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.
+ *
+ * @author kmourao
+ *
+ */
public class HiddenColumns
{
private static final int HASH_MULTIPLIER = 31;
* Methods which change the hiddenColumns collection. These methods should
* use a writeLock to prevent other threads accessing the hiddenColumns
* collection while changes are being made. They should also reset the hidden
- * columns cursor, and either update the hidden columns count, or set it to 0.
+ * columns cursor, and either update the hidden columns count, or set it to 0
+ * (so that it will later be updated when needed).
*/
/**
wasAlreadyLocked = true;
}
+ int previndex = 0;
+ int prevHiddenCount = 0;
+ int regionindex = 0;
if (hiddenColumns == null)
{
hiddenColumns = new ArrayList<>();
}
+ else
+ {
+ // set up cursor reset values
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+ regionindex = cursorPos.getRegionIndex();
+
+ if (regionindex > 0)
+ {
+ // 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
* appropriate
*/
boolean added = false;
- for (int i = 0; !added && i < hiddenColumns.size(); i++)
+ if (regionindex > 0)
+ {
+ added = insertRangeAtRegion(regionindex - 1, start, end);
+ }
+ if (!added && regionindex < hiddenColumns.size())
{
- added = insertRangeAtRegion(i, start, end);
- } // for
+ insertRangeAtRegion(regionindex, start, end);
+ }
}
- if (!wasAlreadyLocked)
- {
- cursor.resetCursor(hiddenColumns);
- // reset the number of columns so they will be recounted
- numColumns = 0;
- }
+ // 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
{
if (!wasAlreadyLocked)
break;
}
region[1] = Math.max(nextRegion[1], end);
+
+ // in theory this is faster than hiddenColumns.remove(i+1)
+ // benchmarking results a bit ambivalent
hiddenColumns.subList(i + 1, i + 2).clear();
}
added = true;
{
// numColumns is out of date, so recalculate
int size = 0;
- if (hiddenColumns != null)
+
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
- {
- int[] range = it.next();
- size += range[1] - range[0] + 1;
- }
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
}
+
numColumns = size;
}
if (hiddenColumns != null)
{
- result += cursor.getHiddenOffset(column).getHiddenSoFar();
+ result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
}
return result;
* @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)
{
if (regionindex > -1 && regionindex < hiddenColumns.size())
{
int[] region = hiddenColumns.get(regionindex);
- if (column >= region[0] && column <= region[1])
+ // already know that column <= region[1] as cursor returns containing
+ // region or region to right
+ if (column >= region[0])
{
return false;
}
*/
public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+ if (alignmentAnnotation != null
+ && alignmentAnnotation.annotations != null)
+ {
+ makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
alignmentAnnotation);
+ }
}
/**
int startFrom = start;
int endAt = end;
- if (alignmentAnnotation.annotations != null)
+ if (alignmentAnnotation != null
+ && alignmentAnnotation.annotations != null)
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
try
{
LOCK.readLock().lock();
+
+ // we don't use getSize()>0 here because it has to iterate over
+ // the full hiddenColumns collection and so will be much slower
return hiddenColumns != null && hiddenColumns.size() > 0;
} finally
{
/**
*
- * @return true if there are more than one set of columns hidden
+ * @return true if there is more than one hidden column region
*/
- public boolean hasManyHiddenColumns()
+ public boolean hasMultiHiddenColumnRegions()
{
try
{
higestRange = (range[1] >= endPos) ? range : higestRange;
}
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
{
startPos = alignmentStartEnd[0];
}
startPos = lowestRange[1] + 1;
}
- if (higestRange[0] == -1 && higestRange[1] == -1)
+ if (higestRange[0] == -1) // includes (higestRange[1] == -1)
{
endPos = alignmentStartEnd[1];
}
{
reveal = hiddenColumns.get(regionindex);
}
- // or try the next region
- else
- {
- regionindex++;
- if (regionindex < hiddenColumns.size()
- && hiddenColumns.get(regionindex)[0] == adjres + 1)
- {
- reveal = hiddenColumns.get(regionindex);
- }
- }
}
return reveal;
try
{
LOCK.readLock().lock();
- return new BoundedHiddenColsIterator(hiddenColumns);
+ return new HiddenColsIterator(hiddenColumns);
} finally
{
LOCK.readLock().unlock();
try
{
LOCK.readLock().lock();
- return new BoundedHiddenColsIterator(start, end, hiddenColumns);
+ return new HiddenColsIterator(start, end, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
* boundaries
*
* @param start
- * first column, inclusive from 0, absolute value
- * @param end
- * last column - not inclusive, absolute value
- */
- public Iterator<int[]> 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<int[]> getVisibleBlocksIterator(int start, int end,
+ public Iterator<int[]> getVisContigsIterator(int start, int end,
boolean useVisibleCoords)
{
int adjstart = start;
try
{
LOCK.readLock().lock();
-
- return new VisibleContigsIterator(adjstart, adjend + 1,
- hiddenColumns);
+ return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
git://source.jalview.org / jalview.git / blobdiff