X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=93791e44f8691559f2895f28ceff4f1b32c2de6c;hb=d4e62e67024759a6452c10521a113f578832b9c0;hp=fb1961eca932ae4bfbf359e2841fb392e67e0f09;hpb=a3c835f0495ade5c3ae7968dd9727c03710d870b;p=jalview.git diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java index fb1961e..93791e4 100644 --- a/src/jalview/datamodel/HiddenColumns.java +++ b/src/jalview/datamodel/HiddenColumns.java @@ -24,9 +24,29 @@ import java.util.ArrayList; import java.util.BitSet; import java.util.Iterator; import java.util.List; -import java.util.NoSuchElementException; import java.util.concurrent.locks.ReentrantReadWriteLock; +/** + * This class manages the collection of hidden columns associated with an + * alignment. To iterate over the collection, or over visible columns/regions, + * use an iterator obtained from one of: + * + * - getBoundedIterator: iterates over the hidden regions, within some bounds, + * returning absolute positions + * + * - getBoundedStartIterator: iterates over the start positions of hidden + * regions, within some bounds, returning visible positions + * + * - getVisContigsIterator: iterates over visible regions in a range, returning + * absolute positions + * + * - getVisibleColsIterator: iterates over the visible *columns* + * + * For performance reasons, provide bounds where possible. + * + * @author kmourao + * + */ public class HiddenColumns { private static final int HASH_MULTIPLIER = 31; @@ -34,6 +54,17 @@ public class HiddenColumns private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock(); /* + * Cursor which tracks the last used hidden columns region, and the number + * of hidden columns up to (but not including) that region. + */ + private HiddenColumnsCursor cursor = new HiddenColumnsCursor(); + + /* + * cache of the number of hidden columns + */ + private int numColumns = 0; + + /* * list of hidden column [start, end] ranges; the list is maintained in * ascending start column order */ @@ -46,16 +77,26 @@ 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 * * @param copy + * the HiddenColumns object to copy from */ public HiddenColumns(HiddenColumns copy) { try { LOCK.writeLock().lock(); + numColumns = 0; if (copy != null) { if (copy.hiddenColumns != null) @@ -64,8 +105,11 @@ public class HiddenColumns Iterator it = copy.iterator(); while (it.hasNext()) { - hiddenColumns.add(it.next()); + int[] region = it.next(); + hiddenColumns.add(region); + numColumns += region[1] - region[0] + 1; } + cursor.resetCursor(hiddenColumns); } } } finally @@ -97,6 +141,7 @@ public class HiddenColumns if (copy != null) { hiddenColumns = new ArrayList<>(); + numColumns = 0; Iterator it = copy.getBoundedIterator(start, end); while (it.hasNext()) { @@ -108,8 +153,10 @@ public class HiddenColumns hiddenColumns.add( new int[] { region[0] - offset, region[1] - offset }); + numColumns += region[1] - region[0] + 1; } } + cursor.resetCursor(hiddenColumns); } } finally { @@ -118,723 +165,464 @@ public class HiddenColumns } /** - * Output regions data as a string. String is in the format: - * reg0[0]reg0[1]reg1[0]reg1[1] ... regn[1] + * Adds the specified column range to the hidden columns collection * - * @param delimiter - * string to delimit regions - * @param betweenstring - * to put between start and end region values - * @return regions formatted according to delimiter and between strings + * @param start + * start of range to add (absolute position in alignment) + * @param end + * end of range to add (absolute position in alignment) */ - public String regionsToString(String delimiter, String between) + public void hideColumns(int start, int end) { + boolean wasAlreadyLocked = false; try { - LOCK.readLock().lock(); - StringBuilder regionBuilder = new StringBuilder(); - Iterator it = new RegionsIterator(); - while (it.hasNext()) + // 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()) { - int[] range = it.next(); - regionBuilder.append(delimiter).append(range[0]).append(between) - .append(range[1]); - if (!it.hasNext()) + LOCK.writeLock().lock(); + } + else + { + wasAlreadyLocked = true; + } + + int previndex = 0; + int prevHiddenCount = 0; + int regionindex = 0; + if (hiddenColumns == null) + { + hiddenColumns = new ArrayList<>(); + } + else + { + // set up cursor reset values + HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start); + regionindex = cursorPos.getRegionIndex(); + + if (regionindex > 0) { - regionBuilder.deleteCharAt(0); + // get previous index and hidden count for updating the cursor later + previndex = regionindex - 1; + int[] prevRegion = hiddenColumns.get(previndex); + prevHiddenCount = cursorPos.getHiddenSoFar() + - (prevRegion[1] - prevRegion[0] + 1); } } - return regionBuilder.toString(); - } finally - { - LOCK.readLock().unlock(); - } - } - /** - * Find the number of hidden columns - * - * @return number of hidden columns - */ - public int getSize() - { - try - { - LOCK.readLock().lock(); - int size = 0; - Iterator it = new RegionsIterator(); - while (it.hasNext()) + /* + * new range follows everything else; check first to avoid looping over whole hiddenColumns collection + */ + if (hiddenColumns.isEmpty() + || start > hiddenColumns.get(hiddenColumns.size() - 1)[1]) { - int[] range = it.next(); - size += range[1] - range[0] + 1; + hiddenColumns.add(new int[] { start, end }); + } + else + { + /* + * traverse existing hidden ranges and insert / amend / append as + * appropriate + */ + boolean added = false; + if (regionindex > 0) + { + added = insertRangeAtRegion(regionindex - 1, start, end); + } + if (!added && regionindex < hiddenColumns.size()) + { + insertRangeAtRegion(regionindex, start, end); + } } - return size; + // reset the cursor to just before our insertion point: this saves + // a lot of reprocessing in large alignments + cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount); + + // reset the number of columns so they will be recounted + numColumns = 0; + } finally { - LOCK.readLock().unlock(); + if (!wasAlreadyLocked) + { + LOCK.writeLock().unlock(); + } } } /** - * Get the number of distinct hidden regions + * Insert [start, range] at the region at index i in hiddenColumns, if + * feasible * - * @return number of regions + * @param i + * index to insert at + * @param start + * start of range to insert + * @param end + * end of range to insert + * @return true if range was successfully inserted */ - public int getNumberOfRegions() + private boolean insertRangeAtRegion(int i, int start, int end) { - try + boolean added = false; + + int[] region = hiddenColumns.get(i); + if (end < region[0] - 1) { - LOCK.readLock().lock(); - int num = 0; - if (hasHiddenColumns()) - { - num = hiddenColumns.size(); - } - return num; - } finally + /* + * insert discontiguous preceding range + */ + hiddenColumns.add(i, new int[] { start, end }); + added = true; + } + else if (end <= region[1]) { - LOCK.readLock().unlock(); + /* + * new range overlaps existing, or is contiguous preceding it - adjust + * start column + */ + region[0] = Math.min(region[0], start); + added = true; } - } - - @Override - public boolean equals(Object obj) - { - try + else if (start <= region[1] + 1) { - LOCK.readLock().lock(); - - if (!(obj instanceof HiddenColumns)) - { - return false; - } - HiddenColumns that = (HiddenColumns) obj; - /* - * check hidden columns are either both null, or match + * new range overlaps existing, or is contiguous following it - adjust + * start and end columns */ - if (this.hiddenColumns == null) - { - return (that.hiddenColumns == null); - } - if (that.hiddenColumns == null - || that.hiddenColumns.size() != this.hiddenColumns.size()) - { - return false; - } + region[0] = Math.min(region[0], start); + region[1] = Math.max(region[1], end); - Iterator it = new RegionsIterator(); - Iterator thatit = that.iterator(); - while (it.hasNext()) + /* + * also update or remove any subsequent ranges + * that are overlapped + */ + while (i < hiddenColumns.size() - 1) { - int[] thisRange = it.next(); - int[] thatRange = thatit.next(); - if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) + int[] nextRegion = hiddenColumns.get(i + 1); + if (nextRegion[0] > end + 1) { - return false; + /* + * gap to next hidden range - no more to update + */ + break; } + 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(); } - return true; - } finally - { - LOCK.readLock().unlock(); + added = true; } + return added; } /** - * Return absolute column index for a visible column index + * mark the columns corresponding to gap characters as hidden in the column + * selection * - * @param column - * int column index in alignment view (count from zero) - * @return alignment column index for column + * @param sr */ - public int adjustForHiddenColumns(int column) + public void hideInsertionsFor(SequenceI sr) { try { - LOCK.readLock().lock(); - int result = column; - - Iterator it = new RegionsIterator(); - while (it.hasNext()) + LOCK.writeLock().lock(); + List inserts = sr.getInsertions(); + for (int[] r : inserts) { - int[] region = it.next(); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } + hideColumns(r[0], r[1]); } - - return result; + cursor.resetCursor(hiddenColumns); + numColumns = 0; } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } /** - * Use this method to find out where a column will appear in the visible - * alignment when hidden columns exist. If the column is not visible, then the - * left-most visible column will always be returned. - * - * @param hiddenColumn - * the column index in the full alignment including hidden columns - * @return the position of the column in the visible alignment + * Unhides, and adds to the selection list, all hidden columns */ - public int findColumnPosition(int hiddenColumn) + public void revealAllHiddenColumns(ColumnSelection sel) { try { - LOCK.readLock().lock(); - int result = hiddenColumn; - int[] region = null; + LOCK.writeLock().lock(); if (hiddenColumns != null) { - Iterator it = new RegionsIterator(0, - hiddenColumn); + Iterator it = hiddenColumns.iterator(); while (it.hasNext()) { - region = it.next(); - if (hiddenColumn > region[1]) - { - result -= region[1] + 1 - region[0]; - } - } - - if (region != null && hiddenColumn >= region[0] - && hiddenColumn <= region[1]) - { - // Here the hidden column is within a region, so - // we want to return the position of region[0]-1, adjusted for any - // earlier hidden columns. - // Calculate the difference between the actual hidden col position - // and region[0]-1, and then subtract from result to convert result - // from the adjusted hiddenColumn value to the adjusted region[0]-1 - // value. - - // However, if the region begins at 0 we cannot return region[0]-1 - // just return 0 - if (region[0] == 0) - { - return 0; - } - else + int[] region = it.next(); + for (int j = region[0]; j < region[1] + 1; j++) { - return result - (hiddenColumn - region[0] + 1); + sel.addElement(j); } } + hiddenColumns = null; + cursor.resetCursor(hiddenColumns); + numColumns = 0; } - return result; // return the shifted position after removing hidden - // columns. } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } /** - * 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. + * Reveals, and marks as selected, the hidden column range with the given + * start column * - * @param visibleDistance - * the number of visible columns to offset by - * @param startColumn - * the column to start from - * @return the position of the column in the visible alignment + * @param start + * the start column to look for + * @param sel + * the column selection to add the hidden column range to */ - public int subtractVisibleColumns(int visibleDistance, int startColumn) + public void revealHiddenColumns(int start, ColumnSelection sel) { try { - LOCK.readLock().lock(); - int distance = visibleDistance; - - // in case startColumn is in a hidden region, move it to the left - int start = adjustForHiddenColumns(findColumnPosition(startColumn)); - - Iterator it = new ReverseRegionsIterator(0, start); + LOCK.writeLock().lock(); - while (it.hasNext() && (distance > 0)) + if (hiddenColumns != null) { - int[] region = it.next(); + int regionIndex = cursor.findRegionForColumn(start) + .getRegionIndex(); - if (start > region[1]) + if (regionIndex != -1 && regionIndex != hiddenColumns.size()) { - // subtract the gap to right of region from distance - if (start - region[1] <= distance) - { - distance -= start - region[1]; - start = region[0] - 1; - } - else + // regionIndex is the region which either contains start + // or lies to the right of start + int[] region = hiddenColumns.get(regionIndex); + if (start == region[0]) { - start = start - distance; - distance = 0; - } - } - } - - return start - distance; - - } finally - { - LOCK.readLock().unlock(); - } - } + for (int j = region[0]; j < region[1] + 1; j++) + { + sel.addElement(j); + } + int colsToRemove = region[1] - region[0] + 1; + hiddenColumns.remove(regionIndex); - /** - * This method returns the rightmost limit of a region of an alignment with - * hidden columns. In otherwords, the next hidden column. - * - * @param alPos - * the (visible) alignmentPosition to find the next hidden column for - */ - public int getHiddenBoundaryRight(int alPos) - { - try - { - LOCK.readLock().lock(); - if (hiddenColumns != null) - { - Iterator it = new RegionsIterator(); - while (it.hasNext()) - { - int[] region = it.next(); - if (alPos < region[0]) - { - return region[0]; + if (hiddenColumns.isEmpty()) + { + hiddenColumns = null; + numColumns = 0; + } + else + { + numColumns -= colsToRemove; + } + cursor.updateForDeletedRegion(hiddenColumns); } } } - return alPos; } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } /** - * This method returns the leftmost limit of a region of an alignment with - * hidden columns. In otherwords, the previous hidden column. + * Add gaps into the sequences aligned to profileseq under the given + * AlignmentView * - * @param alPos - * the (visible) alignmentPosition to find the previous hidden column - * for + * @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 int getHiddenBoundaryLeft(int alPos) + public static HiddenColumns propagateInsertions(SequenceI profileseq, + AlignmentI al, AlignmentView input) { - try - { - LOCK.readLock().lock(); - - Iterator it = new ReverseRegionsIterator(0, alPos); - while (it.hasNext()) - { - int[] region = it.next(); - if (alPos > region[1]) - { - return region[1]; - } - } + int profsqpos = 0; - return alPos; - } finally - { - LOCK.readLock().unlock(); - } + 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; } /** - * Adds the specified column range to the hidden columns collection * - * @param start - * start of range to add (absolute position in alignment) - * @param end - * end of range to add (absolute position in alignment) + * @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 */ - public void hideColumns(int start, int end) + private void propagateInsertions(SequenceI profileseq, AlignmentI al, + SequenceI origseq) { - 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; - } - - if (hiddenColumns == null) - { - hiddenColumns = new ArrayList<>(); - } - - /* - * new range follows everything else; check first to avoid looping over whole hiddenColumns collection - */ - if (hiddenColumns.isEmpty() - || start > hiddenColumns.get(hiddenColumns.size() - 1)[1]) - { - hiddenColumns.add(new int[] { start, end }); - } - else - { - /* - * traverse existing hidden ranges and insert / amend / append as - * appropriate - */ - boolean added = false; - for (int i = 0; !added && i < hiddenColumns.size(); i++) - { - added = insertRangeAtRegion(i, start, end); - } // for - } - } finally - { - if (!wasAlreadyLocked) - { - LOCK.writeLock().unlock(); - } - } - } - - private boolean insertRangeAtRegion(int i, int start, int end) - { - boolean added = false; + LOCK.writeLock().lock(); - int[] region = hiddenColumns.get(i); - if (end < region[0] - 1) - { - /* - * insert discontiguous preceding range - */ - hiddenColumns.add(i, new int[] { start, end }); - added = true; - } - else if (end <= region[1]) - { - /* - * new range overlaps existing, or is contiguous preceding it - adjust - * start column - */ - region[0] = Math.min(region[0], start); - added = true; - } - else if (start <= region[1] + 1) - { - /* - * new range overlaps existing, or is contiguous following it - adjust - * start and end columns - */ - region[0] = Math.min(region[0], start); - region[1] = Math.max(region[1], end); + char gc = al.getGapCharacter(); - /* - * also update or remove any subsequent ranges - * that are overlapped - */ - while (i < hiddenColumns.size() - 1) - { - int[] nextRegion = hiddenColumns.get(i + 1); - if (nextRegion[0] > end + 1) - { - /* - * gap to next hidden range - no more to update - */ - break; - } - region[1] = Math.max(nextRegion[1], end); - hiddenColumns.remove(i + 1); - } - added = true; - } - return added; - } + // take the set of hidden columns, and the set of gaps in origseq, + // and remove all the hidden gaps from hiddenColumns - /** - * Answers if a column in the alignment is visible - * - * @param column - * absolute position of column in the alignment - * @return true if column is visible - */ - public boolean isVisible(int column) - { - try - { - LOCK.readLock().lock(); + // first get the gaps as a Bitset + BitSet gaps = origseq.gapBitset(); - Iterator it = new RegionsIterator(); - while (it.hasNext()) - { - int[] region = it.next(); - if (column >= region[0] && column <= region[1]) - { - return false; - } - } + // now calculate hidden ^ not(gap) + BitSet hidden = new BitSet(); + markHiddenRegions(hidden); + hidden.andNot(gaps); + hiddenColumns = null; + this.hideMarkedBits(hidden); - return true; - } finally - { - LOCK.readLock().unlock(); - } - } + // 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 + Iterator regions = hiddenColumns.iterator(); + ArrayList newhidden = new ArrayList<>(); - /** - * 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 != null && hiddenColumns.size() > 0) + int numGapsBefore = 0; + int gapPosition = 0; + while (regions.hasNext()) { - for (int i = 0; i < iSize; i++) + // get region coordinates accounting for gaps + // we can rely on gaps not being *in* hidden regions because we already + // removed those + int[] region = regions.next(); + while (gapPosition < region[0]) { - StringBuffer visibleSeq = new StringBuffer(); - - Iterator blocks = new VisibleContigsIterator(start, - end + 1, false); - - while (blocks.hasNext()) + gapPosition++; + if (gaps.get(gapPosition)) { - 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])); - } + numGapsBefore++; } - - 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 == null || hiddenColumns.size() == 0) - { - return seq.findIndex(seq.getStart()) - 1; - } - - // Simply walk along the sequence whilst watching for hidden column - // boundaries - Iterator regions = new RegionsIterator(); - 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; + int left = region[0] - numGapsBefore; + int right = region[1] - numGapsBefore; + newhidden.add(new int[] { left, right }); - // 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) + // make a string with number of gaps = length of hidden region + StringBuffer sb = new StringBuffer(); + for (int s = 0; s < right - left + 1; s++) { - start = p; - foundStart = true; + sb.append(gc); } - } + padGaps(sb, left, profileseq, al); - if (foundStart) - { - return findColumnPosition(start); } - // otherwise, sequence was completely hidden - return visPrev; + hiddenColumns = newhidden; + cursor.resetCursor(hiddenColumns); + numColumns = 0; } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param alignmentAnnotation - */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) - { - makeVisibleAnnotation(0, alignmentAnnotation.annotations.length, - alignmentAnnotation); - } - - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). + * Pad gaps in all sequences in alignment except profileseq * - * @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 + * @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 */ - public void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) - { - try - { - LOCK.readLock().lock(); - - int startFrom = start; - int endAt = end; - - if (alignmentAnnotation.annotations != null) - { - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation); - } - else - { - alignmentAnnotation.restrict(startFrom, endAt); - } - } - } finally - { - LOCK.readLock().unlock(); - } - } - - private void removeHiddenAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) + private void padGaps(StringBuffer sb, int pos, SequenceI profileseq, + AlignmentI al) { - // mangle the alignmentAnnotation annotation array - ArrayList annels = new ArrayList<>(); - Annotation[] els = null; - - int w = 0; - - Iterator blocks = new VisibleContigsIterator(start, end + 1, - false); - - int copylength; - int annotationLength; - while (blocks.hasNext()) + // loop over the sequences and pad with gaps where required + for (int s = 0, ns = al.getHeight(); s < ns; s++) { - 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 + SequenceI sqobj = al.getSequenceAt(s); + if (sqobj != profileseq) { - if (annotationLength + block[0] <= alignmentAnnotation.annotations.length) + String sq = al.getSequenceAt(s).getSequenceAsString(); + if (sq.length() <= pos) { - // copy just the visible segment of the annotation row - copylength = annotationLength; + // 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 { - // copy to the end of the annotation row - copylength = alignmentAnnotation.annotations.length - block[0]; + al.getSequenceAt(s).setSequence( + sq.substring(0, pos) + sb.toString() + sq.substring(pos)); } } - - 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; - } } } + /* + * 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] * - * @return true if there are columns hidden + * @param delimiter + * string to delimit regions + * @param betweenstring + * to put between start and end region values + * @return regions formatted according to delimiter and between strings */ - public boolean hasHiddenColumns() + public String regionsToString(String delimiter, String between) { try { LOCK.readLock().lock(); - return hiddenColumns != null && hiddenColumns.size() > 0; + StringBuilder regionBuilder = new StringBuilder(); + if (hiddenColumns != null) + { + Iterator it = hiddenColumns.iterator(); + while (it.hasNext()) + { + int[] range = it.next(); + regionBuilder.append(delimiter).append(range[0]).append(between) + .append(range[1]); + if (!it.hasNext()) + { + regionBuilder.deleteCharAt(0); + } + } + } + return regionBuilder.toString(); } finally { LOCK.readLock().unlock(); @@ -842,15 +630,32 @@ public class HiddenColumns } /** + * Find the number of hidden columns * - * @return true if there are more than one set of columns hidden + * @return number of hidden columns */ - public boolean hasManyHiddenColumns() + public int getSize() { try { LOCK.readLock().lock(); - return hiddenColumns != null && hiddenColumns.size() > 1; + + if (numColumns == 0 && hiddenColumns != null) + { + // numColumns is out of date, so recalculate + int size = 0; + + Iterator it = hiddenColumns.iterator(); + while (it.hasNext()) + { + int[] range = it.next(); + size += range[1] - range[0] + 1; + } + + numColumns = size; + } + + return numColumns; } finally { LOCK.readLock().unlock(); @@ -858,320 +663,366 @@ public class HiddenColumns } /** - * mark the columns corresponding to gap characters as hidden in the column - * selection + * Get the number of distinct hidden regions * - * @param sr + * @return number of regions */ - public void hideInsertionsFor(SequenceI sr) + public int getNumberOfRegions() { try { - LOCK.writeLock().lock(); - List inserts = sr.getInsertions(); - for (int[] r : inserts) + LOCK.readLock().lock(); + int num = 0; + if (hasHiddenColumns()) { - hideColumns(r[0], r[1]); + num = hiddenColumns.size(); } + return num; } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } - /** - * Unhides, and adds to the selection list, all hidden columns - */ - public void revealAllHiddenColumns(ColumnSelection sel) + @Override + public boolean equals(Object obj) { try { - LOCK.writeLock().lock(); - Iterator it = new RegionsIterator(); + LOCK.readLock().lock(); + + if (!(obj instanceof HiddenColumns)) + { + return false; + } + HiddenColumns that = (HiddenColumns) obj; + + /* + * check hidden columns are either both null, or match + */ + if (this.hiddenColumns == null) + { + return (that.hiddenColumns == null); + } + if (that.hiddenColumns == null + || that.hiddenColumns.size() != this.hiddenColumns.size()) + { + return false; + } + + Iterator it = hiddenColumns.iterator(); + Iterator thatit = that.iterator(); while (it.hasNext()) { - int[] region = it.next(); - for (int j = region[0]; j < region[1] + 1; j++) + int[] thisRange = it.next(); + int[] thatRange = thatit.next(); + if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) { - sel.addElement(j); + return false; } } - - hiddenColumns = null; + return true; } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } /** - * Reveals, and marks as selected, the hidden column range with the given - * start column + * Return absolute column index for a visible column index * - * @param start + * @param column + * int column index in alignment view (count from zero) + * @return alignment column index for column */ - public void revealHiddenColumns(int start, ColumnSelection sel) + public int visibleToAbsoluteColumn(int column) { try { - LOCK.writeLock().lock(); - Iterator it = new RegionsIterator(); - while (it.hasNext()) - { - int[] region = it.next(); - if (start == region[0]) - { - for (int j = region[0]; j < region[1] + 1; j++) - { - sel.addElement(j); - } - - hiddenColumns.remove(region); - break; - } - else if (start < region[0]) - { - break; // passed all possible matching regions - } - } + LOCK.readLock().lock(); + int result = column; - if (hiddenColumns.size() == 0) + if (hiddenColumns != null) { - hiddenColumns = null; + result += cursor.findRegionForVisColumn(column).getHiddenSoFar(); } + + return result; } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } /** - * Add gaps into the sequences aligned to profileseq under the given - * AlignmentView + * Use this method to find out where a column will appear in the visible + * alignment when hidden columns exist. If the column is not visible, then the + * index of the next visible column on the left will be returned (or 0 if + * there is no visible column on the left) * - * @param profileseq - * @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. + * @param hiddenColumn + * the column index in the full alignment including hidden columns + * @return the position of the column in the visible alignment */ - public static HiddenColumns propagateInsertions(SequenceI profileseq, - AlignmentI al, AlignmentView input) + public int absoluteToVisibleColumn(int hiddenColumn) { - int profsqpos = 0; + try + { + LOCK.readLock().lock(); + int result = hiddenColumn; - 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; + if (hiddenColumns != null) + { + HiddenCursorPosition cursorPos = cursor + .findRegionForColumn(hiddenColumn); + int index = cursorPos.getRegionIndex(); + int hiddenBeforeCol = cursorPos.getHiddenSoFar(); + + // just subtract hidden cols count - this works fine if column is + // visible + result = hiddenColumn - hiddenBeforeCol; + + // now check in case column is hidden - it will be in the returned + // hidden region + if (index < hiddenColumns.size()) + { + int[] region = hiddenColumns.get(index); + if (hiddenColumn >= region[0] && hiddenColumn <= region[1]) + { + // actually col is hidden, return region[0]-1 + // unless region[0]==0 in which case return 0 + if (region[0] == 0) + { + result = 0; + } + else + { + result = region[0] - 1 - hiddenBeforeCol; + } + } + } + } + + return result; // return the shifted position after removing hidden + // columns. + } finally + { + LOCK.readLock().unlock(); + } } /** + * 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. * - * @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 + * @param visibleDistance + * the number of visible columns to offset by + * @param startColumn + * the column to start from + * @return the position of the column in the visible alignment */ - private void propagateInsertions(SequenceI profileseq, AlignmentI al, - SequenceI origseq) + public int subtractVisibleColumns(int visibleDistance, int startColumn) { 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 = null; - this.hideMarkedBits(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 - Iterator regions = new RegionsIterator(); - ArrayList newhidden = new ArrayList<>(); + LOCK.readLock().lock(); + int distance = visibleDistance; - int numGapsBefore = 0; - int gapPosition = 0; - while (regions.hasNext()) - { - // get region coordinates accounting for gaps - // we can rely on gaps not being *in* hidden regions because we already - // removed those - int[] region = regions.next(); - while (gapPosition < region[0]) - { - gapPosition++; - if (gaps.get(gapPosition)) - { - numGapsBefore++; - } - } + // in case startColumn is in a hidden region, move it to the left + int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn)); - int left = region[0] - numGapsBefore; - int right = region[1] - numGapsBefore; - newhidden.add(new int[] { left, right }); + Iterator it = new ReverseRegionsIterator(0, start, + hiddenColumns); - // make a string with number of gaps = length of hidden region - StringBuffer sb = new StringBuffer(); - for (int s = 0; s < right - left + 1; s++) + while (it.hasNext() && (distance > 0)) + { + int[] region = it.next(); + + if (start > region[1]) { - sb.append(gc); + // 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; + } } - padGaps(sb, left, profileseq, al); - } - hiddenColumns = newhidden; + return start - distance; + } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } /** - * Pad gaps in all sequences in alignment except profileseq + * This method returns the rightmost limit of a region of an alignment with + * hidden columns. In otherwords, the next hidden column. * - * @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 + * @param alPos + * the absolute (visible) alignmentPosition to find the next hidden + * column for + * @return the index of the next hidden column, or alPos if there is no next + * hidden column */ - private void padGaps(StringBuffer sb, int pos, SequenceI profileseq, - AlignmentI al) + public int getHiddenBoundaryRight(int alPos) { - // loop over the sequences and pad with gaps where required - for (int s = 0, ns = al.getHeight(); s < ns; s++) + try { - SequenceI sqobj = al.getSequenceAt(s); - if (sqobj != profileseq) + LOCK.readLock().lock(); + if (hiddenColumns != null) { - String sq = al.getSequenceAt(s).getSequenceAsString(); - if (sq.length() <= pos) + int index = cursor.findRegionForColumn(alPos).getRegionIndex(); + if (index < hiddenColumns.size()) { - // pad sequence - int diff = pos - sq.length() - 1; - if (diff > 0) + int[] region = hiddenColumns.get(index); + if (alPos < region[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(); - } - } + return region[0]; + } + else if ((alPos <= region[1]) + && (index + 1 < hiddenColumns.size())) + { + // alPos is within a hidden region, return the next one + // if there is one + region = hiddenColumns.get(index + 1); + return region[0]; } - sq += sb.toString(); - } - else - { - al.getSequenceAt(s).setSequence( - sq.substring(0, pos) + sb.toString() + sq.substring(pos)); } } + return alPos; + } finally + { + LOCK.readLock().unlock(); } } /** - * Returns a hashCode built from hidden column ranges + * 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 */ - @Override - public int hashCode() + public int getHiddenBoundaryLeft(int alPos) { try { LOCK.readLock().lock(); - int hashCode = 1; - Iterator it = new RegionsIterator(); - while (it.hasNext()) + + if (hiddenColumns != null) { - int[] hidden = it.next(); - hashCode = HASH_MULTIPLIER * hashCode + hidden[0]; - hashCode = HASH_MULTIPLIER * hashCode + hidden[1]; + int index = cursor.findRegionForColumn(alPos).getRegionIndex(); + + if (index > 0) + { + int[] region = hiddenColumns.get(index - 1); + return region[1]; + } } - return hashCode; + return alPos; } finally { LOCK.readLock().unlock(); } } + /** - * Hide columns corresponding to the marked bits + * Answers if a column in the alignment is visible * - * @param inserts - * - columns map to bits starting from zero + * @param column + * absolute position of column in the alignment + * @return true if column is visible */ - public void hideMarkedBits(BitSet inserts) + public boolean isVisible(int column) { try { - LOCK.writeLock().lock(); - for (int firstSet = inserts - .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts - .nextSetBit(lastSet)) + LOCK.readLock().lock(); + + int regionindex = cursor.findRegionForColumn(column).getRegionIndex(); + if (regionindex > -1 && regionindex < hiddenColumns.size()) { - lastSet = inserts.nextClearBit(firstSet); - hideColumns(firstSet, lastSet - 1); + int[] region = hiddenColumns.get(regionindex); + // already know that column <= region[1] as cursor returns containing + // region or region to right + if (column >= region[0]) + { + return false; + } } + return true; + } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } /** + * Get the visible sections of a set of sequences * - * @param inserts - * BitSet where hidden columns will be marked + * @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 void markHiddenRegions(BitSet inserts) + public String[] getVisibleSequenceStrings(int start, int end, + SequenceI[] seqs) { try { LOCK.readLock().lock(); - if (hiddenColumns == null) + int iSize = seqs.length; + String[] selections = new String[iSize]; + if (hiddenColumns != null && hiddenColumns.size() > 0) { - return; + 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(); + } } - Iterator it = new RegionsIterator(); - while (it.hasNext()) + else { - int[] range = it.next(); - inserts.set(range[0], range[1] + 1); + for (int i = 0; i < iSize; i++) + { + selections[i] = seqs[i].getSequenceAsString(start, end); + } } + + return selections; } finally { LOCK.readLock().unlock(); @@ -1179,920 +1030,517 @@ public class HiddenColumns } /** - * Calculate the visible start and end index of an alignment. + * 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 width - * full alignment width - * @return integer array where: int[0] = startIndex, and int[1] = endIndex + * @param seq + * sequence to find position for + * @return visible start position */ - public int[] getVisibleStartAndEndIndex(int width) + public int locateVisibleStartOfSequence(SequenceI seq) { 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 }; + int start = 0; - if (hiddenColumns == null) + if (hiddenColumns == null || hiddenColumns.size() == 0) { - return new int[] { startPos, endPos }; + return seq.findIndex(seq.getStart()) - 1; } - Iterator it = new RegionsIterator(); - while (it.hasNext()) - { - int[] range = it.next(); - lowestRange = (range[0] <= startPos) ? range : lowestRange; - higestRange = (range[1] >= endPos) ? range : higestRange; - } + // 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; - if (lowestRange[0] == -1 && lowestRange[1] == -1) - { - startPos = alignmentStartEnd[0]; - } - else + // step through the non-gapped positions of the sequence + for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++) { - startPos = lowestRange[1] + 1; - } + // get alignment position of this residue in the sequence + int p = seq.findIndex(i) - 1; - if (higestRange[0] == -1 && higestRange[1] == -1) - { - endPos = alignmentStartEnd[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; + } } - else + + if (foundStart) { - endPos = higestRange[0] - 1; + return absoluteToVisibleColumn(start); } - return new int[] { startPos, endPos }; + // 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); + } } /** - * Finds the hidden region (if any) which starts or ends at res + * delete any columns in alignmentAnnotation that are hidden (including + * sequence associated annotation). * - * @param res - * visible residue position, unadjusted for hidden columns - * @return region as [start,end] or null if no matching region is found + * @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 int[] getRegionWithEdgeAtRes(int res) + public void makeVisibleAnnotation(int start, int end, + AlignmentAnnotation alignmentAnnotation) { try { LOCK.readLock().lock(); - int adjres = adjustForHiddenColumns(res); - int[] reveal = null; - Iterator it = new RegionsIterator(adjres - 2, - adjres + 2); - while (it.hasNext()) + int startFrom = start; + int endAt = end; + + if (alignmentAnnotation != null + && alignmentAnnotation.annotations != null) { - int[] region = it.next(); - if (adjres + 1 == region[0] || adjres - 1 == region[1]) + if (hiddenColumns != null && hiddenColumns.size() > 0) { - reveal = region; - break; + removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation); + } + else + { + alignmentAnnotation.restrict(startFrom, endAt); } } - return reveal; } finally { LOCK.readLock().unlock(); } } - /** - * Return an iterator over the hidden regions - */ - public Iterator iterator() + private void removeHiddenAnnotation(int start, int end, + AlignmentAnnotation alignmentAnnotation) { - return new BoundedHiddenColsIterator(); - } + // mangle the alignmentAnnotation annotation array + ArrayList annels = new ArrayList<>(); + Annotation[] els = null; - /** - * Return a bounded iterator over the hidden regions - * - * @param start - * position to start from (inclusive, absolute column position) - * @param end - * position to end at (inclusive, absolute column position) - * @return - */ - public Iterator getBoundedIterator(int start, int end) - { - return new BoundedHiddenColsIterator(start, end); - } + int w = 0; + + Iterator blocks = new VisibleContigsIterator(start, end + 1, + hiddenColumns); - /** - * Return a bounded iterator over the *visible* start positions of hidden - * regions - * - * @param start - * position to start from (inclusive, visible column position) - * @param end - * position to end at (inclusive, visible column position) - */ - public Iterator getBoundedStartIterator(int start, int end) - { - return new BoundedStartRegionIterator(start, end, true); - } + 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]; - /** - * Return an iterator over visible *columns* (not regions) between the given - * start and end boundaries - * - * @param start - * first column (inclusive) - * @param end - * last column (inclusive) - */ - public Iterator getVisibleColsIterator(int start, int end) - { - return new VisibleColsIterator(start, end); + w = 0; + for (Annotation[] chnk : annels) + { + System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, + chnk.length); + w += chnk.length; + } + } } /** - * return an iterator over visible segments between the given start and end - * boundaries * - * @param start - * (first column inclusive from 0) - * @param end - * (last column - not inclusive) + * @return true if there are columns hidden */ - public Iterator getVisContigsIterator(int start, int end) + public boolean hasHiddenColumns() { - // return new VisibleBlocksIterator(start, end, true) - return new VisibleContigsIterator(start, end, true); + try + { + LOCK.readLock().lock(); + + // we don't use getSize()>0 here because it has to iterate over + // the full hiddenColumns collection and so will be much slower + return hiddenColumns != null && hiddenColumns.size() > 0; + } finally + { + LOCK.readLock().unlock(); + } } /** - * return an iterator over visible segments between the given start and end - * boundaries * - * @param start - * (first column - inclusive from 0) - * @param end - * (last column - inclusive) - * @param useVisibleCoords - * if true, start and end are visible column positions, not absolute - * positions + * @return true if there is more than one hidden column region */ - public Iterator getVisibleBlocksIterator(int start, int end, - boolean useVisibleCoords) + public boolean hasMultiHiddenColumnRegions() { - if (useVisibleCoords) + try { - // TODO - // we should really just convert start and end here with - // adjustForHiddenColumns - // and then create a VisibleContigsIterator - // but without a cursor this will be horribly slow in some situations - // ... so until then... - return new VisibleBlocksVisBoundsIterator(start, end, true); - } - else + LOCK.readLock().lock(); + return hiddenColumns != null && hiddenColumns.size() > 1; + } finally { - return new VisibleContigsIterator(start, end - 1, true); + LOCK.readLock().unlock(); } } + /** - * A local iterator which iterates over hidden column regions in a range. - * Intended for use ONLY within the HiddenColumns class, because it works - * directly with the hiddenColumns collection without locking (callers should - * lock hiddenColumns). + * Returns a hashCode built from hidden column ranges */ - private class RegionsIterator implements Iterator + @Override + public int hashCode() { - // start position to iterate from - private int start; - - // end position to iterate to - private int end; - - // current index in hiddenColumns - private int currentPosition = 0; - - // current column in hiddenColumns - private int[] nextRegion = null; - - // Constructor with bounds - RegionsIterator(int lowerBound, int upperBound) - { - init(lowerBound, upperBound); - } - - // Unbounded constructor - RegionsIterator() - { - if (hiddenColumns != null) - { - // iterator over full hiddenColumns collection - int last = hiddenColumns.get(hiddenColumns.size() - 1)[1]; - init(0, last); - } - else - { - // empty iterator - init(0, 0); - } - } - - /** - * Construct an iterator over hiddenColums bounded at - * [lowerBound,upperBound] - * - * @param lowerBound - * lower bound to iterate from - * @param upperBound - * upper bound to iterate to - */ - private void init(int lowerBound, int upperBound) + try { - start = lowerBound; - end = upperBound; - - if (hiddenColumns != null) + LOCK.readLock().lock(); + int hashCode = 1; + Iterator it = hiddenColumns.iterator(); + while (it.hasNext()) { - // iterate until a region overlaps with [start,end] - currentPosition = 0; - while ((currentPosition < hiddenColumns.size()) - && (hiddenColumns.get(currentPosition)[1] < start)) - { - currentPosition++; - } - if (currentPosition < hiddenColumns.size()) - { - nextRegion = hiddenColumns.get(currentPosition); - } + int[] hidden = it.next(); + hashCode = HASH_MULTIPLIER * hashCode + hidden[0]; + hashCode = HASH_MULTIPLIER * hashCode + hidden[1]; } - } - - @Override - public boolean hasNext() - { - return (hiddenColumns != null) && (nextRegion != null) - && (nextRegion[0] <= end); - } - - @Override - public int[] next() + return hashCode; + } finally { - int[] region = nextRegion; - currentPosition++; - if (currentPosition < hiddenColumns.size()) - { - nextRegion = hiddenColumns.get(currentPosition); - } - else - { - nextRegion = null; - } - return region; + LOCK.readLock().unlock(); } - } /** - * A local iterator which reverse iterates over hidden column regions in a - * range. Intended for use ONLY within the HiddenColumns class, because it - * works directly with the hiddenColumns collection without locking (callers - * should lock hiddenColumns). + * Hide columns corresponding to the marked bits + * + * @param inserts + * - columns map to bits starting from zero */ - private class ReverseRegionsIterator implements Iterator + public void hideMarkedBits(BitSet inserts) { - // start position to iterate to - private int start; - - // end position to iterate from - private int end; - - // current index in hiddenColumns - private int currentPosition = 0; - - // current column in hiddenColumns - private int[] nextRegion = null; - - // Constructor with bounds - ReverseRegionsIterator(int lowerBound, int upperBound) - { - init(lowerBound, upperBound); - } - - /** - * Construct an iterator over hiddenColums bounded at - * [lowerBound,upperBound] - * - * @param lowerBound - * lower bound to iterate to - * @param upperBound - * upper bound to iterate from - */ - private void init(int lowerBound, int upperBound) + try { - start = lowerBound; - end = upperBound; - - if (hiddenColumns != null) + LOCK.writeLock().lock(); + for (int firstSet = inserts + .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts + .nextSetBit(lastSet)) { - // iterate until a region overlaps with [start,end] - currentPosition = hiddenColumns.size() - 1; - while (currentPosition >= 0 - && hiddenColumns.get(currentPosition)[1] > end) - { - currentPosition--; - } - if (currentPosition >= 0) - { - nextRegion = hiddenColumns.get(currentPosition); - } + lastSet = inserts.nextClearBit(firstSet); + hideColumns(firstSet, lastSet - 1); } - } - - @Override - public boolean hasNext() + cursor.resetCursor(hiddenColumns); + numColumns = 0; + } finally { - return (hiddenColumns != null) && (nextRegion != null) - && (nextRegion[1] >= start); + LOCK.writeLock().unlock(); } + } - @Override - public int[] next() + /** + * + * @param inserts + * BitSet where hidden columns will be marked + */ + public void markHiddenRegions(BitSet inserts) + { + try { - int[] region = nextRegion; - currentPosition--; - if (currentPosition >= 0) + LOCK.readLock().lock(); + if (hiddenColumns == null) { - nextRegion = hiddenColumns.get(currentPosition); + return; } - else + Iterator it = hiddenColumns.iterator(); + while (it.hasNext()) { - nextRegion = null; + int[] range = it.next(); + inserts.set(range[0], range[1] + 1); } - return region; + } finally + { + LOCK.readLock().unlock(); } - } /** - * An iterator which iterates over hidden column regions in a range. Works - * with a copy of the hidden columns collection. Intended to be used by - * callers OUTSIDE of HiddenColumns. + * Calculate the visible start and end index of an alignment. + * + * @param width + * full alignment width + * @return integer array where: int[0] = startIndex, and int[1] = endIndex */ - private class BoundedHiddenColsIterator implements Iterator + public int[] getVisibleStartAndEndIndex(int width) { - // start position to iterate from - private int start; - - // end position to iterate to - private int end; + try + { + LOCK.readLock().lock(); + int[] alignmentStartEnd = new int[] { 0, width - 1 }; + int startPos = alignmentStartEnd[0]; + int endPos = alignmentStartEnd[1]; - // current index in hiddenColumns - private int currentPosition = 0; + int[] lowestRange = new int[] { -1, -1 }; + int[] higestRange = new int[] { -1, -1 }; - // current column in hiddenColumns - private int[] currentRegion; + if (hiddenColumns == null) + { + return new int[] { startPos, endPos }; + } - // local copy or reference to hiddenColumns - private List localHidden; + Iterator it = hiddenColumns.iterator(); + while (it.hasNext()) + { + int[] range = it.next(); + lowestRange = (range[0] <= startPos) ? range : lowestRange; + higestRange = (range[1] >= endPos) ? range : higestRange; + } - /** - * Unbounded constructor - */ - BoundedHiddenColsIterator() - { - if (hiddenColumns != null) + if (lowestRange[0] == -1) // includes (lowestRange[1] == -1) { - int last = hiddenColumns.get(hiddenColumns.size() - 1)[1]; - init(0, last); + startPos = alignmentStartEnd[0]; } else { - init(0, 0); + startPos = lowestRange[1] + 1; } - } - - /** - * Construct an iterator over hiddenColums bounded at - * [lowerBound,upperBound] - * - * @param lowerBound - * lower bound to iterate from - * @param upperBound - * upper bound to iterate to - */ - BoundedHiddenColsIterator(int lowerBound, int upperBound) - { - init(lowerBound, upperBound); - } - /** - * Construct an iterator over hiddenColums bounded at - * [lowerBound,upperBound] - * - * @param lowerBound - * lower bound to iterate from - * @param upperBound - * upper bound to iterate to - */ - private void init(int lowerBound, int upperBound) - { - start = lowerBound; - end = upperBound; - - try + if (higestRange[0] == -1) // includes (higestRange[1] == -1) { - LOCK.readLock().lock(); - - if (hiddenColumns != null) - { - localHidden = new ArrayList<>(); - - // iterate until a region overlaps with [start,end] - int i = 0; - while ((i < hiddenColumns.size()) - && (hiddenColumns.get(i)[1] < start)) - { - i++; - } - - // iterate from start to end, adding each hidden region. Positions are - // absolute, and all regions which *overlap* [start,end] are added. - while (i < hiddenColumns.size() - && (hiddenColumns.get(i)[0] <= end)) - { - int[] rh = hiddenColumns.get(i); - int[] cp = new int[2]; - System.arraycopy(rh, 0, cp, 0, rh.length); - localHidden.add(cp); - i++; - } - } + endPos = alignmentStartEnd[1]; } - finally + else { - LOCK.readLock().unlock(); + endPos = higestRange[0] - 1; } - } - - @Override - public boolean hasNext() - { - return (localHidden != null) - && (currentPosition < localHidden.size()); - } - - @Override - public int[] next() + return new int[] { startPos, endPos }; + } finally { - currentRegion = localHidden.get(currentPosition); - currentPosition++; - return currentRegion; + LOCK.readLock().unlock(); } } /** - * An iterator which iterates over visible start positions of hidden column - * regions in a range. + * Finds the hidden region (if any) which starts or ends at res + * + * @param res + * visible residue position, unadjusted for hidden columns + * @return region as [start,end] or null if no matching region is found */ - private class BoundedStartRegionIterator implements Iterator + public int[] getRegionWithEdgeAtRes(int res) { - // start position to iterate from - private int start; - - // end position to iterate to - private int end; - - // current index in hiddenColumns - private int currentPosition = 0; - - // local copy or reference to hiddenColumns - private List positions = null; - - /** - * Construct an iterator over hiddenColums bounded at - * [lowerBound,upperBound] - * - * @param lowerBound - * lower bound to iterate from - * @param upperBound - * upper bound to iterate to - * @param useCopyCols - * whether to make a local copy of hiddenColumns for iteration (set - * to true if calling from outwith the HiddenColumns class) - */ - BoundedStartRegionIterator(int lowerBound, int upperBound, - boolean useCopy) - { - start = lowerBound; - end = upperBound; - - try - { - if (useCopy) - { - // assume that if useCopy is false the calling code has locked - // hiddenColumns - LOCK.readLock().lock(); - } - - if (hiddenColumns != null) - { - positions = new ArrayList<>(hiddenColumns.size()); + try + { + LOCK.readLock().lock(); + int adjres = visibleToAbsoluteColumn(res); - // navigate to start, keeping count of hidden columns - int i = 0; - int hiddenSoFar = 0; - while ((i < hiddenColumns.size()) - && (hiddenColumns.get(i)[0] < start + hiddenSoFar)) - { - int[] region = hiddenColumns.get(i); - hiddenSoFar += region[1] - region[0] + 1; - i++; - } + int[] reveal = null; - // iterate from start to end, adding start positions of each - // hidden region. Positions are visible columns count, not absolute - while (i < hiddenColumns.size() - && (hiddenColumns.get(i)[0] <= end + hiddenSoFar)) - { - int[] region = hiddenColumns.get(i); - positions.add(region[0] - hiddenSoFar); - hiddenSoFar += region[1] - region[0] + 1; - i++; - } - } - else + if (hiddenColumns != null) + { + // look for a region ending just before adjres + int regionindex = cursor.findRegionForColumn(adjres - 1) + .getRegionIndex(); + if (regionindex < hiddenColumns.size() + && hiddenColumns.get(regionindex)[1] == adjres - 1) { - positions = new ArrayList<>(); + reveal = hiddenColumns.get(regionindex); } - } finally - { - if (useCopy) + // check if the region ends just after adjres + else if (regionindex < hiddenColumns.size() + && hiddenColumns.get(regionindex)[0] == adjres + 1) { - LOCK.readLock().unlock(); + reveal = hiddenColumns.get(regionindex); } } - } - - @Override - public boolean hasNext() - { - return (currentPosition < positions.size()); - } + return reveal; - /** - * Get next hidden region start position - * - * @return the start position in *visible* coordinates - */ - @Override - public Integer next() + } finally { - int result = positions.get(currentPosition); - currentPosition++; - return result; + LOCK.readLock().unlock(); } } /** - * Iterator over the visible *columns* (not regions) as determined by the set - * of hidden columns. Uses a local copy of hidden columns. - * - * @author kmourao - * + * Return an iterator over the hidden regions */ - private class VisibleColsIterator implements Iterator + public Iterator iterator() { - private int last; - - private int current; - - private int next; - - private List localHidden = new ArrayList<>(); - - private int nexthiddenregion; - - VisibleColsIterator(int firstcol, int lastcol) + try { - last = lastcol; - current = firstcol; - next = firstcol; - nexthiddenregion = 0; - LOCK.readLock().lock(); - - if (hiddenColumns != null) - { - int i = 0; - for (i = 0; i < hiddenColumns.size() - && (current <= hiddenColumns.get(i)[0]); ++i) - { - if (current >= hiddenColumns.get(i)[0] - && current <= hiddenColumns.get(i)[1]) - { - // current is hidden, move to right - current = hiddenColumns.get(i)[1] + 1; - next = current; - nexthiddenregion = i + 1; - } - } - - for (i = hiddenColumns.size() - 1; i >= 0 - && (last >= hiddenColumns.get(i)[1]); --i) - { - if (last >= hiddenColumns.get(i)[0] - && last <= hiddenColumns.get(i)[1]) - { - // last is hidden, move to left - last = hiddenColumns.get(i)[0] - 1; - } - } - - // make a local copy of the bit we need - i = nexthiddenregion; - while (i < hiddenColumns.size() && hiddenColumns.get(i)[0] <= last) - { - int[] region = new int[] { hiddenColumns.get(i)[0], - hiddenColumns.get(i)[1] }; - localHidden.add(region); - i++; - } - } - - LOCK.readLock().unlock(); - } - - @Override - public boolean hasNext() + return new HiddenColsIterator(hiddenColumns); + } finally { - return next <= last; + LOCK.readLock().unlock(); } + } - @Override - public Integer next() + /** + * Return a bounded iterator over the hidden regions + * + * @param start + * position to start from (inclusive, absolute column position) + * @param end + * position to end at (inclusive, absolute column position) + * @return + */ + public Iterator getBoundedIterator(int start, int end) + { + try { - if (next > last) - { - throw new NoSuchElementException(); - } - current = next; - if ((localHidden != null) - && (nexthiddenregion < localHidden.size())) - { - // still some more hidden regions - if (next + 1 < localHidden.get(nexthiddenregion)[0]) - { - // next+1 is still before the next hidden region - next++; - } - else if ((next + 1 >= localHidden.get(nexthiddenregion)[0]) - && (next + 1 <= localHidden.get(nexthiddenregion)[1])) - { - // next + 1 is in the next hidden region - next = localHidden.get(nexthiddenregion)[1] + 1; - nexthiddenregion++; - } - } - else - { - // finished with hidden regions, just increment normally - next++; - } - return current; - } - - @Override - public void remove() + LOCK.readLock().lock(); + return new HiddenColsIterator(start, end, hiddenColumns); + } finally { - throw new UnsupportedOperationException(); + LOCK.readLock().unlock(); } } /** - * An iterator which iterates over visible regions in a range. + * Return a bounded iterator over the *visible* start positions of hidden + * regions + * + * @param start + * position to start from (inclusive, visible column position) + * @param end + * position to end at (inclusive, visible column position) */ - private class VisibleContigsIterator implements Iterator + public Iterator getBoundedStartIterator(int start, int end) { - private List vcontigs = new ArrayList<>(); - - private int currentPosition = 0; - - VisibleContigsIterator(int start, int end, boolean usecopy) + try { - try - { - if (usecopy) - { - LOCK.readLock().lock(); - } - - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - int vstart = start; - int hideStart; - int hideEnd; - - for (int[] region : hiddenColumns) - { - hideStart = region[0]; - hideEnd = region[1]; - - // navigate to start - if (hideEnd < vstart) - { - continue; - } - if (hideStart > vstart) - { - int[] contig = new int[] { vstart, hideStart - 1 }; - vcontigs.add(contig); - } - vstart = hideEnd + 1; + LOCK.readLock().lock(); - // exit if we're past the end - if (vstart >= end) - { - break; - } - } + // get absolute position of column in alignment + int absoluteStart = visibleToAbsoluteColumn(start); - if (vstart < end) - { - int[] contig = new int[] { vstart, end - 1 }; - vcontigs.add(contig); - } - } - else - { - int[] contig = new int[] { start, end - 1 }; - vcontigs.add(contig); - } - } finally - { - if (usecopy) - { - LOCK.readLock().unlock(); - } - } - } + // Get cursor position and supply it to the iterator: + // Since we want visible region start, we look for a cursor for the + // (absoluteStart-1), then if absoluteStart is the start of a visible + // region we'll get the cursor pointing to the region before, which is + // what we want + HiddenCursorPosition pos = cursor + .findRegionForColumn(absoluteStart - 1); - @Override - public boolean hasNext() + return new BoundedStartRegionIterator(pos, start, end, + hiddenColumns); + } finally { - return (currentPosition < vcontigs.size()); + LOCK.readLock().unlock(); } + } - @Override - public int[] next() + /** + * Return an iterator over visible *columns* (not regions) between the given + * start and end boundaries + * + * @param start + * first column (inclusive) + * @param end + * last column (inclusive) + */ + public Iterator getVisibleColsIterator(int start, int end) + { + try { - int[] result = vcontigs.get(currentPosition); - currentPosition++; - return result; + LOCK.readLock().lock(); + return new VisibleColsIterator(start, end, hiddenColumns); + } finally + { + LOCK.readLock().unlock(); } } /** - * An iterator which iterates over visible regions in a range. The range is - * specified in terms of visible column positions. Provides a special - * "endsAtHidden" indicator to allow callers to determine if the final visible - * column is adjacent to a hidden region. + * return an iterator over visible segments between the given start and end + * boundaries + * + * @param start + * first column, inclusive from 0 + * @param end + * last column - not inclusive + * @param useVisibleCoords + * if true, start and end are visible column positions, not absolute + * positions* */ - public class VisibleBlocksVisBoundsIterator implements Iterator + public Iterator getVisContigsIterator(int start, int end, + boolean useVisibleCoords) { - private List vcontigs = new ArrayList<>(); - - private int currentPosition = 0; - - private boolean endsAtHidden = false; - - /** - * Constructor for iterator over visible regions in a range. - * - * @param start - * start position in terms of visible column position - * @param end - * end position in terms of visible column position - * @param usecopy - * whether to use a local copy of hidden columns - */ - VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy) - { - /* actually this implementation always uses a local copy but this may change in future */ - try - { - if (usecopy) - { - LOCK.readLock().lock(); - } - - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - int blockStart = start; - int blockEnd = end; - int hiddenSoFar = 0; - int visSoFar = 0; - - // iterate until a region begins within (start,end] - int i = 0; - while ((i < hiddenColumns.size()) - && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar)) - { - hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0] - + 1; - i++; - } - - blockStart += hiddenSoFar; // convert start to absolute position - blockEnd += hiddenSoFar; // convert end to absolute position - - // iterate from start to end, adding each visible region. Positions - // are - // absolute, and all hidden regions which overlap [start,end] are - // used. - while (i < hiddenColumns.size() - && (hiddenColumns.get(i)[0] <= blockEnd)) - { - int[] region = hiddenColumns.get(i); - - // end position of this visible region is either just before the - // start of the next hidden region, or the absolute position of - // 'end', whichever is lowest - blockEnd = Math.min(blockEnd, region[0] - 1); - - vcontigs.add(new int[] { blockStart, blockEnd }); - - visSoFar += blockEnd - blockStart + 1; - - // next visible region starts after this hidden region - blockStart = region[1] + 1; - - hiddenSoFar += region[1] - region[0] + 1; - - // reset blockEnd to absolute position of 'end', assuming we've now - // passed all hidden regions before end - blockEnd = end + hiddenSoFar; - - i++; - } - if (visSoFar < end - start) - { - // the number of visible columns we've accounted for is less than - // the number specified by end-start; work out the end position of - // the last visible region - blockEnd = blockStart + end - start - visSoFar; - vcontigs.add(new int[] { blockStart, blockEnd }); - - // if the last visible region ends at the next hidden region, set - // endsAtHidden=true - if (i < hiddenColumns.size() - && hiddenColumns.get(i)[0] - 1 == blockEnd) - { - endsAtHidden = true; - } - } - } - else - { - // there are no hidden columns, return a single visible contig - vcontigs.add(new int[] { start, end }); - endsAtHidden = false; - } - } finally - { - if (usecopy) - { - LOCK.readLock().unlock(); - } - } - } - - @Override - public boolean hasNext() + int adjstart = start; + int adjend = end; + if (useVisibleCoords) { - return (currentPosition < vcontigs.size()); + adjstart = visibleToAbsoluteColumn(start); + adjend = visibleToAbsoluteColumn(end); } - @Override - public int[] next() + try { - int[] result = vcontigs.get(currentPosition); - currentPosition++; - return result; - } - - public boolean endsAtHidden() + LOCK.readLock().lock(); + return new VisibleContigsIterator(adjstart, adjend, hiddenColumns); + } finally { - return endsAtHidden; + LOCK.readLock().unlock(); } } }