import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
-import java.util.Vector;
import java.util.concurrent.locks.ReentrantReadWriteLock;
public class HiddenColumns
{
if (copy.hiddenColumns != null)
{
- hiddenColumns = copy.copyHiddenRegionsToArrayList(0);
+ hiddenColumns = new ArrayList<>();
+ Iterator<int[]> it = copy.iterator();
+ while (it.hasNext())
+ {
+ hiddenColumns.add(it.next());
+ }
}
}
} finally
{
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())
{
// 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
+ // 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
{
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));
- // 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;
- }
-
- // walk backwards through the alignment subtracting the counts of visible
- // columns from distance
- int[] region;
- int gap = 0;
- int nextstart = start;
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start);
- while ((index > -1) && (distance - gap > 0))
+ while (it.hasNext() && (distance > 0))
{
- // subtract the gap to right of region from distance
- distance -= gap;
- start = nextstart;
-
- // calculate the next gap
- region = hiddenColumns.get(index);
- gap = start - region[1];
+ int[] region = it.next();
- // set start to just to left of current region
- nextstart = region[0] - 1;
- index--;
+ 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;
+ }
+ }
}
- if (distance - gap > 0)
- {
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - 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;
}
/**
- * This method returns the index of the hidden region to the left of a column
- * position. If the column is in a hidden region it returns the index of the
- * region to the left. If there is no hidden region to the left it returns -1.
- *
- * @param pos
- * int
- */
- private int getHiddenIndexLeft(int pos)
- {
- try
- {
-
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (pos > region[1])
- {
- return index;
- }
-
- index--;
- } while (index > -1);
- }
-
- return -1;
- } finally
- {
- LOCK.readLock().unlock();
- }
-
- }
-
- /**
- * Adds the specified column range to the hidden columns
+ * Adds the specified column range to the hidden columns collection
*
* @param start
+ * start of range to add (absolute position in alignment)
* @param end
+ * end of range to add (absolute position in alignment)
*/
public void hideColumns(int start, int end)
{
boolean added = false;
for (int i = 0; !added && i < hiddenColumns.size(); i++)
{
- int[] region = hiddenColumns.get(i);
-
- if (end < region[0] - 1)
- {
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.add(i, new int[] { start, end });
- added = true;
- }
- else if (end <= region[1])
- {
- /*
- * new range overlaps existing, or is contiguous preceding it - adjust
- * start column
- */
- region[0] = Math.min(region[0], start);
- added = true;
- }
- else if (start <= region[1] + 1)
- {
- /*
- * new range overlaps existing, or is contiguous following it - adjust
- * start and end columns
- */
- region[0] = Math.min(region[0], start);
- region[1] = Math.max(region[1], end);
-
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
- {
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
- {
- /*
- * gap to next hidden range - no more to update
- */
- break;
- }
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
- }
- added = true;
- }
+ added = insertRangeAtRegion(i, start, end);
} // for
}
} finally
}
}
+ private boolean insertRangeAtRegion(int i, int start, int end)
+ {
+ boolean added = false;
+
+ int[] region = hiddenColumns.get(i);
+ if (end < region[0] - 1)
+ {
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.add(i, new int[] { start, end });
+ added = true;
+ }
+ else if (end <= region[1])
+ {
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ added = true;
+ }
+ else if (start <= region[1] + 1)
+ {
+ /*
+ * new range overlaps existing, or is contiguous following it - adjust
+ * start and end columns
+ */
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
+ {
+ int[] nextRegion = hiddenColumns.get(i + 1);
+ if (nextRegion[0] > end + 1)
+ {
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
+ }
+ region[1] = Math.max(nextRegion[1], end);
+ hiddenColumns.remove(i + 1);
+ }
+ added = true;
+ }
+ return added;
+ }
+
+ /**
+ * Answers if a column in the alignment is visible
+ *
+ * @param column
+ * absolute position of column in the alignment
+ * @return true if column is visible
+ */
public boolean isVisible(int column)
{
try
{
LOCK.readLock().lock();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = new RegionsIterator();
while (it.hasNext())
{
int[] region = it.next();
}
}
- private ArrayList<int[]> copyHiddenRegionsToArrayList(int startIndex)
- {
- int size = 0;
- if (hiddenColumns != null)
- {
- size = hiddenColumns.size();
- }
- ArrayList<int[]> copy = new ArrayList<>(size);
-
- for (int i = startIndex, j = size; i < j; i++)
- {
- int[] rh;
- int[] cp;
- rh = hiddenColumns.get(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- copy.add(cp);
- }
- }
-
- return copy;
- }
-
+ /**
+ * Get the visible sections of a set of sequences
+ *
+ * @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
+ */
public String[] getVisibleSequenceStrings(int start, int end,
SequenceI[] seqs)
{
// 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;
AlignmentAnnotation alignmentAnnotation)
{
// mangle the alignmentAnnotation annotation array
- Vector<Annotation[]> annels = new Vector<>();
+ ArrayList<Annotation[]> annels = new ArrayList<>();
Annotation[] els = null;
int w = 0;
}
els = new Annotation[annotationLength];
- annels.addElement(els);
+ annels.add(els);
System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
copylength);
w += annotationLength;
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);
+ }
+
+ /**
+ * 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)
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