X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=402ea2542a8a94d7b9c7550bac4457f7a51ee1e6;hb=6f39eb8080a04854744d9f167104a525b4a38520;hp=66771516c3e304454f5419ec287c8b69916c02b3;hpb=8874aa9fd956f7bc248fe15a669a6d8d81d6891b;p=jalview.git diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java index 6677151..402ea25 100644 --- a/src/jalview/datamodel/HiddenColumns.java +++ b/src/jalview/datamodel/HiddenColumns.java @@ -21,6 +21,7 @@ package jalview.datamodel; import java.util.ArrayList; +import java.util.Arrays; import java.util.BitSet; import java.util.Iterator; import java.util.List; @@ -32,13 +33,13 @@ import java.util.concurrent.locks.ReentrantReadWriteLock; * use an iterator obtained from one of: * * - getBoundedIterator: iterates over the hidden regions, within some bounds, - * returning absolute positions + * returning *absolute* positions * * - getBoundedStartIterator: iterates over the start positions of hidden - * regions, within some bounds, returning visible positions + * regions, within some bounds, returning *visible* positions * * - getVisContigsIterator: iterates over visible regions in a range, returning - * absolute positions + * *absolute* positions * * - getVisibleColsIterator: iterates over the visible *columns* * @@ -46,7 +47,20 @@ import java.util.concurrent.locks.ReentrantReadWriteLock; * numbering begins at 0 throughout this class. * * @author kmourao - * + */ + +/* Implementation notes: + * + * Methods which change the hiddenColumns collection should use a writeLock to + * prevent other threads accessing the hiddenColumns collection while changes + * are being made. They should also reset the hidden columns cursor, and either + * update the hidden columns count, or set it to 0 (so that it will later be + * updated when needed). + * + * + * Methods which only need read access to the hidden columns collection should + * use a readLock to prevent other threads changing the hidden columns + * collection while it is in use. */ public class HiddenColumns { @@ -78,14 +92,6 @@ public class HiddenColumns { } - /* - * Methods which change the hiddenColumns collection. These methods should - * use a writeLock to prevent other threads accessing the hiddenColumns - * collection while changes are being made. They should also reset the hidden - * columns cursor, and either update the hidden columns count, or set it to 0 - * (so that it will later be updated when needed). - */ - /** * Copy constructor * @@ -134,7 +140,7 @@ public class HiddenColumns numColumns += region[1] - region[0] + 1; } } - cursor.resetCursor(hiddenColumns); + cursor = new HiddenColumnsCursor(hiddenColumns); } } finally { @@ -152,19 +158,9 @@ public class HiddenColumns */ public void hideColumns(int start, int end) { - boolean wasAlreadyLocked = false; try { - // check if the write lock was already locked by this thread, - // as this method can be called internally in loops within HiddenColumns - if (!LOCK.isWriteLockedByCurrentThread()) - { - LOCK.writeLock().lock(); - } - else - { - wasAlreadyLocked = true; - } + LOCK.writeLock().lock(); int previndex = 0; int prevHiddenCount = 0; @@ -212,17 +208,15 @@ public class HiddenColumns // reset the cursor to just before our insertion point: this saves // a lot of reprocessing in large alignments - cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount); + cursor = new HiddenColumnsCursor(hiddenColumns, previndex, + prevHiddenCount); // reset the number of columns so they will be recounted numColumns = 0; } finally { - if (!wasAlreadyLocked) - { - LOCK.writeLock().unlock(); - } + LOCK.writeLock().unlock(); } } @@ -285,9 +279,9 @@ public class HiddenColumns } region[1] = Math.max(nextRegion[1], end); - // in theory this is faster than hiddenColumns.remove(i+1) - // benchmarking results a bit ambivalent - hiddenColumns.subList(i + 1, i + 2).clear(); + // in theory hiddenColumns.subList(i + 1, i + 2).clear() is faster than + // hiddenColumns.remove(i+1) but benchmarking results a bit ambivalent + hiddenColumns.remove(i + 1); } added = true; } @@ -308,7 +302,7 @@ public class HiddenColumns { hideColumns(r[0], r[1]); } - cursor.resetCursor(hiddenColumns); + cursor = new HiddenColumnsCursor(hiddenColumns); numColumns = 0; } finally { @@ -333,7 +327,7 @@ public class HiddenColumns } } hiddenColumns.clear(); - cursor.resetCursor(hiddenColumns); + cursor = new HiddenColumnsCursor(hiddenColumns); numColumns = 0; } finally @@ -378,7 +372,6 @@ public class HiddenColumns if (hiddenColumns.isEmpty()) { - hiddenColumns.clear(); numColumns = 0; } else @@ -396,170 +389,6 @@ public class HiddenColumns } /** - * Add gaps into the sequences aligned to profileseq under the given - * AlignmentView - * - * @param profileseq - * sequence in al which sequences are aligned to - * @param al - * alignment to have gaps inserted into it - * @param input - * alignment view where sequence corresponding to profileseq is first - * entry - * @return new HiddenColumns for new alignment view, with insertions into - * profileseq marked as hidden. - */ - public static HiddenColumns propagateInsertions(SequenceI profileseq, - AlignmentI al, AlignmentView input) - { - int profsqpos = 0; - - char gc = al.getGapCharacter(); - Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc); - HiddenColumns nview = (HiddenColumns) alandhidden[1]; - SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos]; - nview.propagateInsertions(profileseq, al, origseq); - return nview; - } - - /** - * - * @param profileseq - * sequence in al which corresponds to origseq - * @param al - * alignment which is to have gaps inserted into it - * @param origseq - * sequence corresponding to profileseq which defines gap map for - * modifying al - */ - private void propagateInsertions(SequenceI profileseq, AlignmentI al, - SequenceI origseq) - { - try - { - LOCK.writeLock().lock(); - - char gc = al.getGapCharacter(); - - // take the set of hidden columns, and the set of gaps in origseq, - // and remove all the hidden gaps from hiddenColumns - - // first get the gaps as a Bitset - BitSet gaps = origseq.gapBitset(); - - // now calculate hidden ^ not(gap) - BitSet hidden = new BitSet(); - markHiddenRegions(hidden); - hidden.andNot(gaps); - hiddenColumns.clear(); - this.hideColumns(hidden); - - // for each sequence in the alignment, except the profile sequence, - // insert gaps corresponding to each hidden region but where each hidden - // column region is shifted backwards by the number of preceding visible - // gaps update hidden columns at the same time - List newhidden = new ArrayList<>(); - - int numGapsBefore = 0; - int gapPosition = 0; - for (int[] region : hiddenColumns) - { - // get region coordinates accounting for gaps - // we can rely on gaps not being *in* hidden regions because we already - // removed those - while (gapPosition < region[0]) - { - gapPosition++; - if (gaps.get(gapPosition)) - { - numGapsBefore++; - } - } - - int left = region[0] - numGapsBefore; - int right = region[1] - numGapsBefore; - newhidden.add(new int[] { left, right }); - - // make a string with number of gaps = length of hidden region - StringBuffer sb = new StringBuffer(); - for (int s = 0; s < right - left + 1; s++) - { - sb.append(gc); - } - padGaps(sb, left, profileseq, al); - - } - hiddenColumns = newhidden; - cursor.resetCursor(hiddenColumns); - numColumns = 0; - } finally - { - LOCK.writeLock().unlock(); - } - } - - /** - * Pad gaps in all sequences in alignment except profileseq - * - * @param sb - * gap string to insert - * @param left - * position to insert at - * @param profileseq - * sequence not to pad - * @param al - * alignment to pad sequences in - */ - private void padGaps(StringBuffer sb, int pos, SequenceI profileseq, - AlignmentI al) - { - // loop over the sequences and pad with gaps where required - for (int s = 0, ns = al.getHeight(); s < ns; s++) - { - SequenceI sqobj = al.getSequenceAt(s); - if (sqobj != profileseq) - { - String sq = al.getSequenceAt(s).getSequenceAsString(); - if (sq.length() <= pos) - { - // pad sequence - int diff = pos - sq.length() - 1; - if (diff > 0) - { - // pad gaps - sq = sq + sb; - while ((diff = pos - sq.length() - 1) > 0) - { - if (diff >= sb.length()) - { - sq += sb.toString(); - } - else - { - char[] buf = new char[diff]; - sb.getChars(0, diff, buf, 0); - sq += buf.toString(); - } - } - } - sq += sb.toString(); - } - else - { - al.getSequenceAt(s).setSequence( - sq.substring(0, pos) + sb.toString() + sq.substring(pos)); - } - } - } - } - - /* - * Methods which only need read access to the hidden columns collection. - * These methods should use a readLock to prevent other threads changing - * the hidden columns collection while it is in use. - */ - - /** * Output regions data as a string. String is in the format: * reg0[0]reg0[1]reg1[0]reg1[1] ... regn[1] * @@ -639,12 +468,7 @@ public class HiddenColumns try { LOCK.readLock().lock(); - int num = 0; - if (hasHiddenColumns()) - { - num = hiddenColumns.size(); - } - return num; + return hiddenColumns.size(); } finally { LOCK.readLock().unlock(); @@ -673,16 +497,17 @@ public class HiddenColumns return false; } + Iterator it = this.iterator(); Iterator thatit = that.iterator(); - for (int[] thisRange : hiddenColumns) + while (it.hasNext()) { - int[] thatRange = thatit.next(); - if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) + if (!(Arrays.equals(it.next(), thatit.next()))) { return false; } } return true; + } finally { LOCK.readLock().unlock(); @@ -774,48 +599,25 @@ public class HiddenColumns /** * Find the visible column which is a given visible number of columns to the - * left of another visible column. i.e. for a startColumn x, the column which - * is distance 1 away will be column x-1. + * left (negative visibleDistance) or right (positive visibleDistance) of + * startColumn. If startColumn is not visible, we use the visible column at + * the left boundary of the hidden region containing startColumn. * * @param visibleDistance - * the number of visible columns to offset by + * the number of visible columns to offset by (left offset = negative + * value; right offset = positive value) * @param startColumn - * the column to start from - * @return the position of the column in the visible alignment + * the position of the column to start from (absolute position) + * @return the position of the column which is away + * (absolute position) */ - public int subtractVisibleColumns(int visibleDistance, int startColumn) + public int offsetByVisibleColumns(int visibleDistance, int startColumn) { try { LOCK.readLock().lock(); - int distance = visibleDistance; - - // in case startColumn is in a hidden region, move it to the left - int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn)); - - Iterator it = new ReverseRegionsIterator(0, start, - hiddenColumns); - - while (it.hasNext() && (distance > 0)) - { - int[] region = it.next(); - - if (start > region[1]) - { - // subtract the gap to right of region from distance - if (start - region[1] <= distance) - { - distance -= start - region[1]; - start = region[0] - 1; - } - else - { - start = start - distance; - distance = 0; - } - } - } - return start - distance; + int start = absoluteToVisibleColumn(startColumn); + return visibleToAbsoluteColumn(start + visibleDistance); } finally { @@ -833,7 +635,7 @@ public class HiddenColumns * @return the index of the next hidden column, or alPos if there is no next * hidden column */ - public int getHiddenBoundaryRight(int alPos) + public int getNextHiddenBoundary(boolean left, int alPos) { try { @@ -841,7 +643,13 @@ public class HiddenColumns if (!hiddenColumns.isEmpty()) { int index = cursor.findRegionForColumn(alPos).getRegionIndex(); - if (index < hiddenColumns.size()) + + if (left && index > 0) + { + int[] region = hiddenColumns.get(index - 1); + return region[1]; + } + else if (!left && index < hiddenColumns.size()) { int[] region = hiddenColumns.get(index); if (alPos < region[0]) @@ -866,38 +674,6 @@ public class HiddenColumns } /** - * This method returns the leftmost limit of a region of an alignment with - * hidden columns. In otherwords, the previous hidden column. - * - * @param alPos - * the absolute (visible) alignmentPosition to find the previous - * hidden column for - */ - public int getHiddenBoundaryLeft(int alPos) - { - try - { - LOCK.readLock().lock(); - - if (!hiddenColumns.isEmpty()) - { - int index = cursor.findRegionForColumn(alPos).getRegionIndex(); - - if (index > 0) - { - int[] region = hiddenColumns.get(index - 1); - return region[1]; - } - } - return alPos; - } finally - { - LOCK.readLock().unlock(); - } - } - - - /** * Answers if a column in the alignment is visible * * @param column @@ -930,249 +706,6 @@ public class HiddenColumns } /** - * Get the visible sections of a set of sequences - * - * @param start - * sequence position to start from - * @param end - * sequence position to end at - * @param seqs - * an array of sequences - * @return an array of strings encoding the visible parts of each sequence - */ - public String[] getVisibleSequenceStrings(int start, int end, - SequenceI[] seqs) - { - try - { - LOCK.readLock().lock(); - int iSize = seqs.length; - String[] selections = new String[iSize]; - if (!hiddenColumns.isEmpty()) - { - for (int i = 0; i < iSize; i++) - { - StringBuffer visibleSeq = new StringBuffer(); - - Iterator blocks = new VisibleContigsIterator(start, - end + 1, hiddenColumns); - - while (blocks.hasNext()) - { - int[] block = blocks.next(); - if (blocks.hasNext()) - { - visibleSeq - .append(seqs[i].getSequence(block[0], block[1] + 1)); - } - else - { - visibleSeq - .append(seqs[i].getSequence(block[0], block[1])); - } - } - - selections[i] = visibleSeq.toString(); - } - } - else - { - for (int i = 0; i < iSize; i++) - { - selections[i] = seqs[i].getSequenceAsString(start, end); - } - } - - return selections; - } finally - { - LOCK.readLock().unlock(); - } - } - - /** - * Locate the first position visible for this sequence. If seq isn't visible - * then return the position of the left side of the hidden boundary region. - * - * @param seq - * sequence to find position for - * @return visible start position - */ - public int locateVisibleStartOfSequence(SequenceI seq) - { - try - { - LOCK.readLock().lock(); - int start = 0; - - if (hiddenColumns.isEmpty()) - { - return seq.findIndex(seq.getStart()) - 1; - } - - // Simply walk along the sequence whilst watching for hidden column - // boundaries - Iterator regions = hiddenColumns.iterator(); - int hideStart = seq.getLength(); - int hideEnd = -1; - int visPrev = 0; - int visNext = 0; - boolean foundStart = false; - - // step through the non-gapped positions of the sequence - for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++) - { - // get alignment position of this residue in the sequence - int p = seq.findIndex(i) - 1; - - // update hidden region start/end - while (hideEnd < p && regions.hasNext()) - { - int[] region = regions.next(); - visPrev = visNext; - visNext += region[0] - visPrev; - hideStart = region[0]; - hideEnd = region[1]; - } - if (hideEnd < p) - { - hideStart = seq.getLength(); - } - // update visible boundary for sequence - if (p < hideStart) - { - start = p; - foundStart = true; - } - } - - if (foundStart) - { - return absoluteToVisibleColumn(start); - } - // otherwise, sequence was completely hidden - return visPrev; - } finally - { - LOCK.readLock().unlock(); - } - } - - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param alignmentAnnotation - */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) - { - if (alignmentAnnotation != null - && alignmentAnnotation.annotations != null) - { - makeVisibleAnnotation(0, alignmentAnnotation.annotations.length, - alignmentAnnotation); - } - } - - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param start - * remove any annotation to the right of this column - * @param end - * remove any annotation to the left of this column - * @param alignmentAnnotation - * the annotation to operate on - */ - public void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) - { - try - { - LOCK.readLock().lock(); - - int startFrom = start; - int endAt = end; - - if (alignmentAnnotation != null - && alignmentAnnotation.annotations != null) - { - if (!hiddenColumns.isEmpty()) - { - removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation); - } - else - { - alignmentAnnotation.restrict(startFrom, endAt); - } - } - } finally - { - LOCK.readLock().unlock(); - } - } - - private void removeHiddenAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) - { - // mangle the alignmentAnnotation annotation array - ArrayList annels = new ArrayList<>(); - Annotation[] els = null; - - int w = 0; - - Iterator blocks = new VisibleContigsIterator(start, end + 1, - hiddenColumns); - - int copylength; - int annotationLength; - while (blocks.hasNext()) - { - int[] block = blocks.next(); - annotationLength = block[1] - block[0] + 1; - - if (blocks.hasNext()) - { - // copy just the visible segment of the annotation row - copylength = annotationLength; - } - else - { - if (annotationLength + block[0] <= alignmentAnnotation.annotations.length) - { - // copy just the visible segment of the annotation row - copylength = annotationLength; - } - else - { - // copy to the end of the annotation row - copylength = alignmentAnnotation.annotations.length - block[0]; - } - } - - els = new Annotation[annotationLength]; - annels.add(els); - System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0, - copylength); - w += annotationLength; - } - - if (w != 0) - { - alignmentAnnotation.annotations = new Annotation[w]; - - w = 0; - for (Annotation[] chnk : annels) - { - System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, - chnk.length); - w += chnk.length; - } - } - } - - /** * * @return true if there are columns hidden */ @@ -1218,6 +751,7 @@ public class HiddenColumns { LOCK.readLock().lock(); int hashCode = 1; + for (int[] hidden : hiddenColumns) { hashCode = HASH_MULTIPLIER * hashCode + hidden[0]; @@ -1234,7 +768,7 @@ public class HiddenColumns * Hide columns corresponding to the marked bits * * @param inserts - * - columns map to bits starting from zero + * - columns mapped to bits starting from zero */ public void hideColumns(BitSet inserts) { @@ -1248,7 +782,7 @@ public class HiddenColumns lastSet = inserts.nextClearBit(firstSet); hideColumns(firstSet, lastSet - 1); } - cursor.resetCursor(hiddenColumns); + cursor = new HiddenColumnsCursor(hiddenColumns); numColumns = 0; } finally { @@ -1257,23 +791,112 @@ public class HiddenColumns } /** + * Hide columns corresponding to the marked bits, within the range + * [start,end]. Entries in tohide which are outside [start,end] are ignored. * - * @param inserts + * @param tohide + * columns mapped to bits starting from zero + * @param start + * start of range to hide columns within + * @param end + * end of range to hide columns within + */ + public void hideColumns(BitSet tohide, int start, int end) + { + clearHiddenColumnsInRange(start, end); + + // make sure only bits between start and end are set + if (!tohide.isEmpty()) + { + tohide.clear(0, start); + tohide.clear(Math.min(end + 1, tohide.length() + 1), + tohide.length() + 1); + } + + hideColumns(tohide); + } + + /** + * Make all columns in the range [start,end] visible + * + * @param start + * start of range to show columns + * @param end + * end of range to show columns + */ + private void clearHiddenColumnsInRange(int start, int end) + { + try + { + LOCK.writeLock().lock(); + + if (!hiddenColumns.isEmpty()) + { + HiddenCursorPosition pos = cursor.findRegionForColumn(start); + int index = pos.getRegionIndex(); + int startindex = index; // first index in hiddenColumns to remove + + if (index != -1 && index != hiddenColumns.size()) + { + // regionIndex is the region which either contains start + // or lies to the right of start + int[] region = hiddenColumns.get(index); + if (region[0] < start && region[1] >= start) + { + // region contains start, truncate so that it ends just before start + region[1] = start - 1; + startindex++; + } + } + + pos = cursor.findRegionForColumn(end); + index = pos.getRegionIndex(); + int endindex = index - 1; // last index in hiddenColumns to remove + + if (index != -1 && index != hiddenColumns.size()) + { + // regionIndex is the region which either contains end + // or lies to the right of end + int[] region = hiddenColumns.get(index); + if (region[0] <= end && region[1] > end) + { + // region contains end, truncate so that it starts just after end + region[0] = end + 1; + } + } + + hiddenColumns.subList(startindex, endindex + 1).clear(); + cursor = new HiddenColumnsCursor(hiddenColumns); + numColumns = 0; + } + } finally + { + LOCK.writeLock().unlock(); + } + } + + /** + * + * @param updates * BitSet where hidden columns will be marked */ - public void markHiddenRegions(BitSet inserts) + protected void andNot(BitSet updates) { try { - LOCK.readLock().lock(); + LOCK.writeLock().lock(); + BitSet hiddenBitSet = new BitSet(); for (int[] range : hiddenColumns) { - inserts.set(range[0], range[1] + 1); + hiddenBitSet.set(range[0], range[1] + 1); } + hiddenBitSet.andNot(updates); + hiddenColumns.clear(); + hideColumns(hiddenBitSet); } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } @@ -1289,42 +912,27 @@ public class HiddenColumns try { LOCK.readLock().lock(); - int[] alignmentStartEnd = new int[] { 0, width - 1 }; - int startPos = alignmentStartEnd[0]; - int endPos = alignmentStartEnd[1]; - int[] lowestRange = new int[] { -1, -1 }; - int[] higestRange = new int[] { -1, -1 }; - - if (hiddenColumns.isEmpty()) - { - return new int[] { startPos, endPos }; - } + int firstVisible = 0; + int lastVisible = width - 1; - for (int[] range : hiddenColumns) + if (!hiddenColumns.isEmpty()) { - lowestRange = (range[0] <= startPos) ? range : lowestRange; - higestRange = (range[1] >= endPos) ? range : higestRange; - } + // first visible col with index 0, convert to absolute index + firstVisible = visibleToAbsoluteColumn(0); - if (lowestRange[0] == -1) // includes (lowestRange[1] == -1) - { - startPos = alignmentStartEnd[0]; - } - else - { - startPos = lowestRange[1] + 1; + // last visible column is either immediately to left of + // last hidden region, or is just the last column in the alignment + int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1); + if (lastregion[1] == width - 1) + { + // last region is at very end of alignment + // last visible column immediately precedes it + lastVisible = lastregion[0] - 1; + } } + return new int[] { firstVisible, lastVisible }; - if (higestRange[0] == -1) // includes (higestRange[1] == -1) - { - endPos = alignmentStartEnd[1]; - } - else - { - endPos = higestRange[0] - 1; - } - return new int[] { startPos, endPos }; } finally { LOCK.readLock().unlock();