{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- for (int[] range : hiddenColumns)
- {
- regionBuilder.append(delimiter).append(range[0]).append(between)
+ int[] range = it.next();
+ regionBuilder.append(delimiter).append(range[0]).append(between)
.append(range[1]);
+ if (!it.hasNext())
+ {
+ regionBuilder.deleteCharAt(0);
}
-
- regionBuilder.deleteCharAt(0);
}
return regionBuilder.toString();
} finally
{
LOCK.readLock().lock();
int size = 0;
- if (hasHiddenColumns())
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- for (int[] range : hiddenColumns)
- {
- size += range[1] - range[0] + 1;
- }
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
}
+
return size;
} finally
{
{
return false;
}
- int i = 0;
- for (int[] thisRange : hiddenColumns)
+
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> thatit = that.iterator();
+ while (it.hasNext())
{
- int[] thatRange = that.hiddenColumns.get(i++);
+ int[] thisRange = it.next();
+ int[] thatRange = thatit.next();
if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
{
return false;
{
LOCK.readLock().lock();
int result = column;
- if (hiddenColumns != null)
+
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] region = it.next();
+ if (result >= region[0])
{
- int[] region = hiddenColumns.get(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
+ result += region[1] - region[0] + 1;
}
}
+
return result;
} finally
{
{
LOCK.readLock().lock();
int result = hiddenColumn;
+ int[] region = null;
if (hiddenColumns != null)
{
- int index = 0;
- int[] region;
- do
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator(0,
+ hiddenColumn);
+ while (it.hasNext())
{
- region = hiddenColumns.get(index++);
+ region = it.next();
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 (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
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- for (int[] region : hiddenColumns)
+ int[] region = it.next();
+ if (column >= region[0] && column <= region[1])
{
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
+ return false;
}
}
{
StringBuffer visibleSeq = new StringBuffer();
- Iterator<int[]> blocks = new VisibleBlocksIterator(start,
- end, false);
+ Iterator<int[]> blocks = new VisibleContigsIterator(start,
+ end + 1, false);
+
while (blocks.hasNext())
{
int[] block = blocks.next();
- visibleSeq.append(seqs[i].getSequence(block[0], block[1]));
+ if (blocks.hasNext())
+ {
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1] + 1));
+ }
+ else
+ {
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1]));
+ }
}
selections[i] = visibleSeq.toString();
// Simply walk along the sequence whilst watching for hidden column
// boundaries
- Iterator<int[]> regions = iterator();
+ Iterator<int[]> regions = new LocalBoundedHiddenColsIterator();
int hideStart = seq.getLength();
int hideEnd = -1;
int visPrev = 0;
int w = 0;
- Iterator<int[]> blocks = new VisibleBlocksIterator(start, end,
+ Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
false);
+
int copylength;
int annotationLength;
while (blocks.hasNext())
{
int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
if (blocks.hasNext())
{
- annotationLength = block[1] - block[0];
// copy just the visible segment of the annotation row
copylength = annotationLength;
}
else
{
- annotationLength = block[1] - block[0] + 1;
if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
{
// copy just the visible segment of the annotation row
try
{
LOCK.writeLock().lock();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] region = it.next();
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- int[] region = hiddenColumns.get(i);
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
+ sel.addElement(j);
}
}
try
{
LOCK.writeLock().lock();
- for (int i = 0; i < hiddenColumns.size(); i++)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- int[] region = hiddenColumns.get(i);
+ int[] region = it.next();
if (start == region[0])
{
for (int j = region[0]; j < region[1] + 1; j++)
hiddenColumns.remove(region);
break;
}
+ else if (start < region[0])
+ {
+ break; // passed all possible matching regions
+ }
}
+
if (hiddenColumns.size() == 0)
{
hiddenColumns = null;
// of
// preceding visible gaps
// update hidden columns at the same time
- Iterator<int[]> regions = iterator();
+ Iterator<int[]> regions = new LocalBoundedHiddenColsIterator();
ArrayList<int[]> newhidden = new ArrayList<>();
int numGapsBefore = 0;
{
LOCK.readLock().lock();
int hashCode = 1;
- if (hiddenColumns != null)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- for (int[] hidden : hiddenColumns)
- {
- hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
- hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
- }
+ int[] hidden = it.next();
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
return hashCode;
} finally
{
return;
}
- for (int[] range : hiddenColumns)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
+ int[] range = it.next();
inserts.set(range[0], range[1] + 1);
}
} finally
return new int[] { startPos, endPos };
}
- for (int[] hiddenCol : hiddenColumns)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ while (it.hasNext())
{
- lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
- higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ int[] range = it.next();
+ lowestRange = (range[0] <= startPos) ? range : lowestRange;
+ higestRange = (range[1] >= endPos) ? range : higestRange;
}
if (lowestRange[0] == -1 && lowestRange[1] == -1)
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
- if (hiddenColumns != null)
+ Iterator<int[]> it = new LocalBoundedHiddenColsIterator(adjres - 2,
+ adjres + 2);
+ while (it.hasNext())
{
- for (int[] region : hiddenColumns)
+ int[] region = it.next();
+ if (adjres + 1 == region[0] || adjres - 1 == region[1])
{
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
- {
- reveal = region;
- break;
- }
+ reveal = region;
+ break;
}
}
return reveal;
*/
public Iterator<int[]> 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 new BoundedHiddenColsIterator();
}
/**
*/
public Iterator<int[]> getBoundedIterator(int start, int end)
{
- return new BoundedHiddenColsIterator(start, end, true);
+ return new BoundedHiddenColsIterator(start, end);
}
/**
}
/**
- * Return an iterator over visible columns between the given start and end
- * boundaries
+ * Return an iterator over visible *columns* (not regions) between the given
+ * start and end boundaries
*
* @param start
* first column (inclusive)
*/
public Iterator<Integer> getVisibleColsIterator(int start, int end)
{
- return new VisibleColsIterator(start, end, true);
+ return new VisibleColsIterator(start, end);
}
/**
*/
public Iterator<int[]> getVisContigsIterator(int start, int end)
{
+ // return new VisibleBlocksIterator(start, end, true)
return new VisibleContigsIterator(start, end, true);
}
// TODO
// we should really just convert start and end here with
// adjustForHiddenColumns
- // and then create a VisibleBlocksIterator
+ // 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
{
- return new VisibleBlocksIterator(start, end, true);
+ return new VisibleContigsIterator(start, end - 1, true);
}
}
/**
- * An iterator which iterates over hidden column regions in a range.
+ * A local iterator which iterates over hidden column regions in a range.
+ * Works with the actual hidden columns collection (so locking before use may
+ * be required).
*/
- private class BoundedHiddenColsIterator implements Iterator<int[]>
+ private class LocalBoundedHiddenColsIterator implements Iterator<int[]>
{
private int start; // start position to iterate from
private int currentPosition = 0;
// current column in hiddenColumns
- private int[] currentRegion;
+ private int[] nextRegion = null;
- // whether to make a local copy of hiddenColumns
- private final boolean useCopy;
+ LocalBoundedHiddenColsIterator(int lowerBound, int upperBound)
+ {
+ init(lowerBound, upperBound);
+ }
- // local copy or reference to hiddenColumns
- private List<int[]> localHidden;
+ LocalBoundedHiddenColsIterator()
+ {
+ if (hiddenColumns != null)
+ {
+ int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
+ init(0, last);
+ }
+ else
+ {
+ init(0, 0);
+ }
+ }
/**
* Construct an iterator over hiddenColums bounded at
* 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)
+ private void init(int lowerBound, int upperBound)
{
start = lowerBound;
end = upperBound;
- useCopy = useCopyCols;
- try
+ if (hiddenColumns != null)
{
- if (useCopy)
+ // iterate until a region overlaps with [start,end]
+ currentPosition = 0;
+ while ((currentPosition < hiddenColumns.size())
+ && (hiddenColumns.get(currentPosition)[1] < start))
{
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- LOCK.readLock().lock();
+ currentPosition++;
+ }
+ if (currentPosition < hiddenColumns.size())
+ {
+ nextRegion = hiddenColumns.get(currentPosition);
}
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (hiddenColumns != null) && (nextRegion != null)
+ && (nextRegion[0] <= end);
+ }
+
+ @Override
+ public int[] next()
+ {
+ int[] region = nextRegion;
+ currentPosition++;
+ if (currentPosition < hiddenColumns.size())
+ {
+ nextRegion = hiddenColumns.get(currentPosition);
+ }
+ else
+ {
+ nextRegion = null;
+ }
+ return region;
+ }
+
+ }
+
+ /**
+ * An iterator which iterates over hidden column regions in a range. Works
+ * with a copy of the hidden columns collection.
+ */
+ private class BoundedHiddenColsIterator implements Iterator<int[]>
+ {
+ 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;
+
+ // local copy or reference to hiddenColumns
+ private List<int[]> localHidden;
+
+ BoundedHiddenColsIterator()
+ {
+ if (hiddenColumns != null)
+ {
+ int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
+ init(0, last);
+ }
+ else
+ {
+ init(0, 0);
+ }
+ }
+
+ /**
+ * Construct an iterator over hiddenColums bounded at
+ * [lowerBound,upperBound]
+ *
+ * @param lowerBound
+ * lower bound to iterate from
+ * @param upperBound
+ * upper bound to iterate to
+ */
+ BoundedHiddenColsIterator(int lowerBound, int upperBound)
+ {
+ init(lowerBound, upperBound);
+ }
+
+ /**
+ * Construct an iterator over hiddenColums bounded at
+ * [lowerBound,upperBound]
+ *
+ * @param lowerBound
+ * lower bound to iterate from
+ * @param upperBound
+ * upper bound to iterate to
+ */
+ private void init(int lowerBound, int upperBound)
+ {
+ start = lowerBound;
+ end = upperBound;
+
+ try
+ {
+ LOCK.readLock().lock();
if (hiddenColumns != null)
{
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);
- }
+ int[] rh = hiddenColumns.get(i);
+ int[] cp = new int[2];
+ System.arraycopy(rh, 0, cp, 0, rh.length);
+ localHidden.add(cp);
i++;
}
}
}
finally
{
- if (useCopy)
- {
- LOCK.readLock().unlock();
- }
+ LOCK.readLock().unlock();
}
}
}
}
+ /**
+ * Iterator over the visible *columns* (not regions) as determined by the set
+ * of hidden columns. Uses a local copy of hidden columns.
+ *
+ * @author kmourao
+ *
+ */
private class VisibleColsIterator implements Iterator<Integer>
{
private int last;
private int nexthiddenregion;
- VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
+ VisibleColsIterator(int firstcol, int lastcol)
{
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();
- }
+ LOCK.readLock().lock();
- if (hiddenColumns != null)
+ if (hiddenColumns != null)
+ {
+ int i = 0;
+ for (i = 0; i < hiddenColumns.size()
+ && (current <= hiddenColumns.get(i)[0]); ++i)
{
- 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])
{
- 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;
- }
+ // current is hidden, move to right
+ current = hiddenColumns.get(i)[1] + 1;
+ next = current;
+ nexthiddenregion = i + 1;
}
+ }
- // make a local copy of the bit we need
- i = nexthiddenregion;
- while (i < hiddenColumns.size()
- && hiddenColumns.get(i)[0] <= last)
+ for (i = hiddenColumns.size() - 1; i >= 0
+ && (last >= hiddenColumns.get(i)[1]); --i)
+ {
+ if (last >= hiddenColumns.get(i)[0]
+ && last <= hiddenColumns.get(i)[1])
{
- int[] region = new int[] { hiddenColumns.get(i)[0],
- hiddenColumns.get(i)[1] };
- localHidden.add(region);
- i++;
+ // last is hidden, move to left
+ last = hiddenColumns.get(i)[0] - 1;
}
}
- } finally
- {
- if (useCopy)
+
+ // make a local copy of the bit we need
+ i = nexthiddenregion;
+ while (i < hiddenColumns.size() && hiddenColumns.get(i)[0] <= last)
{
- LOCK.readLock().unlock();
+ int[] region = new int[] { hiddenColumns.get(i)[0],
+ hiddenColumns.get(i)[1] };
+ localHidden.add(region);
+ i++;
}
}
+
+ LOCK.readLock().unlock();
}
@Override
}
/**
- * An iterator which iterates over visible regions in a range.
- */
- private class VisibleBlocksIterator implements Iterator<int[]>
- {
- private List<int[]> 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
return endsAtHidden;
}
}
-
}
git://source.jalview.org / jalview.git / commitdiff