of hidden columns
169 LOCK.readLock().lock();
171 if (hiddenColumns != null)
173 Iterator<int[]> it = hiddenColumns.iterator();
176 int[] range = it.next();
177 size += range[1] - range[0] + 1;
183 LOCK.readLock().unlock();
188 * Get the number of distinct hidden regions
190 * @return number of regions
192 public int getNumberOfRegions()
196 LOCK.readLock().lock();
198 if (hasHiddenColumns())
200 num = hiddenColumns.size();
205 LOCK.readLock().unlock();
210 public boolean equals(Object obj)
214 LOCK.readLock().lock();
216 if (!(obj instanceof HiddenColumns))
220 HiddenColumns that = (HiddenColumns) obj;
223 * check hidden columns are either both null, or match
225 if (this.hiddenColumns == null)
227 return (that.hiddenColumns == null);
229 if (that.hiddenColumns == null
230 || that.hiddenColumns.size() != this.hiddenColumns.size())
235 Iterator<int[]> it = hiddenColumns.iterator();
236 Iterator<int[]> thatit = that.iterator();
239 int[] thisRange = it.next();
240 int[] thatRange = thatit.next();
241 if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
249 LOCK.readLock().unlock();
254 * Return absolute column index for a visible column index
257 * int column index in alignment view (count from zero)
258 * @return alignment column index for column
260 public int adjustForHiddenColumns(int column)
264 LOCK.readLock().lock();
267 if (hiddenColumns != null)
269 result += cursor.getHiddenOffset(column);
275 LOCK.readLock().unlock();
280 * Use this method to find out where a column will appear in the visible
281 * alignment when hidden columns exist. If the column is not visible, then the
282 * left-most visible column will always be returned.
284 * @param hiddenColumn
285 * the column index in the full alignment including hidden columns
286 * @return the position of the column in the visible alignment
288 public int findColumnPosition(int hiddenColumn)
292 /* LOCK.readLock().lock();
293 int result = hiddenColumn;
295 if (hiddenColumns != null)
297 Iterator<int[]> it = new RegionsIterator(0, hiddenColumn,
298 hiddenColumns, cursor);
302 if (hiddenColumn > region[1])
304 result -= region[1] + 1 - region[0];
308 if (region != null && hiddenColumn >= region[0]
309 && hiddenColumn <= region[1])
311 // Here the hidden column is within a region, so
312 // we want to return the position of region[0]-1, adjusted for any
313 // earlier hidden columns.
314 // Calculate the difference between the actual hidden col position
315 // and region[0]-1, and then subtract from result to convert result
316 // from the adjusted hiddenColumn value to the adjusted region[0]-1
319 // However, if the region begins at 0 we cannot return region[0]-1
327 return result - (hiddenColumn - region[0] + 1);
331 return result; // return the shifted position after removing hidden
335 LOCK.readLock().unlock();
338 LOCK.readLock().lock();
339 int result = hiddenColumn;
340 // int[] region = null;
341 if (hiddenColumns != null)
343 int index = cursor.findRegionForColumn(hiddenColumn);
344 int hiddenBeforeCol = cursor.getHiddenSoFar();
346 // just subtract hidden cols count - this works fine if column is
348 result = hiddenColumn - hiddenBeforeCol;
350 // now check in case column is hidden - it will be in the returned
352 if (index < hiddenColumns.size())
354 int[] region = hiddenColumns.get(index);
355 if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
357 // actually col is hidden, return region[0]-1
358 // unless region[0]==0 in which case return 0
365 result = region[0] - 1 - hiddenBeforeCol;
370 System.out.println(hiddenColumn + " " + result);
371 return result; // return the shifted position after removing hidden
375 LOCK.readLock().unlock();
380 * Find the visible column which is a given visible number of columns to the
381 * left of another visible column. i.e. for a startColumn x, the column which
382 * is distance 1 away will be column x-1.
384 * @param visibleDistance
385 * the number of visible columns to offset by
387 * the column to start from
388 * @return the position of the column in the visible alignment
390 public int subtractVisibleColumns(int visibleDistance, int startColumn)
394 LOCK.readLock().lock();
395 int distance = visibleDistance;
397 // in case startColumn is in a hidden region, move it to the left
398 int start = adjustForHiddenColumns(findColumnPosition(startColumn));
400 Iterator<int[]> it = new ReverseRegionsIterator(0, start,
403 while (it.hasNext() && (distance > 0))
405 int[] region = it.next();
407 if (start > region[1])
409 // subtract the gap to right of region from distance
410 if (start - region[1] <= distance)
412 distance -= start - region[1];
413 start = region[0] - 1;
417 start = start - distance;
423 return start - distance;
427 LOCK.readLock().unlock();
432 * This method returns the rightmost limit of a region of an alignment with
433 * hidden columns. In otherwords, the next hidden column.
436 * the absolute (visible) alignmentPosition to find the next hidden
439 public int getHiddenBoundaryRight(int alPos)
443 LOCK.readLock().lock();
444 if (hiddenColumns != null)
446 int index = cursor.findRegionForColumn(alPos);
447 if (index < hiddenColumns.size())
449 int[] region = hiddenColumns.get(index);
450 if (alPos < region[0])
454 else if ((alPos <= region[1])
455 && (index + 1 < hiddenColumns.size()))
457 // alPos is within a hidden region, return the next one
459 region = hiddenColumns.get(index + 1);
467 LOCK.readLock().unlock();
472 * This method returns the leftmost limit of a region of an alignment with
473 * hidden columns. In otherwords, the previous hidden column.
476 * the absolute (visible) alignmentPosition to find the previous
479 public int getHiddenBoundaryLeft(int alPos)
483 LOCK.readLock().lock();
485 if (hiddenColumns != null)
487 int index = cursor.findRegionForColumn(alPos);
491 int[] region = hiddenColumns.get(index - 1);
498 LOCK.readLock().unlock();
503 * Adds the specified column range to the hidden columns collection
506 * start of range to add (absolute position in alignment)
508 * end of range to add (absolute position in alignment)
510 public void hideColumns(int start, int end)
512 boolean wasAlreadyLocked = false;
515 // check if the write lock was already locked by this thread,
516 // as this method can be called internally in loops within HiddenColumns
517 if (!LOCK.isWriteLockedByCurrentThread())
519 LOCK.writeLock().lock();
523 wasAlreadyLocked = true;
526 if (hiddenColumns == null)
528 hiddenColumns = new ArrayList<>();
532 * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
534 if (hiddenColumns.isEmpty()
535 || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
537 hiddenColumns.add(new int[] { start, end });
542 * traverse existing hidden ranges and insert / amend / append as
545 boolean added = false;
546 for (int i = 0; !added && i < hiddenColumns.size(); i++)
548 added = insertRangeAtRegion(i, start, end);
551 if (!wasAlreadyLocked)
553 cursor.resetCursor(hiddenColumns);
557 if (!wasAlreadyLocked)
559 LOCK.writeLock().unlock();
565 * Insert [start, range] at the region at index i in hiddenColumns, if
571 * start of range to insert
573 * end of range to insert
574 * @return true if range was successfully inserted
576 private boolean insertRangeAtRegion(int i, int start, int end)
578 boolean added = false;
580 int[] region = hiddenColumns.get(i);
581 if (end < region[0] - 1)
584 * insert discontiguous preceding range
586 hiddenColumns.add(i, new int[] { start, end });
589 else if (end <= region[1])
592 * new range overlaps existing, or is contiguous preceding it - adjust
595 region[0] = Math.min(region[0], start);
598 else if (start <= region[1] + 1)
601 * new range overlaps existing, or is contiguous following it - adjust
602 * start and end columns
604 region[0] = Math.min(region[0], start);
605 region[1] = Math.max(region[1], end);
608 * also update or remove any subsequent ranges
609 * that are overlapped
611 while (i < hiddenColumns.size() - 1)
613 int[] nextRegion = hiddenColumns.get(i + 1);
614 if (nextRegion[0] > end + 1)
617 * gap to next hidden range - no more to update
621 region[1] = Math.max(nextRegion[1], end);
622 hiddenColumns.subList(i + 1, i + 2).clear();
630 * Answers if a column in the alignment is visible
633 * absolute position of column in the alignment
634 * @return true if column is visible
636 public boolean isVisible(int column)
640 LOCK.readLock().lock();
642 Iterator<int[]> it = new RegionsIterator(column, column,
643 hiddenColumns, cursor);
646 int[] region = it.next();
647 if (column >= region[0] && column <= region[1])
656 LOCK.readLock().unlock();
661 * Get the visible sections of a set of sequences
664 * sequence position to start from
666 * sequence position to end at
668 * an array of sequences
669 * @return an array of strings encoding the visible parts of each sequence
671 public String[] getVisibleSequenceStrings(int start, int end,
676 LOCK.readLock().lock();
677 int iSize = seqs.length;
678 String[] selections = new String[iSize];
679 if (hiddenColumns != null && hiddenColumns.size() > 0)
681 for (int i = 0; i < iSize; i++)
683 StringBuffer visibleSeq = new StringBuffer();
685 Iterator<int[]> blocks = new VisibleContigsIterator(start,
686 end + 1, hiddenColumns);
688 while (blocks.hasNext())
690 int[] block = blocks.next();
691 if (blocks.hasNext())
694 .append(seqs[i].getSequence(block[0], block[1] + 1));
699 .append(seqs[i].getSequence(block[0], block[1]));
703 selections[i] = visibleSeq.toString();
708 for (int i = 0; i < iSize; i++)
710 selections[i] = seqs[i].getSequenceAsString(start, end);
717 LOCK.readLock().unlock();
722 * Locate the first position visible for this sequence. If seq isn't visible
723 * then return the position of the left side of the hidden boundary region.
726 * sequence to find position for
727 * @return visible start position
729 public int locateVisibleStartOfSequence(SequenceI seq)
733 LOCK.readLock().lock();
736 if (hiddenColumns == null || hiddenColumns.size() == 0)
738 return seq.findIndex(seq.getStart()) - 1;
741 // Simply walk along the sequence whilst watching for hidden column
743 Iterator<int[]> regions = hiddenColumns.iterator();
744 int hideStart = seq.getLength();
748 boolean foundStart = false;
750 // step through the non-gapped positions of the sequence
751 for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
753 // get alignment position of this residue in the sequence
754 int p = seq.findIndex(i) - 1;
756 // update hidden region start/end
757 while (hideEnd < p && regions.hasNext())
759 int[] region = regions.next();
761 visNext += region[0] - visPrev;
762 hideStart = region[0];
767 hideStart = seq.getLength();
769 // update visible boundary for sequence
779 return findColumnPosition(start);
781 // otherwise, sequence was completely hidden
785 LOCK.readLock().unlock();
790 * delete any columns in alignmentAnnotation that are hidden (including
791 * sequence associated annotation).
793 * @param alignmentAnnotation
795 public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
797 makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
798 alignmentAnnotation);
802 * delete any columns in alignmentAnnotation that are hidden (including
803 * sequence associated annotation).
806 * remove any annotation to the right of this column
808 * remove any annotation to the left of this column
809 * @param alignmentAnnotation
810 * the annotation to operate on
812 public void makeVisibleAnnotation(int start, int end,
813 AlignmentAnnotation alignmentAnnotation)
817 LOCK.readLock().lock();
819 int startFrom = start;
822 if (alignmentAnnotation.annotations != null)
824 if (hiddenColumns != null && hiddenColumns.size() > 0)
826 removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
830 alignmentAnnotation.restrict(startFrom, endAt);
835 LOCK.readLock().unlock();
839 private void removeHiddenAnnotation(int start, int end,
840 AlignmentAnnotation alignmentAnnotation)
842 // mangle the alignmentAnnotation annotation array
843 ArrayList<Annotation[]> annels = new ArrayList<>();
844 Annotation[] els = null;
848 Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
852 int annotationLength;
853 while (blocks.hasNext())
855 int[] block = blocks.next();
856 annotationLength = block[1] - block[0] + 1;
858 if (blocks.hasNext())
860 // copy just the visible segment of the annotation row
861 copylength = annotationLength;
865 if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
867 // copy just the visible segment of the annotation row
868 copylength = annotationLength;
872 // copy to the end of the annotation row
873 copylength = alignmentAnnotation.annotations.length - block[0];
877 els = new Annotation[annotationLength];
879 System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
881 w += annotationLength;
886 alignmentAnnotation.annotations = new Annotation[w];
889 for (Annotation[] chnk : annels)
891 System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
900 * @return true if there are columns hidden
902 public boolean hasHiddenColumns()
906 LOCK.readLock().lock();
907 return hiddenColumns != null && hiddenColumns.size() > 0;
910 LOCK.readLock().unlock();
916 * @return true if there are more than one set of columns hidden
918 public boolean hasManyHiddenColumns()
922 LOCK.readLock().lock();
923 return hiddenColumns != null && hiddenColumns.size() > 1;
926 LOCK.readLock().unlock();
931 * mark the columns corresponding to gap characters as hidden in the column
936 public void hideInsertionsFor(SequenceI sr)
940 LOCK.writeLock().lock();
941 List<int[]> inserts = sr.getInsertions();
942 for (int[] r : inserts)
944 hideColumns(r[0], r[1]);
946 cursor.resetCursor(hiddenColumns);
949 LOCK.writeLock().unlock();
954 * Unhides, and adds to the selection list, all hidden columns
956 public void revealAllHiddenColumns(ColumnSelection sel)
960 LOCK.writeLock().lock();
961 if (hiddenColumns != null)
963 Iterator<int[]> it = hiddenColumns.iterator();
966 int[] region = it.next();
967 for (int j = region[0]; j < region[1] + 1; j++)
972 hiddenColumns = null;
973 cursor.resetCursor(hiddenColumns);
977 LOCK.writeLock().unlock();
982 * Reveals, and marks as selected, the hidden column range with the given
987 public void revealHiddenColumns(int start, ColumnSelection sel)
991 LOCK.writeLock().lock();
992 Iterator<int[]> it = new RegionsIterator(start, start, hiddenColumns,
996 int[] region = it.next();
997 if (start == region[0])
999 for (int j = region[0]; j < region[1] + 1; j++)
1006 else if (start < region[0])
1008 break; // passed all possible matching regions
1012 if (hiddenColumns.size() == 0)
1014 hiddenColumns = null;
1016 cursor.resetCursor(hiddenColumns);
1019 LOCK.writeLock().unlock();
1024 * Add gaps into the sequences aligned to profileseq under the given
1029 * - alignment to have gaps inserted into it
1031 * - alignment view where sequence corresponding to profileseq is
1033 * @return new HiddenColumns for new alignment view, with insertions into
1034 * profileseq marked as hidden.
1036 public static HiddenColumns propagateInsertions(SequenceI profileseq,
1037 AlignmentI al, AlignmentView input)
1041 char gc = al.getGapCharacter();
1042 Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
1043 HiddenColumns nview = (HiddenColumns) alandhidden[1];
1044 SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
1045 nview.propagateInsertions(profileseq, al, origseq);
1052 * - sequence in al which corresponds to origseq
1054 * - alignment which is to have gaps inserted into it
1056 * - sequence corresponding to profileseq which defines gap map for
1059 private void propagateInsertions(SequenceI profileseq, AlignmentI al,
1064 LOCK.writeLock().lock();
1066 char gc = al.getGapCharacter();
1068 // take the set of hidden columns, and the set of gaps in origseq,
1069 // and remove all the hidden gaps from hiddenColumns
1071 // first get the gaps as a Bitset
1072 BitSet gaps = origseq.gapBitset();
1074 // now calculate hidden ^ not(gap)
1075 BitSet hidden = new BitSet();
1076 markHiddenRegions(hidden);
1077 hidden.andNot(gaps);
1078 hiddenColumns = null;
1079 this.hideMarkedBits(hidden);
1081 // for each sequence in the alignment, except the profile sequence,
1082 // insert gaps corresponding to each hidden region
1083 // but where each hidden column region is shifted backwards by the number
1085 // preceding visible gaps
1086 // update hidden columns at the same time
1087 Iterator<int[]> regions = hiddenColumns.iterator();
1088 ArrayList<int[]> newhidden = new ArrayList<>();
1090 int numGapsBefore = 0;
1091 int gapPosition = 0;
1092 while (regions.hasNext())
1094 // get region coordinates accounting for gaps
1095 // we can rely on gaps not being *in* hidden regions because we already
1097 int[] region = regions.next();
1098 while (gapPosition < region[0])
1101 if (gaps.get(gapPosition))
1107 int left = region[0] - numGapsBefore;
1108 int right = region[1] - numGapsBefore;
1109 newhidden.add(new int[] { left, right });
1111 // make a string with number of gaps = length of hidden region
1112 StringBuffer sb = new StringBuffer();
1113 for (int s = 0; s < right - left + 1; s++)
1117 padGaps(sb, left, profileseq, al);
1120 hiddenColumns = newhidden;
1121 cursor.resetCursor(hiddenColumns);
1124 LOCK.writeLock().unlock();
1129 * Pad gaps in all sequences in alignment except profileseq
1132 * gap string to insert
1134 * position to insert at
1136 * sequence not to pad
1138 * alignment to pad sequences in
1140 private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
1143 // loop over the sequences and pad with gaps where required
1144 for (int s = 0, ns = al.getHeight(); s < ns; s++)
1146 SequenceI sqobj = al.getSequenceAt(s);
1147 if (sqobj != profileseq)
1149 String sq = al.getSequenceAt(s).getSequenceAsString();
1150 if (sq.length() <= pos)
1153 int diff = pos - sq.length() - 1;
1158 while ((diff = pos - sq.length() - 1) > 0)
1160 if (diff >= sb.length())
1162 sq += sb.toString();
1166 char[] buf = new char[diff];
1167 sb.getChars(0, diff, buf, 0);
1168 sq += buf.toString();
1172 sq += sb.toString();
1176 al.getSequenceAt(s).setSequence(
1177 sq.substring(0, pos) + sb.toString() + sq.substring(pos));
1184 * Returns a hashCode built from hidden column ranges
1187 public int hashCode()
1191 LOCK.readLock().lock();
1193 Iterator<int[]> it = hiddenColumns.iterator();
1194 while (it.hasNext())
1196 int[] hidden = it.next();
1197 hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
1198 hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
1203 LOCK.readLock().unlock();
1208 * Hide columns corresponding to the marked bits
1211 * - columns map to bits starting from zero
1213 public void hideMarkedBits(BitSet inserts)
1217 LOCK.writeLock().lock();
1218 for (int firstSet = inserts
1219 .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
1220 .nextSetBit(lastSet))
1222 lastSet = inserts.nextClearBit(firstSet);
1223 hideColumns(firstSet, lastSet - 1);
1225 cursor.resetCursor(hiddenColumns);
1228 LOCK.writeLock().unlock();
1235 * BitSet where hidden columns will be marked
1237 public void markHiddenRegions(BitSet inserts)
1241 LOCK.readLock().lock();
1242 if (hiddenColumns == null)
1246 Iterator<int[]> it = hiddenColumns.iterator();
1247 while (it.hasNext())
1249 int[] range = it.next();
1250 inserts.set(range[0], range[1] + 1);
1254 LOCK.readLock().unlock();
1259 * Calculate the visible start and end index of an alignment.
1262 * full alignment width
1263 * @return integer array where: int[0] = startIndex, and int[1] = endIndex
1265 public int[] getVisibleStartAndEndIndex(int width)
1269 LOCK.readLock().lock();
1270 int[] alignmentStartEnd = new int[] { 0, width - 1 };
1271 int startPos = alignmentStartEnd[0];
1272 int endPos = alignmentStartEnd[1];
1274 int[] lowestRange = new int[] { -1, -1 };
1275 int[] higestRange = new int[] { -1, -1 };
1277 if (hiddenColumns == null)
1279 return new int[] { startPos, endPos };
1282 Iterator<int[]> it = hiddenColumns.iterator();
1283 while (it.hasNext())
1285 int[] range = it.next();
1286 lowestRange = (range[0] <= startPos) ? range : lowestRange;
1287 higestRange = (range[1] >= endPos) ? range : higestRange;
1290 if (lowestRange[0] == -1 && lowestRange[1] == -1)
1292 startPos = alignmentStartEnd[0];
1296 startPos = lowestRange[1] + 1;
1299 if (higestRange[0] == -1 && higestRange[1] == -1)
1301 endPos = alignmentStartEnd[1];
1305 endPos = higestRange[0] - 1;
1307 return new int[] { startPos, endPos };
1310 LOCK.readLock().unlock();
1315 * Finds the hidden region (if any) which starts or ends at res
1318 * visible residue position, unadjusted for hidden columns
1319 * @return region as [start,end] or null if no matching region is found
1321 public int[] getRegionWithEdgeAtRes(int res)
1325 LOCK.readLock().lock();
1326 int adjres = adjustForHiddenColumns(res);
1328 int[] reveal = null;
1330 if (hiddenColumns != null)
1332 int regionindex = cursor.findRegionForColumn(adjres - 1);
1333 if (hiddenColumns.get(regionindex)[1] == adjres - 1)
1335 reveal = hiddenColumns.get(regionindex);
1339 regionindex = cursor.findRegionForColumn(adjres + 1);
1340 if (hiddenColumns.get(regionindex)[0] == adjres + 1)
1342 reveal = hiddenColumns.get(regionindex);
1350 LOCK.readLock().unlock();
1355 * Return an iterator over the hidden regions
1357 public Iterator<int[]> iterator()
1361 LOCK.readLock().lock();
1362 return new BoundedHiddenColsIterator(hiddenColumns);
1365 LOCK.readLock().unlock();
1370 * Return a bounded iterator over the hidden regions
1373 * position to start from (inclusive, absolute column position)
1375 * position to end at (inclusive, absolute column position)
1378 public Iterator<int[]> getBoundedIterator(int start, int end)
1382 LOCK.readLock().lock();
1383 return new BoundedHiddenColsIterator(start, end, hiddenColumns);
1386 LOCK.readLock().unlock();
1391 * Return a bounded iterator over the *visible* start positions of hidden
1395 * position to start from (inclusive, visible column position)
1397 * position to end at (inclusive, visible column position)
1399 public Iterator<Integer> getBoundedStartIterator(int start, int end)
1403 LOCK.readLock().lock();
1404 return new BoundedStartRegionIterator(start, end, hiddenColumns);
1407 LOCK.readLock().unlock();
1412 * Return an iterator over visible *columns* (not regions) between the given
1413 * start and end boundaries
1416 * first column (inclusive)
1418 * last column (inclusive)
1420 public Iterator<Integer> getVisibleColsIterator(int start, int end)
1424 LOCK.readLock().lock();
1425 return new VisibleColsIterator(start, end, hiddenColumns);
1428 LOCK.readLock().unlock();
1433 * return an iterator over visible segments between the given start and end
1437 * (first column inclusive from 0)
1439 * (last column - not inclusive)
1441 public Iterator<int[]> getVisContigsIterator(int start, int end)
1445 LOCK.readLock().lock();
1446 return new VisibleContigsIterator(start, end, hiddenColumns);
1449 LOCK.readLock().unlock();
1454 * return an iterator over visible segments between the given start and end
1458 * (first column - inclusive from 0)
1460 * (last column - inclusive)
1461 * @param useVisibleCoords
1462 * if true, start and end are visible column positions, not absolute
1465 public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
1466 boolean useVisibleCoords)
1468 if (useVisibleCoords)
1471 // we should really just convert start and end here with
1472 // adjustForHiddenColumns
1473 // and then create a VisibleContigsIterator
1474 // but without a cursor this will be horribly slow in some situations
1475 // ... so until then...
1476 return new VisibleBlocksVisBoundsIterator(start, end, true);
1482 LOCK.readLock().lock();
1483 return new VisibleContigsIterator(start, end + 1, hiddenColumns);
1486 LOCK.readLock().unlock();
1492 * An iterator which iterates over visible regions in a range. The range is
1493 * specified in terms of visible column positions. Provides a special
1494 * "endsAtHidden" indicator to allow callers to determine if the final visible
1495 * column is adjacent to a hidden region.
1497 public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
1499 private List<int[]> vcontigs = new ArrayList<>();
1501 private int currentPosition = 0;
1503 private boolean endsAtHidden = false;
1506 * Constructor for iterator over visible regions in a range.
1509 * start position in terms of visible column position
1511 * end position in terms of visible column position
1513 * whether to use a local copy of hidden columns
1515 VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
1517 /* actually this implementation always uses a local copy but this may change in future */
1522 LOCK.readLock().lock();
1525 if (hiddenColumns != null && hiddenColumns.size() > 0)
1527 int blockStart = start;
1529 int hiddenSoFar = 0;
1532 // iterate until a region begins within (start,end]
1534 while ((i < hiddenColumns.size())
1535 && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar))
1537 hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0]
1542 blockStart += hiddenSoFar; // convert start to absolute position
1543 blockEnd += hiddenSoFar; // convert end to absolute position
1545 // iterate from start to end, adding each visible region. Positions
1547 // absolute, and all hidden regions which overlap [start,end] are
1549 while (i < hiddenColumns.size()
1550 && (hiddenColumns.get(i)[0] <= blockEnd))
1552 int[] region = hiddenColumns.get(i);
1554 // end position of this visible region is either just before the
1555 // start of the next hidden region, or the absolute position of
1556 // 'end', whichever is lowest
1557 blockEnd = Math.min(blockEnd, region[0] - 1);
1559 vcontigs.add(new int[] { blockStart, blockEnd });
1561 visSoFar += blockEnd - blockStart + 1;
1563 // next visible region starts after this hidden region
1564 blockStart = region[1] + 1;
1566 hiddenSoFar += region[1] - region[0] + 1;
1568 // reset blockEnd to absolute position of 'end', assuming we've now
1569 // passed all hidden regions before end
1570 blockEnd = end + hiddenSoFar;
1574 if (visSoFar < end - start + 1)
1576 // the number of visible columns we've accounted for is less than
1577 // the number specified by end-start; work out the end position of
1578 // the last visible region
1579 blockEnd = blockStart + end - start - visSoFar;
1580 vcontigs.add(new int[] { blockStart, blockEnd });
1582 // if the last visible region ends at the next hidden region, set
1583 // endsAtHidden=true
1584 if (i < hiddenColumns.size()
1585 && hiddenColumns.get(i)[0] - 1 == blockEnd)
1587 endsAtHidden = true;
1593 // there are no hidden columns, return a single visible contig
1594 vcontigs.add(new int[] { start, end });
1595 endsAtHidden = false;
1601 LOCK.readLock().unlock();
1607 public boolean hasNext()
1609 return (currentPosition < vcontigs.size());
1615 int[] result = vcontigs.get(currentPosition);
1620 public boolean endsAtHidden()
1622 return endsAtHidden;