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// numColumns is out of date, so recalculate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();