{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] range = it.next();
{
LOCK.readLock().lock();
int size = 0;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] range = it.next();
return false;
}
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
Iterator<int[]> thatit = that.iterator();
while (it.hasNext())
{
LOCK.readLock().lock();
int result = column;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] region = it.next();
int[] region = null;
if (hiddenColumns != null)
{
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator(0,
+ Iterator<int[]> it = new RegionsIterator(0,
hiddenColumn);
while (it.hasNext())
{
// 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;
- }
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start);
- // 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))
+ while (it.hasNext() && (distance - gap > 0))
{
- // subtract the gap to right of region from distance
- distance -= gap;
- start = nextstart;
+ region = it.next();
+
+ if (start > region[1])
+ {
+
+
+ // subtract the gap to right of region from distance
+ distance -= start - region[1]; // gap;
+
+ start = nextstart;
+ nextstart = region[0] - 1;// nextstart;
+
- // calculate the next gap
- region = hiddenColumns.get(index);
- gap = start - region[1];
+ // calculate the next gap
- // set start to just to left of current region
- nextstart = region[0] - 1;
- index--;
+ // gap = start - region[1];
+
+ // set start to just to left of current region
+ // nextstart = region[0] - 1;
+ }
}
- if (distance - gap > 0)
+ if (!it.hasNext())
{
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - distance;
+ // no hidden regions to left of startColumn
+ return start - distance;
+ }
+ else
+ {
+
+ /* // walk backwards through the alignment subtracting the counts of
+ // visible
+ // columns from distance
+ int[] region;
+ int gap = 0;
+ int nextstart = start;
+
+ while (it.hasNext() && (distance - gap > 0))
+ {
+ region = it.next();
+
+ // subtract the gap to right of region from distance
+ distance -= gap;
+ start = nextstart;
+
+ // calculate the next gap
+
+ gap = start - region[1];
+
+ // set start to just to left of current region
+ nextstart = region[0] - 1;
+ }
+ */
+ if (distance - gap > 0)
+ {
+ // fell out of loop because there are no more hidden regions
+ distance -= gap;
+ return nextstart - distance;
+ }
+ return start - 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 (visible) alignmentPosition to find the next hidden column for
*/
public int getHiddenBoundaryRight(int alPos)
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
- int index = 0;
- do
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- int[] region = hiddenColumns.get(index);
+ int[] region = it.next();
if (alPos < region[0])
{
return region[0];
}
-
- index++;
- } while (index < hiddenColumns.size());
+ }
}
-
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 index
- * int
+ * @param alPos
+ * the (visible) alignmentPosition to find the previous hidden column
+ * for
*/
public int getHiddenBoundaryLeft(int alPos)
{
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new ReverseRegionsIterator(0, alPos);
+ while (it.hasNext())
{
- int index = hiddenColumns.size() - 1;
- do
+ int[] region = it.next();
+ if (alPos > region[1])
{
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
+ return region[1];
+ }
}
return alPos;
* region to the left. If there is no hidden region to the left it returns -1.
*
* @param pos
- * int
+ * position to find index relative to
*/
private int getHiddenIndexLeft(int pos)
{
try
{
-
LOCK.readLock().lock();
- if (hiddenColumns != null)
+
+
+ Iterator<int[]> it = new ReverseRegionsIterator(0, pos);
+ if (it.hasNext())
{
- int index = hiddenColumns.size() - 1;
- do
+ int index = hiddenColumns.size() - 1; // need index of region not last
+ // one
+ while (it.hasNext())
{
- int[] region = hiddenColumns.get(index);
+ int[] region = it.next();
if (pos > region[1])
{
return index;
}
-
index--;
- } while (index > -1);
+ }
}
-
return -1;
} finally
{
{
LOCK.readLock().lock();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] region = it.next();
// Simply walk along the sequence whilst watching for hidden column
// boundaries
- Iterator<int[]> regions = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> regions = new RegionsIterator();
int hideStart = seq.getLength();
int hideEnd = -1;
int visPrev = 0;
try
{
LOCK.writeLock().lock();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] region = it.next();
try
{
LOCK.writeLock().lock();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] region = it.next();
// of
// preceding visible gaps
// update hidden columns at the same time
- Iterator<int[]> regions = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> regions = new RegionsIterator();
ArrayList<int[]> newhidden = new ArrayList<>();
int numGapsBefore = 0;
{
LOCK.readLock().lock();
int hashCode = 1;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] hidden = it.next();
{
return;
}
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] range = it.next();
return new int[] { startPos, endPos };
}
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] range = it.next();
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator(adjres - 2,
+ Iterator<int[]> it = new RegionsIterator(adjres - 2,
adjres + 2);
while (it.hasNext())
{
/**
* 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).
+ * Intended for use ONLY within the HiddenColumns class, because it works
+ * directly with the hiddenColumns collection without locking (callers should
+ * lock hiddenColumns).
*/
- private class LocalBoundedHiddenColsIterator implements Iterator<int[]>
+ private class RegionsIterator implements Iterator<int[]>
{
- private int start; // start position to iterate from
+ // start position to iterate from
+ private int start;
- private int end; // end position to iterate to
+ // end position to iterate to
+ private int end;
// current index in hiddenColumns
private int currentPosition = 0;
// current column in hiddenColumns
private int[] nextRegion = null;
- LocalBoundedHiddenColsIterator(int lowerBound, int upperBound)
+ // Constructor with bounds
+ RegionsIterator(int lowerBound, int upperBound)
{
init(lowerBound, upperBound);
}
- LocalBoundedHiddenColsIterator()
+ // Unbounded constructor
+ RegionsIterator()
{
if (hiddenColumns != null)
{
+ // iterator over full hiddenColumns collection
int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
init(0, last);
}
else
{
+ // empty iterator
init(0, 0);
}
}
* 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)
*/
private void init(int lowerBound, int upperBound)
{
}
/**
+ * A local iterator which reverse iterates over hidden column regions in a
+ * range. Intended for use ONLY within the HiddenColumns class, because it
+ * works directly with the hiddenColumns collection without locking (callers
+ * should lock hiddenColumns).
+ */
+ private class ReverseRegionsIterator implements Iterator<int[]>
+ {
+ // start position to iterate to
+ private int start;
+
+ // end position to iterate from
+ private int end;
+
+ // current index in hiddenColumns
+ private int currentPosition = 0;
+
+ // current column in hiddenColumns
+ private int[] nextRegion = null;
+
+ // Constructor with bounds
+ ReverseRegionsIterator(int lowerBound, int upperBound)
+ {
+ init(lowerBound, upperBound);
+ }
+
+ // Unbounded constructor
+ ReverseRegionsIterator()
+ {
+ if (hiddenColumns != null)
+ {
+ // iterator over full hiddenColumns collection
+ int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
+ init(0, last);
+ }
+ else
+ {
+ // empty iterator
+ init(0, 0);
+ }
+ }
+
+ /**
+ * Construct an iterator over hiddenColums bounded at
+ * [lowerBound,upperBound]
+ *
+ * @param lowerBound
+ * lower bound to iterate to
+ * @param upperBound
+ * upper bound to iterate from
+ */
+ private void init(int lowerBound, int upperBound)
+ {
+ start = lowerBound;
+ end = upperBound;
+
+ if (hiddenColumns != null)
+ {
+ // iterate until a region overlaps with [start,end]
+ currentPosition = hiddenColumns.size() - 1;
+ while (currentPosition >= 0
+ && hiddenColumns.get(currentPosition)[1] > end)
+ {
+ currentPosition--;
+ }
+ if (currentPosition >= 0)
+ {
+ nextRegion = hiddenColumns.get(currentPosition);
+ }
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (hiddenColumns != null) && (nextRegion != null)
+ && (nextRegion[1] >= start);
+ }
+
+ @Override
+ public int[] next()
+ {
+ int[] region = nextRegion;
+ currentPosition--;
+ if (currentPosition >= 0)
+ {
+ 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.
+ * with a copy of the hidden columns collection. Intended to be used by
+ * callers OUTSIDE of HiddenColumns.
*/
private class BoundedHiddenColsIterator implements Iterator<int[]>
{
- private int start; // start position to iterate from
+ // start position to iterate from
+ private int start;
- private int end; // end position to iterate to
+ // end position to iterate to
+ private int end;
// current index in hiddenColumns
private int currentPosition = 0;
// local copy or reference to hiddenColumns
private List<int[]> localHidden;
+ /**
+ * Unbounded constructor
+ */
BoundedHiddenColsIterator()
{
if (hiddenColumns != null)
git://source.jalview.org / jalview.git / commitdiff