X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=b903826c83071cb44cfb966b2dc037fc8ef041ae;hb=e48cf231d302b758416cc9a3b38939853cf6b3bf;hp=09f2ec5077a578ee509b72ef46bf9232e59acff4;hpb=02bdd4e842db62a0c9c3a36bbddd2b4f7249df92;p=jalview.git diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java index 09f2ec5..b903826 100644 --- a/src/jalview/datamodel/HiddenColumns.java +++ b/src/jalview/datamodel/HiddenColumns.java @@ -20,16 +20,48 @@ */ package jalview.datamodel; -import jalview.util.Comparison; - import java.util.ArrayList; +import java.util.Arrays; import java.util.BitSet; import java.util.Iterator; import java.util.List; -import java.util.NoSuchElementException; -import java.util.Vector; 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. Note that column + * 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 { private static final int HASH_MULTIPLIER = 31; @@ -37,10 +69,21 @@ 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 */ - private ArrayList hiddenColumns; + private List hiddenColumns = new ArrayList<>(); /** * Constructor @@ -53,23 +96,11 @@ public class HiddenColumns * Copy constructor * * @param copy + * the HiddenColumns object to copy from */ public HiddenColumns(HiddenColumns copy) { - try - { - LOCK.writeLock().lock(); - if (copy != null) - { - if (copy.hiddenColumns != null) - { - hiddenColumns = copy.copyHiddenRegionsToArrayList(0); - } - } - } finally - { - LOCK.writeLock().unlock(); - } + this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0); } /** @@ -94,7 +125,7 @@ public class HiddenColumns LOCK.writeLock().lock(); if (copy != null) { - hiddenColumns = new ArrayList<>(); + numColumns = 0; Iterator it = copy.getBoundedIterator(start, end); while (it.hasNext()) { @@ -106,6 +137,248 @@ public class HiddenColumns hiddenColumns.add( new int[] { region[0] - offset, region[1] - offset }); + numColumns += region[1] - region[0] + 1; + } + } + cursor.resetCursor(hiddenColumns); + } + } finally + { + LOCK.writeLock().unlock(); + } + } + + /** + * 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) + */ + public void hideColumns(int start, int end) + { + try + { + LOCK.writeLock().lock(); + + int previndex = 0; + int prevHiddenCount = 0; + int regionindex = 0; + if (!hiddenColumns.isEmpty()) + { + // set up cursor reset values + HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start); + regionindex = cursorPos.getRegionIndex(); + + if (regionindex > 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); + } + } + + /* + * 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; + if (regionindex > 0) + { + added = insertRangeAtRegion(regionindex - 1, start, end); + } + if (!added && regionindex < hiddenColumns.size()) + { + insertRangeAtRegion(regionindex, start, end); + } + } + + // 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.writeLock().unlock(); + } + } + + /** + * Insert [start, range] at the region at index i in hiddenColumns, if + * feasible + * + * @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 + */ + private boolean insertRangeAtRegion(int i, int start, int end) + { + boolean added = false; + + 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); + + /* + * 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); + + // 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; + } + return added; + } + + /** + * hide a list of ranges + * + * @param ranges + */ + public void hideList(List ranges) + { + try + { + LOCK.writeLock().lock(); + for (int[] r : ranges) + { + hideColumns(r[0], r[1]); + } + cursor.resetCursor(hiddenColumns); + numColumns = 0; + } finally + { + LOCK.writeLock().unlock(); + } + } + + /** + * Unhides, and adds to the selection list, all hidden columns + */ + public void revealAllHiddenColumns(ColumnSelection sel) + { + try + { + LOCK.writeLock().lock(); + + for (int[] region : hiddenColumns) + { + for (int j = region[0]; j < region[1] + 1; j++) + { + sel.addElement(j); + } + } + hiddenColumns.clear(); + cursor.resetCursor(hiddenColumns); + numColumns = 0; + + } finally + { + LOCK.writeLock().unlock(); + } + } + + /** + * Reveals, and marks as selected, the hidden column range with the given + * start column + * + * @param start + * the start column to look for + * @param sel + * the column selection to add the hidden column range to + */ + public void revealHiddenColumns(int start, ColumnSelection sel) + { + try + { + LOCK.writeLock().lock(); + + if (!hiddenColumns.isEmpty()) + { + int regionIndex = cursor.findRegionForColumn(start) + .getRegionIndex(); + + if (regionIndex != -1 && regionIndex != hiddenColumns.size()) + { + // regionIndex is the region which either contains start + // or lies to the right of start + int[] region = hiddenColumns.get(regionIndex); + if (start == region[0]) + { + for (int j = region[0]; j < region[1] + 1; j++) + { + sel.addElement(j); + } + int colsToRemove = region[1] - region[0] + 1; + hiddenColumns.remove(regionIndex); + + if (hiddenColumns.isEmpty()) + { + hiddenColumns.clear(); + numColumns = 0; + } + else + { + numColumns -= colsToRemove; + } + cursor.updateForDeletedRegion(hiddenColumns); } } } @@ -131,16 +404,22 @@ public class HiddenColumns { LOCK.readLock().lock(); StringBuilder regionBuilder = new StringBuilder(); - if (hiddenColumns != null) + + boolean first = true; + for (int[] range : hiddenColumns) { - for (int[] range : hiddenColumns) + if (!first) + { + regionBuilder.append(delimiter); + } + else { - regionBuilder.append(delimiter).append(range[0]).append(between) - .append(range[1]); + first = false; } + regionBuilder.append(range[0]).append(between).append(range[1]); - regionBuilder.deleteCharAt(0); } + return regionBuilder.toString(); } finally { @@ -158,15 +437,21 @@ public class HiddenColumns try { LOCK.readLock().lock(); - int size = 0; - if (hasHiddenColumns()) + + if (numColumns == 0) { + // numColumns is out of date, so recalculate + int size = 0; + for (int[] range : hiddenColumns) { size += range[1] - range[0] + 1; } + + numColumns = size; } - return size; + + return numColumns; } finally { LOCK.readLock().unlock(); @@ -183,12 +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(); @@ -211,25 +491,23 @@ public class HiddenColumns /* * 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()) + + if (that.hiddenColumns.size() != this.hiddenColumns.size()) { return false; } - int i = 0; - for (int[] thisRange : hiddenColumns) + + Iterator it = this.iterator(); + Iterator thatit = that.iterator(); + while (it.hasNext()) { - int[] thatRange = that.hiddenColumns.get(i++); - if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) + if (!(Arrays.equals(it.next(), thatit.next()))) { return false; } } return true; + } finally { LOCK.readLock().unlock(); @@ -243,23 +521,18 @@ public class HiddenColumns * int column index in alignment view (count from zero) * @return alignment column index for column */ - public int adjustForHiddenColumns(int column) + public int visibleToAbsoluteColumn(int column) { try { LOCK.readLock().lock(); int result = column; - if (hiddenColumns != null) + + if (!hiddenColumns.isEmpty()) { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.get(i); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } - } + result += cursor.findRegionForVisColumn(column).getHiddenSoFar(); } + return result; } finally { @@ -270,54 +543,52 @@ public class HiddenColumns /** * 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. + * index of the next visible column on the left will be returned (or 0 if + * there is no visible column on the left) * * @param hiddenColumn * the column index in the full alignment including hidden columns * @return the position of the column in the visible alignment */ - public int findColumnPosition(int hiddenColumn) + public int absoluteToVisibleColumn(int hiddenColumn) { try { LOCK.readLock().lock(); int result = hiddenColumn; - if (hiddenColumns != null) - { - int index = 0; - int[] region; - do - { - region = hiddenColumns.get(index++); - if (hiddenColumn > region[1]) - { - result -= region[1] + 1 - region[0]; - } - } while ((hiddenColumn > region[1]) - && (index < hiddenColumns.size())); - if (hiddenColumn >= region[0] && hiddenColumn <= region[1]) + if (!hiddenColumns.isEmpty()) + { + 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()) { - // 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 = hiddenColumns.get(index); + if (hiddenColumn >= region[0] && hiddenColumn <= region[1]) { - return result - (hiddenColumn - region[0] + 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 @@ -328,135 +599,106 @@ 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 = adjustForHiddenColumns(findColumnPosition(startColumn)); - - // get index of hidden region to left of start - int index = getHiddenIndexLeft(start); - if (index == -1) - { - // no hidden regions to left of startColumn - return start - distance; - } - - // walk backwards through the alignment subtracting the counts of visible - // columns from distance - int[] region; - int gap = 0; - int nextstart = start; - - while ((index > -1) && (distance - gap > 0)) - { - // subtract the gap to right of region from distance - distance -= gap; - start = nextstart; + int start = absoluteToVisibleColumn(startColumn); + return visibleToAbsoluteColumn(start + visibleDistance); - // calculate the next gap - region = hiddenColumns.get(index); - gap = start - region[1]; - - // set start to just to left of current region - nextstart = region[0] - 1; - index--; - } - - if (distance - gap > 0) - { - // fell out of loop because there are no more hidden regions - distance -= gap; - return nextstart - distance; - } - return start - distance; } finally { LOCK.readLock().unlock(); } - } - - /** * This method returns the rightmost limit of a region of an alignment with * hidden columns. In otherwords, the next hidden column. * - * @param index - * int + * @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 */ - public int getHiddenBoundaryRight(int alPos) + public int getNextHiddenBoundary(boolean left, int alPos) { try { LOCK.readLock().lock(); - if (hiddenColumns != null) + if (!hiddenColumns.isEmpty()) { - int index = 0; - do + int index = cursor.findRegionForColumn(alPos).getRegionIndex(); + + 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]) { return region[0]; } - - index++; - } while (index < hiddenColumns.size()); + 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]; + } + } } - return alPos; } finally { LOCK.readLock().unlock(); } - } /** - * This method returns the leftmost limit of a region of an alignment with - * hidden columns. In otherwords, the previous hidden column. + * Answers if a column in the alignment is visible * - * @param index - * int + * @param column + * absolute position of column in the alignment + * @return true if column is visible */ - public int getHiddenBoundaryLeft(int alPos) + public boolean isVisible(int column) { try { LOCK.readLock().lock(); - if (hiddenColumns != null) + int regionindex = cursor.findRegionForColumn(column).getRegionIndex(); + if (regionindex > -1 && regionindex < hiddenColumns.size()) { - int index = hiddenColumns.size() - 1; - do + int[] region = hiddenColumns.get(regionindex); + // already know that column <= region[1] as cursor returns containing + // region or region to right + if (column >= region[0]) { - int[] region = hiddenColumns.get(index); - if (alPos > region[1]) - { - return region[1]; - } - - index--; - } while (index > -1); + return false; + } } + return true; - return alPos; } finally { LOCK.readLock().unlock(); @@ -464,222 +706,127 @@ public class HiddenColumns } /** - * This method returns the index of the hidden region to the left of a column - * position. If the column is in a hidden region it returns the index of the - * region to the left. If there is no hidden region to the left it returns -1. + * 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 pos - * int + * @param seq + * sequence to find position for + * @return visible start position */ - private int getHiddenIndexLeft(int pos) + public int locateVisibleStartOfSequence(SequenceI seq) { try { - LOCK.readLock().lock(); - if (hiddenColumns != null) - { - int index = hiddenColumns.size() - 1; - do - { - int[] region = hiddenColumns.get(index); - if (pos > region[1]) - { - return index; - } + int start = 0; - index--; - } while (index > -1); + if (hiddenColumns.isEmpty()) + { + return seq.findIndex(seq.getStart()) - 1; } - return -1; - } finally - { - LOCK.readLock().unlock(); - } - - } - - /** - * Adds the specified column range to the hidden columns - * - * @param start - * @param end - */ - 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; - } - - if (hiddenColumns == null) - { - hiddenColumns = new ArrayList<>(); - } + // 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; - /* - * traverse existing hidden ranges and insert / amend / append as - * appropriate - */ - for (int i = 0; i < hiddenColumns.size(); i++) + // step through the non-gapped positions of the sequence + for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++) { - int[] region = hiddenColumns.get(i); + // get alignment position of this residue in the sequence + int p = seq.findIndex(i) - 1; - if (end < region[0] - 1) + // update hidden region start/end + while (hideEnd < p && regions.hasNext()) { - /* - * insert discontiguous preceding range - */ - hiddenColumns.add(i, new int[] { start, end }); - return; + int[] region = regions.next(); + visPrev = visNext; + visNext += region[0] - visPrev; + hideStart = region[0]; + hideEnd = region[1]; } - - if (end <= region[1]) + if (hideEnd < p) { - /* - * new range overlaps existing, or is contiguous preceding it - adjust - * start column - */ - region[0] = Math.min(region[0], start); - return; + hideStart = seq.getLength(); } - - if (start <= region[1] + 1) + // update visible boundary for sequence + if (p < hideStart) { - /* - * 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); - - /* - * 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); - } - return; + start = p; + foundStart = true; } } - /* - * remaining case is that the new range follows everything else - */ - hiddenColumns.add(new int[] { start, end }); - } finally - { - if (!wasAlreadyLocked) + if (foundStart) { - LOCK.writeLock().unlock(); + return absoluteToVisibleColumn(start); } + // otherwise, sequence was completely hidden + return visPrev; + } finally + { + LOCK.readLock().unlock(); } } - public boolean isVisible(int column) + + /** + * + * @return true if there are columns hidden + */ + public boolean hasHiddenColumns() { try { LOCK.readLock().lock(); - if (hiddenColumns != null) - { - for (int[] region : hiddenColumns) - { - if (column >= region[0] && column <= region[1]) - { - return false; - } - } - } - - return true; + // 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.isEmpty()); } finally { LOCK.readLock().unlock(); } } - private ArrayList copyHiddenRegionsToArrayList(int startIndex) + /** + * + * @return true if there is more than one hidden column region + */ + public boolean hasMultiHiddenColumnRegions() { - int size = 0; - if (hiddenColumns != null) + try { - size = hiddenColumns.size(); - } - ArrayList copy = new ArrayList<>(size); - - for (int i = startIndex, j = size; i < j; i++) + LOCK.readLock().lock(); + return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1; + } finally { - int[] rh; - int[] cp; - rh = hiddenColumns.get(i); - if (rh != null) - { - cp = new int[rh.length]; - System.arraycopy(rh, 0, cp, 0, rh.length); - copy.add(cp); - } + LOCK.readLock().unlock(); } - - return copy; } - public String[] getVisibleSequenceStrings(int start, int end, - SequenceI[] seqs) + + /** + * Returns a hashCode built from hidden column ranges + */ + @Override + public int hashCode() { try { LOCK.readLock().lock(); - int iSize = seqs.length; - String[] selections = new String[iSize]; - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - for (int i = 0; i < iSize; i++) - { - StringBuffer visibleSeq = new StringBuffer(); - - Iterator blocks = new VisibleBlocksIterator(start, - end, false); - while (blocks.hasNext()) - { - int[] block = blocks.next(); - visibleSeq.append(seqs[i].getSequence(block[0], block[1])); - } + int hashCode = 1; - selections[i] = visibleSeq.toString(); - } - } - else + for (int[] hidden : hiddenColumns) { - for (int i = 0; i < iSize; i++) - { - selections[i] = seqs[i].getSequenceAsString(start, end); - } + hashCode = HASH_MULTIPLIER * hashCode + hidden[0]; + hashCode = HASH_MULTIPLIER * hashCode + hidden[1]; } - - return selections; + return hashCode; } finally { LOCK.readLock().unlock(); @@ -687,194 +834,231 @@ public class HiddenColumns } /** - * Locate the first and last position visible for this sequence. if seq isn't - * visible then return the position of the left and right of the hidden - * boundary region, and the corresponding alignment column indices for the - * extent of the sequence + * Hide columns corresponding to the marked bits * - * @param seq - * @return int[] { visible start, first seqpos, last seqpos } + * @param inserts + * - columns mapped to bits starting from zero */ - public int locateVisibleBoundsOfSequence(SequenceI seq) + public void hideColumns(BitSet inserts) { try { - LOCK.readLock().lock(); - int start = 0; - - if (hiddenColumns == null || hiddenColumns.size() == 0) + LOCK.writeLock().lock(); + for (int firstSet = inserts + .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts + .nextSetBit(lastSet)) { - return seq.findIndex(seq.getStart()) - 1; + lastSet = inserts.nextClearBit(firstSet); + hideColumns(firstSet, lastSet - 1); } + cursor.resetCursor(hiddenColumns); + numColumns = 0; + } finally + { + LOCK.writeLock().unlock(); + } + } - // Simply walk along the sequence whilst watching for hidden column - // boundaries - Iterator regions = iterator(); - int spos = seq.getStart(); - int hideStart = seq.getLength(); - int hideEnd = -1; - int visPrev = 0; - int visNext = 0; + /** + * Hide columns corresponding to the marked bits, within the range + * [start,end]. Entries in tohide which are outside [start,end] are ignored. + * + * @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); - boolean foundStart = false; - for (int p = 0; spos <= seq.getEnd() && p < seq.getLength(); p++) + // 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()) { - if (!Comparison.isGap(seq.getCharAt(p))) + HiddenCursorPosition pos = cursor.findRegionForColumn(start); + int index = pos.getRegionIndex(); + int startindex = index; // first index in hiddenColumns to remove + + if (index != -1 && index != hiddenColumns.size()) { - // 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) + // 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) { - hideStart = seq.getLength(); + // region contains start, truncate so that it ends just before start + region[1] = start - 1; + startindex++; } - // update visible boundary for sequence - if ((p < hideStart) && (!foundStart)) + } + + 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) { - start = p; - foundStart = true; + // region contains end, truncate so that it starts just after end + region[0] = end + 1; } - // look for next sequence position - spos++; } + + hiddenColumns.subList(startindex, endindex + 1).clear(); + cursor.resetCursor(hiddenColumns); + numColumns = 0; } - if (foundStart) - { - return findColumnPosition(start); - } - // otherwise, sequence was completely hidden - return visPrev; } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). * - * @param alignmentAnnotation + * @param updates + * BitSet where hidden columns will be marked */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) + protected void andNot(BitSet updates) { - makeVisibleAnnotation(0, alignmentAnnotation.annotations.length, - alignmentAnnotation); + try + { + LOCK.writeLock().lock(); + + BitSet hiddenBitSet = new BitSet(); + for (int[] range : hiddenColumns) + { + hiddenBitSet.set(range[0], range[1] + 1); + } + hiddenBitSet.andNot(updates); + hiddenColumns.clear(); + hideColumns(hiddenBitSet); + } finally + { + LOCK.writeLock().unlock(); + } } /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). + * Calculate the visible start and end index of an alignment. * - * @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 width + * full alignment width + * @return integer array where: int[0] = startIndex, and int[1] = endIndex */ - public void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) + public int[] getVisibleStartAndEndIndex(int width) { try { LOCK.readLock().lock(); - int startFrom = start; - int endAt = end; + int firstVisible = 0; + int lastVisible = width - 1; - if (alignmentAnnotation.annotations != null) + if (!hiddenColumns.isEmpty()) { - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation); - } - else + // first visible col with index 0, convert to absolute index + firstVisible = visibleToAbsoluteColumn(0); + + // 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) { - alignmentAnnotation.restrict(startFrom, endAt); + // last region is at very end of alignment + // last visible column immediately precedes it + lastVisible = lastregion[0] - 1; } } + return new int[] { firstVisible, lastVisible }; + } finally { LOCK.readLock().unlock(); } } - private void removeHiddenAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) + /** + * 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. If + * res is adjacent to two regions, returns the left region. + */ + public int[] getRegionWithEdgeAtRes(int res) { - // mangle the alignmentAnnotation annotation array - Vector annels = new Vector<>(); - Annotation[] els = null; - - int w = 0; - - Iterator blocks = new VisibleBlocksIterator(start, end, - false); - int copylength; - int annotationLength; - while (blocks.hasNext()) + try { - int[] block = blocks.next(); - - if (blocks.hasNext()) - { - annotationLength = block[1] - block[0]; - // copy just the visible segment of the annotation row - copylength = annotationLength; - } - else + LOCK.readLock().lock(); + int adjres = visibleToAbsoluteColumn(res); + + int[] reveal = null; + + if (!hiddenColumns.isEmpty()) { - annotationLength = block[1] - block[0] + 1; - if (annotationLength + block[0] <= alignmentAnnotation.annotations.length) + // 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) { - // copy just the visible segment of the annotation row - copylength = annotationLength; + reveal = hiddenColumns.get(regionindex); } - else + // check if the region ends just after adjres + else if (regionindex < hiddenColumns.size() + && hiddenColumns.get(regionindex)[0] == adjres + 1) { - // copy to the end of the annotation row - copylength = alignmentAnnotation.annotations.length - block[0]; + reveal = hiddenColumns.get(regionindex); } } - - els = new Annotation[annotationLength]; - annels.addElement(els); - System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0, - copylength); - w += annotationLength; - } - - if (w != 0) - { - alignmentAnnotation.annotations = new Annotation[w]; + return reveal; - w = 0; - for (Annotation[] chnk : annels) - { - System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, - chnk.length); - w += chnk.length; - } + } finally + { + LOCK.readLock().unlock(); } } /** - * - * @return true if there are columns hidden + * Return an iterator over the hidden regions */ - public boolean hasHiddenColumns() + public Iterator iterator() { try { LOCK.readLock().lock(); - return hiddenColumns != null && hiddenColumns.size() > 0; + return new HiddenColsIterator(hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -882,15 +1066,20 @@ public class HiddenColumns } /** + * Return a bounded iterator over the hidden regions * - * @return true if there are more than one set of columns hidden + * @param start + * position to start from (inclusive, absolute column position) + * @param end + * position to end at (inclusive, absolute column position) + * @return */ - public boolean hasManyHiddenColumns() + public Iterator getBoundedIterator(int start, int end) { try { LOCK.readLock().lock(); - return hiddenColumns != null && hiddenColumns.size() > 1; + return new HiddenColsIterator(start, end, hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -898,315 +1087,54 @@ public class HiddenColumns } /** - * mark the columns corresponding to gap characters as hidden in the column - * selection + * Return a bounded iterator over the *visible* start positions of hidden + * regions * - * @param sr + * @param start + * position to start from (inclusive, visible column position) + * @param end + * position to end at (inclusive, visible column position) */ - public void hideInsertionsFor(SequenceI sr) + public Iterator getBoundedStartIterator(int start, int end) { try { - LOCK.writeLock().lock(); - List inserts = sr.getInsertions(); - for (int[] r : inserts) - { - hideColumns(r[0], r[1]); - } + LOCK.readLock().lock(); + + // get absolute position of column in alignment + int absoluteStart = visibleToAbsoluteColumn(start); + + // 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); + + return new BoundedStartRegionIterator(pos, start, end, + hiddenColumns); } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } /** - * Unhides, and adds to the selection list, all hidden columns + * 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 void revealAllHiddenColumns(ColumnSelection sel) - { - try - { - LOCK.writeLock().lock(); - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.get(i); - for (int j = region[0]; j < region[1] + 1; j++) - { - sel.addElement(j); - } - } - } - - hiddenColumns = null; - } finally - { - LOCK.writeLock().unlock(); - } - } - - /** - * Reveals, and marks as selected, the hidden column range with the given - * start column - * - * @param start - */ - public void revealHiddenColumns(int start, ColumnSelection sel) - { - try - { - LOCK.writeLock().lock(); - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.get(i); - if (start == region[0]) - { - for (int j = region[0]; j < region[1] + 1; j++) - { - sel.addElement(j); - } - - hiddenColumns.remove(region); - break; - } - } - if (hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - } finally - { - LOCK.writeLock().unlock(); - } - } - - /** - * Add gaps into the sequences aligned to profileseq under the given - * AlignmentView - * - * @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. - */ - 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 = 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 = iterator(); - ArrayList newhidden = new ArrayList<>(); - - 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++; - } - } - - 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; - } 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)); - } - } - } - } - - /** - * Returns a hashCode built from hidden column ranges - */ - @Override - public int hashCode() - { - try - { - LOCK.readLock().lock(); - int hashCode = 1; - if (hiddenColumns != null) - { - for (int[] hidden : hiddenColumns) - { - hashCode = HASH_MULTIPLIER * hashCode + hidden[0]; - hashCode = HASH_MULTIPLIER * hashCode + hidden[1]; - } - } - return hashCode; - } finally - { - LOCK.readLock().unlock(); - } - } - - /** - * Hide columns corresponding to the marked bits - * - * @param inserts - * - columns map to bits starting from zero - */ - public void hideMarkedBits(BitSet inserts) - { - try - { - LOCK.writeLock().lock(); - for (int firstSet = inserts - .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts - .nextSetBit(lastSet)) - { - lastSet = inserts.nextClearBit(firstSet); - hideColumns(firstSet, lastSet - 1); - } - } finally - { - LOCK.writeLock().unlock(); - } - } - - /** - * - * @param inserts - * BitSet where hidden columns will be marked - */ - public void markHiddenRegions(BitSet inserts) + public Iterator getVisibleColsIterator(int start, int end) { try { LOCK.readLock().lock(); - if (hiddenColumns == null) - { - return; - } - for (int[] range : hiddenColumns) - { - inserts.set(range[0], range[1] + 1); - } + return new VisibleColsIterator(start, end, hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -1214,826 +1142,36 @@ public class HiddenColumns } /** - * Calculate the visible start and end index of an alignment. + * return an iterator over visible segments between the given start and end + * boundaries * - * @param width - * full alignment width - * @return integer array where: int[0] = startIndex, and int[1] = endIndex + * @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 int[] getVisibleStartAndEndIndex(int width) + public VisibleContigsIterator getVisContigsIterator(int start, + int end, + boolean useVisibleCoords) { - 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 == null) - { - return new int[] { startPos, endPos }; - } - - for (int[] hiddenCol : hiddenColumns) - { - lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; - higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; - } - - if (lowestRange[0] == -1 && lowestRange[1] == -1) - { - startPos = alignmentStartEnd[0]; - } - else - { - startPos = lowestRange[1] + 1; - } - - if (higestRange[0] == -1 && higestRange[1] == -1) - { - endPos = alignmentStartEnd[1]; - } - else - { - endPos = higestRange[0] - 1; - } - return new int[] { startPos, endPos }; - } finally + int adjstart = start; + int adjend = end; + if (useVisibleCoords) { - LOCK.readLock().unlock(); + adjstart = visibleToAbsoluteColumn(start); + adjend = visibleToAbsoluteColumn(end); } - } - - /** - * 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 - */ - public int[] getRegionWithEdgeAtRes(int res) - { try { LOCK.readLock().lock(); - int adjres = adjustForHiddenColumns(res); - - int[] reveal = null; - if (hiddenColumns != null) - { - for (int[] region : hiddenColumns) - { - if (adjres + 1 == region[0] || adjres - 1 == region[1]) - { - reveal = region; - break; - } - } - } - return reveal; + return new VisibleContigsIterator(adjstart, adjend, hiddenColumns); } finally { LOCK.readLock().unlock(); } } - - /** - * Return an iterator over the hidden regions - */ - public Iterator iterator() - { - if (hiddenColumns != null) - { - int last = hiddenColumns.get(hiddenColumns.size() - 1)[1]; - return new BoundedHiddenColsIterator(0, last, true); - } - else - { - return new BoundedHiddenColsIterator(0, 0, true); - } - } - - /** - * 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, true); - } - - /** - * 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); - } - - /** - * Return an iterator over visible columns 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, true); - } - - /** - * 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) - */ - public Iterator getVisContigsIterator(int start, int end) - { - return new VisibleContigsIterator(start, end, true); - } - - /** - * 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 - */ - public Iterator getVisibleBlocksIterator(int start, int end, - boolean useVisibleCoords) - { - if (useVisibleCoords) - { - // TODO - // we should really just convert start and end here with - // adjustForHiddenColumns - // and then create a VisibleBlocksIterator - // but without a cursor this will be horribly slow in some situations - // ... so until then... - return new VisibleBlocksVisBoundsIterator(start, end, true); - } - else - { - return new VisibleBlocksIterator(start, end, true); - } - } - - /** - * An iterator which iterates over hidden column regions in a range. - */ - private class BoundedHiddenColsIterator implements Iterator - { - private int start; // start position to iterate from - - private int end; // end position to iterate to - - // current index in hiddenColumns - private int currentPosition = 0; - - // current column in hiddenColumns - private int[] currentRegion; - - // whether to make a local copy of hiddenColumns - private final boolean useCopy; - - // local copy or reference to hiddenColumns - private List localHidden; - - /** - * 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) - */ - BoundedHiddenColsIterator(int lowerBound, int upperBound, - boolean useCopyCols) - { - start = lowerBound; - end = upperBound; - useCopy = useCopyCols; - - try - { - if (useCopy) - { - // assume that if useCopy is false the calling code has locked - // hiddenColumns - 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; - int[] cp; - rh = hiddenColumns.get(i); - if (rh != null) - { - cp = new int[rh.length]; - System.arraycopy(rh, 0, cp, 0, rh.length); - localHidden.add(cp); - } - i++; - } - } - } - finally - { - if (useCopy) - { - LOCK.readLock().unlock(); - } - } - } - - @Override - public boolean hasNext() - { - return (localHidden != null) - && (currentPosition < localHidden.size()); - } - - @Override - public int[] next() - { - currentRegion = localHidden.get(currentPosition); - currentPosition++; - return currentRegion; - } - } - - /** - * An iterator which iterates over visible start positions of hidden column - * regions in a range. - */ - private class BoundedStartRegionIterator implements Iterator - { - // 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()); - - // 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++; - } - - // 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 - { - positions = new ArrayList<>(); - } - } finally - { - if (useCopy) - { - LOCK.readLock().unlock(); - } - } - } - - @Override - public boolean hasNext() - { - return (currentPosition < positions.size()); - } - - /** - * Get next hidden region start position - * - * @return the start position in *visible* coordinates - */ - @Override - public Integer next() - { - int result = positions.get(currentPosition); - currentPosition++; - return result; - } - } - - private class VisibleColsIterator implements Iterator - { - private int last; - - private int current; - - private int next; - - private List localHidden = new ArrayList<>(); - - private int nexthiddenregion; - - VisibleColsIterator(int firstcol, int lastcol, boolean useCopy) - { - last = lastcol; - current = firstcol; - next = firstcol; - nexthiddenregion = 0; - - try - { - if (useCopy) - { - // assume that if useCopy is false the calling code has locked - // hiddenColumns - 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++; - } - } - } finally - { - if (useCopy) - { - LOCK.readLock().unlock(); - } - } - } - - @Override - public boolean hasNext() - { - return next <= last; - } - - @Override - public Integer next() - { - 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() - { - throw new UnsupportedOperationException(); - } - } - - /** - * An iterator which iterates over visible regions in a range. - */ - private class VisibleContigsIterator implements Iterator - { - private List vcontigs = new ArrayList<>(); - - private int currentPosition = 0; - - VisibleContigsIterator(int start, int end, boolean usecopy) - { - 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; - - // exit if we're past the end - if (vstart >= end) - { - break; - } - } - - 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(); - } - } - } - - @Override - public boolean hasNext() - { - return (currentPosition < vcontigs.size()); - } - - @Override - public int[] next() - { - int[] result = vcontigs.get(currentPosition); - currentPosition++; - return result; - } - } - - /** - * An iterator which iterates over visible regions in a range. - */ - private class VisibleBlocksIterator implements Iterator - { - private List vcontigs = new ArrayList<>(); - - private int currentPosition = 0; - - VisibleBlocksIterator(int start, int end, boolean usecopy) - { - try - { - if (usecopy) - { - LOCK.readLock().lock(); - } - - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - int blockStart = start; - int blockEnd = end; - - // 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 used. - while (i < hiddenColumns.size() - && (hiddenColumns.get(i)[0] <= end)) - { - int[] region = hiddenColumns.get(i); - - blockStart = Math.min(blockStart, region[1] + 1); - blockEnd = Math.min(blockEnd, region[0]); - - int[] contig = new int[] { blockStart, blockEnd }; - vcontigs.add(contig); - - blockStart = region[1] + 1; - blockEnd = end; - - i++; - } - - if (end > blockStart) - { - int[] contig = new int[] { blockStart, end }; - vcontigs.add(contig); - } - } - else - { - int[] contig = new int[] { start, end }; - vcontigs.add(contig); - } - } finally - { - if (usecopy) - { - LOCK.readLock().unlock(); - } - } - } - - @Override - public boolean hasNext() - { - return (currentPosition < vcontigs.size()); - } - - @Override - public int[] next() - { - int[] result = vcontigs.get(currentPosition); - currentPosition++; - return result; - } - } - - /** - * 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. - */ - public class VisibleBlocksVisBoundsIterator implements Iterator - { - 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() - { - return (currentPosition < vcontigs.size()); - } - - @Override - public int[] next() - { - int[] result = vcontigs.get(currentPosition); - currentPosition++; - return result; - } - - public boolean endsAtHidden() - { - return endsAtHidden; - } - } - }