X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=9a8669f0b863aa9d8c4c96eb4f048969d22990c1;hb=9e064d395de4746f14106c1c296bc94696a6190e;hp=b86a1a1086b6ddea1d85185332713f4750cedacd;hpb=dab7d55392edfa7307e8d7be5f5dde69c9808f30;p=jalview.git diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java index b86a1a1..9a8669f 100644 --- a/src/jalview/datamodel/HiddenColumns.java +++ b/src/jalview/datamodel/HiddenColumns.java @@ -21,24 +21,72 @@ package jalview.datamodel; import java.util.ArrayList; +import java.util.Arrays; import java.util.BitSet; import java.util.Iterator; import java.util.List; 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; + private static final int NUMCOLUMNS_RESET = -1; // value of numColumns if it + // needs to be recalculated + 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 @@ -51,29 +99,11 @@ 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 = new ArrayList<>(); - Iterator it = copy.iterator(); - while (it.hasNext()) - { - hiddenColumns.add(it.next()); - } - cursor.resetCursor(hiddenColumns); - } - } - } finally - { - LOCK.writeLock().unlock(); - } + this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0); } /** @@ -98,7 +128,7 @@ public class HiddenColumns LOCK.writeLock().lock(); if (copy != null) { - hiddenColumns = new ArrayList<>(); + numColumns = 0; Iterator it = copy.getBoundedIterator(start, end); while (it.hasNext()) { @@ -110,9 +140,10 @@ public class HiddenColumns hiddenColumns.add( new int[] { region[0] - offset, region[1] - offset }); + numColumns += region[1] - region[0] + 1; } } - cursor.resetCursor(hiddenColumns); + cursor = new HiddenColumnsCursor(hiddenColumns); } } finally { @@ -121,348 +152,6 @@ public class HiddenColumns } /** - * Output regions data as a string. String is in the format: - * reg0[0]reg0[1]reg1[0]reg1[1] ... regn[1] - * - * @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 String regionsToString(String delimiter, String between) - { - try - { - LOCK.readLock().lock(); - 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(); - } - } - - /** - * Find the number of hidden columns - * - * @return number of hidden columns - */ - public int getSize() - { - try - { - LOCK.readLock().lock(); - int size = 0; - if (hiddenColumns != null) - { - Iterator it = hiddenColumns.iterator(); - while (it.hasNext()) - { - int[] range = it.next(); - size += range[1] - range[0] + 1; - } - } - return size; - } finally - { - LOCK.readLock().unlock(); - } - } - - /** - * Get the number of distinct hidden regions - * - * @return number of regions - */ - public int getNumberOfRegions() - { - try - { - LOCK.readLock().lock(); - int num = 0; - if (hasHiddenColumns()) - { - num = hiddenColumns.size(); - } - return num; - } finally - { - LOCK.readLock().unlock(); - } - } - - @Override - public boolean equals(Object obj) - { - try - { - 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[] thisRange = it.next(); - int[] thatRange = thatit.next(); - if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) - { - return false; - } - } - return true; - } finally - { - LOCK.readLock().unlock(); - } - } - - /** - * Return absolute column index for a visible column index - * - * @param column - * int column index in alignment view (count from zero) - * @return alignment column index for column - */ - public int adjustForHiddenColumns(int column) - { - try - { - LOCK.readLock().lock(); - int result = column; - - if (hiddenColumns != null) - { - result += cursor.getHiddenOffset(column); - - - /*Iterator it = hiddenColumns.iterator(); - while (it.hasNext()) - { - int[] region = it.next(); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } - }*/ - } - - return result; - } finally - { - LOCK.readLock().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 - */ - public int findColumnPosition(int hiddenColumn) - { - try - { - LOCK.readLock().lock(); - int result = hiddenColumn; - int[] region = null; - if (hiddenColumns != null) - { - Iterator it = new RegionsIterator(0, - hiddenColumn, hiddenColumns, cursor); - 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 - { - return result - (hiddenColumn - region[0] + 1); - } - } - } - 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 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 - */ - public int subtractVisibleColumns(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)); - - Iterator it = new ReverseRegionsIterator(0, start, - hiddenColumns); - - while (it.hasNext() && (distance > 0)) - { - int[] region = it.next(); - - if (start > region[1]) - { - // subtract the gap to right of region from distance - if (start - region[1] <= distance) - { - distance -= start - region[1]; - start = region[0] - 1; - } - else - { - start = start - distance; - distance = 0; - } - } - } - - return start - distance; - - } 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 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 = hiddenColumns.iterator(); - while (it.hasNext()) - { - int[] region = it.next(); - if (alPos < region[0]) - { - 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. - * - * @param alPos - * the (visible) alignmentPosition to find the previous hidden column - * for - */ - public int getHiddenBoundaryLeft(int alPos) - { - try - { - LOCK.readLock().lock(); - - Iterator it = new ReverseRegionsIterator(0, alPos, - hiddenColumns); - while (it.hasNext()) - { - int[] region = it.next(); - if (alPos > region[1]) - { - return region[1]; - } - } - - return alPos; - } finally - { - LOCK.readLock().unlock(); - } - } - - /** * Adds the specified column range to the hidden columns collection * * @param start @@ -472,23 +161,27 @@ public class HiddenColumns */ public void hideColumns(int start, int end) { - boolean wasAlreadyLocked = false; try { - // check if the write lock was already locked by this thread, - // as this method can be called internally in loops within HiddenColumns - if (!LOCK.isWriteLockedByCurrentThread()) - { - LOCK.writeLock().lock(); - } - else - { - wasAlreadyLocked = true; - } + LOCK.writeLock().lock(); - if (hiddenColumns == null) + int previndex = 0; + int prevHiddenCount = 0; + int regionindex = 0; + if (!hiddenColumns.isEmpty()) { - hiddenColumns = new ArrayList<>(); + // 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); + } } /* @@ -506,21 +199,27 @@ public class HiddenColumns * appropriate */ boolean added = false; - for (int i = 0; !added && i < hiddenColumns.size(); i++) + if (regionindex > 0) { - added = insertRangeAtRegion(i, start, end); - } // for - } - if (!wasAlreadyLocked) - { - cursor.resetCursor(hiddenColumns); + 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 = new HiddenColumnsCursor(hiddenColumns, previndex, + prevHiddenCount); + + // reset the number of columns so they will be recounted + resetNumColumns(); + } finally { - if (!wasAlreadyLocked) - { - LOCK.writeLock().unlock(); - } + LOCK.writeLock().unlock(); } } @@ -582,7 +281,10 @@ public class HiddenColumns break; } region[1] = Math.max(nextRegion[1], end); - hiddenColumns.subList(i + 1, i + 2).clear(); + + // in theory hiddenColumns.subList(i + 1, i + 2).clear() is faster than + // hiddenColumns.remove(i+1) but benchmarking results a bit ambivalent + hiddenColumns.remove(i + 1); } added = true; } @@ -590,91 +292,138 @@ public class HiddenColumns } /** - * Answers if a column in the alignment is visible + * hide a list of ranges * - * @param column - * absolute position of column in the alignment - * @return true if column is visible + * @param ranges */ - public boolean isVisible(int column) + public void hideList(List ranges) { try { - LOCK.readLock().lock(); + LOCK.writeLock().lock(); + for (int[] r : ranges) + { + hideColumns(r[0], r[1]); + } + cursor = new HiddenColumnsCursor(hiddenColumns); + resetNumColumns(); + } finally + { + LOCK.writeLock().unlock(); + } + } - Iterator it = new RegionsIterator(column, column, - hiddenColumns, cursor); - while (it.hasNext()) + /** + * Unhides, and adds to the selection list, all hidden columns + */ + public void revealAllHiddenColumns(ColumnSelection sel) + { + try + { + LOCK.writeLock().lock(); + + for (int[] region : hiddenColumns) { - int[] region = it.next(); - if (column >= region[0] && column <= region[1]) + for (int j = region[0]; j < region[1] + 1; j++) { - return false; + sel.addElement(j); } } + hiddenColumns.clear(); + cursor = new HiddenColumnsCursor(hiddenColumns); + resetNumColumns(); - return true; } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } /** - * Get the visible sections of a set of sequences + * Reveals, and marks as selected, the hidden column range with the given + * start column * * @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 + * the start column to look for + * @param sel + * the column selection to add the hidden column range to */ - public String[] getVisibleSequenceStrings(int start, int end, - SequenceI[] seqs) + public void revealHiddenColumns(int start, ColumnSelection sel) { 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(); + LOCK.writeLock().lock(); - Iterator blocks = new VisibleContigsIterator(start, - end + 1, hiddenColumns); + if (!hiddenColumns.isEmpty()) + { + int regionIndex = cursor.findRegionForColumn(start) + .getRegionIndex(); - while (blocks.hasNext()) + 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]) { - int[] block = blocks.next(); - if (blocks.hasNext()) + for (int j = region[0]; j < region[1] + 1; j++) { - visibleSeq - .append(seqs[i].getSequence(block[0], block[1] + 1)); + sel.addElement(j); + } + int colsToRemove = region[1] - region[0] + 1; + hiddenColumns.remove(regionIndex); + + if (hiddenColumns.isEmpty()) + { + resetNumColumns(); } else { - visibleSeq - .append(seqs[i].getSequence(block[0], block[1])); + numColumns -= colsToRemove; } + cursor.updateForDeletedRegion(hiddenColumns); } - - selections[i] = visibleSeq.toString(); } } - else + } finally + { + LOCK.writeLock().unlock(); + } + } + + /** + * Output regions data as a string. String is in the format: + * reg0[0]reg0[1]reg1[0]reg1[1] ... regn[1] + * + * @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 String regionsToString(String delimiter, String between) + { + try + { + LOCK.readLock().lock(); + StringBuilder regionBuilder = new StringBuilder(); + + boolean first = true; + for (int[] range : hiddenColumns) { - for (int i = 0; i < iSize; i++) + if (!first) + { + regionBuilder.append(delimiter); + } + else { - selections[i] = seqs[i].getSequenceAsString(start, end); + first = false; } + regionBuilder.append(range[0]).append(between).append(range[1]); + } - return selections; + return regionBuilder.toString(); } finally { LOCK.readLock().unlock(); @@ -682,67 +431,30 @@ public class HiddenColumns } /** - * 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. + * Find the number of hidden columns * - * @param seq - * sequence to find position for - * @return visible start position + * @return number of hidden columns */ - public int locateVisibleStartOfSequence(SequenceI seq) + public int getSize() { try { LOCK.readLock().lock(); - int start = 0; - if (hiddenColumns == null || hiddenColumns.size() == 0) + if (numColumns == NUMCOLUMNS_RESET) { - return seq.findIndex(seq.getStart()) - 1; - } + // numColumns is out of date, so recalculate + int size = 0; - // Simply walk along the sequence whilst watching for hidden column - // boundaries - Iterator regions = hiddenColumns.iterator(); - int hideStart = seq.getLength(); - int hideEnd = -1; - int visPrev = 0; - int visNext = 0; - boolean foundStart = false; - - // step through the non-gapped positions of the sequence - for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++) - { - // get alignment position of this residue in the sequence - int p = seq.findIndex(i) - 1; - - // update hidden region start/end - while (hideEnd < p && regions.hasNext()) - { - int[] region = regions.next(); - visPrev = visNext; - visNext += region[0] - visPrev; - hideStart = region[0]; - hideEnd = region[1]; - } - if (hideEnd < p) + for (int[] range : hiddenColumns) { - hideStart = seq.getLength(); - } - // update visible boundary for sequence - if (p < hideStart) - { - start = p; - foundStart = true; + size += range[1] - range[0] + 1; } - } - if (foundStart) - { - return findColumnPosition(start); + numColumns = size; } - // otherwise, sequence was completely hidden - return visPrev; + + return numColumns; } finally { LOCK.readLock().unlock(); @@ -750,124 +462,149 @@ public class HiddenColumns } /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param alignmentAnnotation + * Reset numColumns so that it gets recalculated. Currently the code does not + * recalculate numColumns on hide/reveal as it requires a full sweep of the + * hidden columns collection / smarter updating. Placeholder here if later on + * a recalculation is added. */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) + private void resetNumColumns() { - makeVisibleAnnotation(0, alignmentAnnotation.annotations.length, - alignmentAnnotation); + numColumns = NUMCOLUMNS_RESET; } /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). + * Get the number of distinct hidden regions * - * @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 + * @return number of regions */ - public void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) + public int getNumberOfRegions() { 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); - } - } + return hiddenColumns.size(); } finally { LOCK.readLock().unlock(); } } - private void removeHiddenAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) + @Override + public boolean equals(Object obj) { - // mangle the alignmentAnnotation annotation array - ArrayList annels = new ArrayList<>(); - Annotation[] els = null; + try + { + LOCK.readLock().lock(); - int w = 0; - - Iterator blocks = new VisibleContigsIterator(start, end + 1, - hiddenColumns); + if (!(obj instanceof HiddenColumns)) + { + return false; + } + HiddenColumns that = (HiddenColumns) obj; - int copylength; - int annotationLength; - while (blocks.hasNext()) - { - int[] block = blocks.next(); - annotationLength = block[1] - block[0] + 1; - - if (blocks.hasNext()) + /* + * check hidden columns are either both null, or match + */ + + if (that.hiddenColumns.size() != this.hiddenColumns.size()) { - // copy just the visible segment of the annotation row - copylength = annotationLength; + return false; } - else + + Iterator it = this.iterator(); + Iterator thatit = that.iterator(); + while (it.hasNext()) { - if (annotationLength + block[0] <= alignmentAnnotation.annotations.length) - { - // copy just the visible segment of the annotation row - copylength = annotationLength; - } - else + if (!(Arrays.equals(it.next(), thatit.next()))) { - // copy to the end of the annotation row - copylength = alignmentAnnotation.annotations.length - block[0]; + return false; } } - - els = new Annotation[annotationLength]; - annels.add(els); - System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0, - copylength); - w += annotationLength; + return true; + + } finally + { + LOCK.readLock().unlock(); } - - if (w != 0) + } + + /** + * Return absolute column index for a visible column index + * + * @param column + * int column index in alignment view (count from zero) + * @return alignment column index for column + */ + public int visibleToAbsoluteColumn(int column) + { + try { - alignmentAnnotation.annotations = new Annotation[w]; + LOCK.readLock().lock(); + int result = column; - w = 0; - for (Annotation[] chnk : annels) + if (!hiddenColumns.isEmpty()) { - System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, - chnk.length); - w += chnk.length; + result += cursor.findRegionForVisColumn(column).getHiddenSoFar(); } + + return result; + } finally + { + LOCK.readLock().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 + * index of the next visible column on the left will be returned (or 0 if + * there is no visible column on the left) * - * @return true if there are columns hidden + * @param hiddenColumn + * the column index in the full alignment including hidden columns + * @return the position of the column in the visible alignment */ - public boolean hasHiddenColumns() + public int absoluteToVisibleColumn(int hiddenColumn) { try { LOCK.readLock().lock(); - return hiddenColumns != null && hiddenColumns.size() > 0; + int result = hiddenColumn; + + 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()) + { + 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(); @@ -875,15 +612,27 @@ public class HiddenColumns } /** + * Find the visible column which is a given visible number of columns to the + * 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. * - * @return true if there are more than one set of columns hidden + * @param visibleDistance + * the number of visible columns to offset by (left offset = negative + * value; right offset = positive value) + * @param startColumn + * the position of the column to start from (absolute position) + * @return the position of the column which is away + * (absolute position) */ - public boolean hasManyHiddenColumns() + public int offsetByVisibleColumns(int visibleDistance, int startColumn) { try { LOCK.readLock().lock(); - return hiddenColumns != null && hiddenColumns.size() > 1; + int start = absoluteToVisibleColumn(startColumn); + return visibleToAbsoluteColumn(start + visibleDistance); + } finally { LOCK.readLock().unlock(); @@ -891,258 +640,121 @@ public class HiddenColumns } /** - * mark the columns corresponding to gap characters as hidden in the column - * selection + * This method returns the rightmost limit of a region of an alignment with + * hidden columns. In otherwords, the next hidden column. * - * @param sr + * @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 void hideInsertionsFor(SequenceI sr) + public int getNextHiddenBoundary(boolean left, int alPos) { try { - LOCK.writeLock().lock(); - List inserts = sr.getInsertions(); - for (int[] r : inserts) + LOCK.readLock().lock(); + if (!hiddenColumns.isEmpty()) { - hideColumns(r[0], r[1]); - } - cursor.resetCursor(hiddenColumns); - } finally - { - LOCK.writeLock().unlock(); - } - } + int index = cursor.findRegionForColumn(alPos).getRegionIndex(); - /** - * Unhides, and adds to the selection list, all hidden columns - */ - public void revealAllHiddenColumns(ColumnSelection sel) - { - try - { - LOCK.writeLock().lock(); - if (hiddenColumns != null) - { - Iterator it = hiddenColumns.iterator(); - while (it.hasNext()) + if (left && index > 0) { - int[] region = it.next(); - for (int j = region[0]; j < region[1] + 1; j++) + 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]; + } + else if ((alPos <= region[1]) + && (index + 1 < hiddenColumns.size())) { - sel.addElement(j); + // alPos is within a hidden region, return the next one + // if there is one + region = hiddenColumns.get(index + 1); + return region[0]; } } - hiddenColumns = null; - cursor.resetCursor(hiddenColumns); } + return alPos; } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().unlock(); } } /** - * Reveals, and marks as selected, the hidden column range with the given - * start column + * Answers if a column in the alignment is visible * - * @param start + * @param column + * absolute position of column in the alignment + * @return true if column is visible */ - public void revealHiddenColumns(int start, ColumnSelection sel) + public boolean isVisible(int column) { try { - LOCK.writeLock().lock(); - Iterator it = new RegionsIterator(start, start, hiddenColumns, - cursor); - while (it.hasNext()) + LOCK.readLock().lock(); + + int regionindex = cursor.findRegionForColumn(column).getRegionIndex(); + if (regionindex > -1 && regionindex < hiddenColumns.size()) { - int[] region = it.next(); - if (start == region[0]) - { - for (int j = region[0]; j < region[1] + 1; j++) - { - sel.addElement(j); - } - it.remove(); - break; - } - else if (start < region[0]) + int[] region = hiddenColumns.get(regionindex); + // already know that column <= region[1] as cursor returns containing + // region or region to right + if (column >= region[0]) { - break; // passed all possible matching regions + return false; } } + return true; - if (hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - cursor.resetCursor(hiddenColumns); } finally { - LOCK.writeLock().unlock(); + LOCK.readLock().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 + * @return true if there are columns hidden */ - private void propagateInsertions(SequenceI profileseq, AlignmentI al, - SequenceI origseq) + public boolean hasHiddenColumns() { 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 = hiddenColumns.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); + LOCK.readLock().lock(); - } - hiddenColumns = newhidden; - cursor.resetCursor(hiddenColumns); + // 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.writeLock().unlock(); + LOCK.readLock().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 + * @return true if there is more than one hidden column region */ - private void padGaps(StringBuffer sb, int pos, SequenceI profileseq, - AlignmentI al) + public boolean hasMultiHiddenColumnRegions() { - // 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) - { - 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)); - } - } + LOCK.readLock().lock(); + return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1; + } finally + { + LOCK.readLock().unlock(); } } + /** * Returns a hashCode built from hidden column ranges */ @@ -1153,10 +765,9 @@ public class HiddenColumns { LOCK.readLock().lock(); int hashCode = 1; - Iterator it = hiddenColumns.iterator(); - while (it.hasNext()) + + for (int[] hidden : hiddenColumns) { - int[] hidden = it.next(); hashCode = HASH_MULTIPLIER * hashCode + hidden[0]; hashCode = HASH_MULTIPLIER * hashCode + hidden[1]; } @@ -1171,9 +782,9 @@ public class HiddenColumns * Hide columns corresponding to the marked bits * * @param inserts - * - columns map to bits starting from zero + * - columns mapped to bits starting from zero */ - public void hideMarkedBits(BitSet inserts) + public void hideColumns(BitSet inserts) { try { @@ -1185,7 +796,8 @@ public class HiddenColumns lastSet = inserts.nextClearBit(firstSet); hideColumns(firstSet, lastSet - 1); } - cursor.resetCursor(hiddenColumns); + cursor = new HiddenColumnsCursor(hiddenColumns); + resetNumColumns(); } finally { LOCK.writeLock().unlock(); @@ -1193,28 +805,112 @@ public class HiddenColumns } /** + * Hide columns corresponding to the marked bits, within the range + * [start,end]. Entries in tohide which are outside [start,end] are ignored. * - * @param inserts - * BitSet where hidden columns will be marked + * @param tohide + * columns mapped to bits starting from zero + * @param start + * start of range to hide columns within + * @param end + * end of range to hide columns within + */ + public void hideColumns(BitSet tohide, int start, int end) + { + clearHiddenColumnsInRange(start, end); + + // make sure only bits between start and end are set + if (!tohide.isEmpty()) + { + tohide.clear(0, start); + tohide.clear(Math.min(end + 1, tohide.length() + 1), + tohide.length() + 1); + } + + hideColumns(tohide); + } + + /** + * Make all columns in the range [start,end] visible + * + * @param start + * start of range to show columns + * @param end + * end of range to show columns */ - public void markHiddenRegions(BitSet inserts) + private void clearHiddenColumnsInRange(int start, int end) { try { - LOCK.readLock().lock(); - if (hiddenColumns == null) + LOCK.writeLock().lock(); + + if (!hiddenColumns.isEmpty()) { - return; + HiddenCursorPosition pos = cursor.findRegionForColumn(start); + int index = pos.getRegionIndex(); + int startindex = index; // first index in hiddenColumns to remove + + if (index != -1 && index != hiddenColumns.size()) + { + // regionIndex is the region which either contains start + // or lies to the right of start + int[] region = hiddenColumns.get(index); + if (region[0] < start && region[1] >= start) + { + // region contains start, truncate so that it ends just before start + region[1] = start - 1; + startindex++; + } + } + + pos = cursor.findRegionForColumn(end); + index = pos.getRegionIndex(); + int endindex = index - 1; // last index in hiddenColumns to remove + + if (index != -1 && index != hiddenColumns.size()) + { + // regionIndex is the region which either contains end + // or lies to the right of end + int[] region = hiddenColumns.get(index); + if (region[0] <= end && region[1] > end) + { + // region contains end, truncate so that it starts just after end + region[0] = end + 1; + } + } + + hiddenColumns.subList(startindex, endindex + 1).clear(); + cursor = new HiddenColumnsCursor(hiddenColumns); + resetNumColumns(); } - Iterator it = hiddenColumns.iterator(); - while (it.hasNext()) + } finally + { + LOCK.writeLock().unlock(); + } + } + + /** + * + * @param updates + * BitSet where hidden columns will be marked + */ + protected void andNot(BitSet updates) + { + try + { + LOCK.writeLock().lock(); + + BitSet hiddenBitSet = new BitSet(); + for (int[] range : hiddenColumns) { - int[] range = it.next(); - inserts.set(range[0], range[1] + 1); + hiddenBitSet.set(range[0], range[1] + 1); } + hiddenBitSet.andNot(updates); + hiddenColumns.clear(); + hideColumns(hiddenBitSet); } finally { - LOCK.readLock().unlock(); + LOCK.writeLock().unlock(); } } @@ -1230,44 +926,27 @@ public class HiddenColumns try { LOCK.readLock().lock(); - int[] alignmentStartEnd = new int[] { 0, width - 1 }; - int startPos = alignmentStartEnd[0]; - int endPos = alignmentStartEnd[1]; - - int[] lowestRange = new int[] { -1, -1 }; - int[] higestRange = new int[] { -1, -1 }; - if (hiddenColumns == null) - { - return new int[] { startPos, endPos }; - } + int firstVisible = 0; + int lastVisible = width - 1; - Iterator it = hiddenColumns.iterator(); - while (it.hasNext()) + if (!hiddenColumns.isEmpty()) { - int[] range = it.next(); - lowestRange = (range[0] <= startPos) ? range : lowestRange; - higestRange = (range[1] >= endPos) ? range : higestRange; - } + // first visible col with index 0, convert to absolute index + firstVisible = visibleToAbsoluteColumn(0); - if (lowestRange[0] == -1 && lowestRange[1] == -1) - { - startPos = alignmentStartEnd[0]; - } - else - { - startPos = lowestRange[1] + 1; + // last visible column is either immediately to left of + // last hidden region, or is just the last column in the alignment + int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1); + if (lastregion[1] == width - 1) + { + // last region is at very end of alignment + // last visible column immediately precedes it + lastVisible = lastregion[0] - 1; + } } + return new int[] { firstVisible, lastVisible }; - if (higestRange[0] == -1 && higestRange[1] == -1) - { - endPos = alignmentStartEnd[1]; - } - else - { - endPos = higestRange[0] - 1; - } - return new int[] { startPos, endPos }; } finally { LOCK.readLock().unlock(); @@ -1279,28 +958,37 @@ public class HiddenColumns * * @param res * visible residue position, unadjusted for hidden columns - * @return region as [start,end] or null if no matching region is found + * @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) { try { LOCK.readLock().lock(); - int adjres = adjustForHiddenColumns(res); + int adjres = visibleToAbsoluteColumn(res); int[] reveal = null; - Iterator it = new RegionsIterator(adjres - 2, - adjres + 2, hiddenColumns, cursor); - while (it.hasNext()) + + if (!hiddenColumns.isEmpty()) { - int[] region = it.next(); - if (adjres + 1 == region[0] || adjres - 1 == region[1]) + // 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) { - reveal = region; - break; + reveal = hiddenColumns.get(regionindex); + } + // check if the region ends just after adjres + else if (regionindex < hiddenColumns.size() + && hiddenColumns.get(regionindex)[0] == adjres + 1) + { + reveal = hiddenColumns.get(regionindex); } } return reveal; + } finally { LOCK.readLock().unlock(); @@ -1315,7 +1003,7 @@ public class HiddenColumns try { LOCK.readLock().lock(); - return new BoundedHiddenColsIterator(hiddenColumns); + return new HiddenColsIterator(hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -1336,7 +1024,7 @@ public class HiddenColumns try { LOCK.readLock().lock(); - return new BoundedHiddenColsIterator(start, end, hiddenColumns); + return new HiddenColsIterator(start, end, hiddenColumns); } finally { LOCK.readLock().unlock(); @@ -1357,7 +1045,20 @@ public class HiddenColumns try { LOCK.readLock().lock(); - return new BoundedStartRegionIterator(start, end, hiddenColumns); + + // 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.readLock().unlock(); @@ -1390,192 +1091,32 @@ public class HiddenColumns * boundaries * * @param start - * (first column inclusive from 0) - * @param end - * (last column - not inclusive) - */ - public Iterator getVisContigsIterator(int start, int end) - { - try - { - LOCK.readLock().lock(); - return new VisibleContigsIterator(start, end, hiddenColumns); - } finally - { - LOCK.readLock().unlock(); - } - } - - /** - * return an iterator over visible segments between the given start and end - * boundaries - * - * @param start - * (first column - inclusive from 0) + * first column, inclusive from 0 * @param end - * (last column - inclusive) + * last column - not inclusive * @param useVisibleCoords * if true, start and end are visible column positions, not absolute - * positions + * positions* */ - public Iterator getVisibleBlocksIterator(int start, int end, + public VisibleContigsIterator getVisContigsIterator(int start, + int end, boolean useVisibleCoords) { + int adjstart = start; + int adjend = end; if (useVisibleCoords) { - // 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 - { - try - { - LOCK.readLock().lock(); - return new VisibleContigsIterator(start, end + 1, 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. - */ - 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()); + 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(); } } }