-
- /**
- * Return an iterator over the hidden regions
- */
- public Iterator<int[]> iterator()
- {
- return new BoundedHiddenColsIterator();
- }
-
- /**
- * Return a bounded iterator over the hidden regions
- *
- * @param start
- * position to start from (inclusive, absolute column position)
- * @param end
- * position to end at (inclusive, absolute column position)
- * @return
- */
- public Iterator<int[]> getBoundedIterator(int start, int end)
- {
- return new BoundedHiddenColsIterator(start, end);
- }
-
- /**
- * Return a bounded iterator over the *visible* start positions of hidden
- * regions
- *
- * @param start
- * position to start from (inclusive, visible column position)
- * @param end
- * position to end at (inclusive, visible column position)
- */
- public Iterator<Integer> getBoundedStartIterator(int start, int end)
- {
- return new BoundedStartRegionIterator(start, end, true);
- }
-
- /**
- * Return an iterator over visible *columns* (not regions) between the given
- * start and end boundaries
- *
- * @param start
- * first column (inclusive)
- * @param end
- * last column (inclusive)
- */
- public Iterator<Integer> getVisibleColsIterator(int start, int end)
- {
- return new VisibleColsIterator(start, end);
- }
-
- /**
- * return an iterator over visible segments between the given start and end
- * boundaries
- *
- * @param start
- * (first column inclusive from 0)
- * @param end
- * (last column - not inclusive)
- */
- public Iterator<int[]> getVisContigsIterator(int start, int end)
- {
- // return new VisibleBlocksIterator(start, end, true)
- return new VisibleContigsIterator(start, end, true);
- }
-
- /**
- * return an iterator over visible segments between the given start and end
- * boundaries
- *
- * @param start
- * (first column - inclusive from 0)
- * @param end
- * (last column - inclusive)
- * @param useVisibleCoords
- * if true, start and end are visible column positions, not absolute
- * positions
- */
- public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
- boolean useVisibleCoords)
- {
- if (useVisibleCoords)
- {
- // TODO
- // we should really just convert start and end here with
- // adjustForHiddenColumns
- // 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 VisibleContigsIterator(start, end + 1, true);
- }
- }
-
- /**
- * A local iterator which 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 RegionsIterator implements Iterator<int[]>
- {
- // start position to iterate from
- private int start;
-
- // end position to iterate to
- private int end;
-
- // current index in hiddenColumns
- private int currentPosition = 0;
-
- // current column in hiddenColumns
- private int[] nextRegion = null;
-
- private int[] currentRegion = null;
-
- private int removedIndex = -1;
-
- // Constructor with bounds
- RegionsIterator(int lowerBound, int upperBound)
- {
- start = lowerBound;
- end = upperBound;
-
- if (hiddenColumns != null)
- {
- // iterate until a region overlaps with [start,end]
- currentPosition = 0;
- while ((currentPosition < hiddenColumns.size())
- && (hiddenColumns.get(currentPosition)[1] < start))
- {
- 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()
- {
- currentRegion = nextRegion;
- currentPosition++;
- if (currentPosition < hiddenColumns.size())
- {
- nextRegion = hiddenColumns.get(currentPosition);
- }
- else
- {
- nextRegion = null;
- }
- return currentRegion;
- }
-
- @Override
- public void remove()
- {
- if ((currentRegion != null) && (removedIndex != currentPosition))
- {
- currentPosition--;
- hiddenColumns.subList(currentPosition, currentPosition + 1).clear();
- removedIndex = currentPosition;
- }
- else
- {
- // already removed element last returned by next()
- // or next() has not yet been called
- throw new IllegalStateException();
- }
- }
-
- }
-
- /**
- * 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. Intended to be used by
- * callers OUTSIDE of HiddenColumns.
- */
- private class BoundedHiddenColsIterator implements Iterator<int[]>
- {
- // start position to iterate from
- private int start;
-
- // end position to iterate to
- private int end;
-
- // 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;
-
- /**
- * Unbounded constructor
- */
- 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)
- {
- localHidden = new ArrayList<>();
-
- // 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 added.
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= end))
- {
- int[] rh = hiddenColumns.get(i);
- int[] cp = new int[2];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- localHidden.add(cp);
- i++;
- }
- }
- }
- finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- @Override
- public boolean hasNext()
- {
- return (localHidden != null)
- && (currentPosition < localHidden.size());
- }
-
- @Override
- public int[] next()
- {
- currentRegion = localHidden.get(currentPosition);
- currentPosition++;
- return currentRegion;
- }
- }
-
- /**
- * An iterator which iterates over visible start positions of hidden column
- * regions in a range.
- */
- private class BoundedStartRegionIterator implements Iterator<Integer>
- {
- // start position to iterate from
- private int start;
-
- // end position to iterate to
- private int end;
-
- // current index in hiddenColumns
- private int currentPosition = 0;
-
- // local copy or reference to hiddenColumns
- private List<Integer> positions = null;
-
- /**
- * Construct an iterator over hiddenColums bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * 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)
- */
- BoundedStartRegionIterator(int lowerBound, int upperBound,
- boolean useCopy)
- {
- start = lowerBound;
- end = upperBound;
-
- try
- {
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null)
- {
- positions = new ArrayList<>(hiddenColumns.size());
-
- // navigate to start, keeping count of hidden columns
- int i = 0;
- int hiddenSoFar = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
- {
- int[] region = hiddenColumns.get(i);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
- }
-
- // iterate from start to end, adding start positions of each
- // hidden region. Positions are visible columns count, not absolute
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
- {
- int[] region = hiddenColumns.get(i);
- positions.add(region[0] - hiddenSoFar);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
- }
- }
- else
- {
- positions = new ArrayList<>();
- }
- } finally
- {
- if (useCopy)
- {
- LOCK.readLock().unlock();
- }
- }
- }
-
- @Override
- public boolean hasNext()
- {
- return (currentPosition < positions.size());
- }
-
- /**
- * Get next hidden region start position
- *
- * @return the start position in *visible* coordinates
- */
- @Override
- public Integer next()
- {
- int result = positions.get(currentPosition);
- currentPosition++;
- return result;
- }
- }
-
- /**
- * 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 current;
-
- private int next;
-
- private List<int[]> localHidden = new ArrayList<>();
-
- private int nexthiddenregion;
-
- VisibleColsIterator(int firstcol, int lastcol)
- {
- last = lastcol;
- current = firstcol;
- next = firstcol;
- nexthiddenregion = 0;
-
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
- {
- 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])
- {
- // 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;
- }
- }
-
- // make a local copy of the bit we need
- i = nexthiddenregion;
- while (i < hiddenColumns.size() && hiddenColumns.get(i)[0] <= last)
- {
- int[] region = new int[] { hiddenColumns.get(i)[0],
- hiddenColumns.get(i)[1] };
- localHidden.add(region);
- i++;
- }
- }
-
- LOCK.readLock().unlock();
- }
-
- @Override
- public boolean hasNext()
- {
- return next <= last;
- }
-
- @Override
- public Integer next()
- {
- if (next > last)
- {
- throw new NoSuchElementException();
- }
- current = next;
- if ((localHidden != null)
- && (nexthiddenregion < localHidden.size()))
- {
- // still some more hidden regions
- if (next + 1 < localHidden.get(nexthiddenregion)[0])
- {
- // next+1 is still before the next hidden region
- next++;
- }
- else if ((next + 1 >= localHidden.get(nexthiddenregion)[0])
- && (next + 1 <= localHidden.get(nexthiddenregion)[1]))
- {
- // next + 1 is in the next hidden region
- next = localHidden.get(nexthiddenregion)[1] + 1;
- nexthiddenregion++;
- }
- }
- else
- {
- // finished with hidden regions, just increment normally
- next++;
- }
- return current;
- }
-
- @Override
- public void remove()
- {
- throw new UnsupportedOperationException();
- }
- }
-
- /**
- * An iterator which iterates over visible regions in a range.
- */
- private class VisibleContigsIterator implements Iterator<int[]>
- {
- private List<int[]> vcontigs = new ArrayList<>();
-
- private int currentPosition = 0;
-
- VisibleContigsIterator(int start, int end, boolean usecopy)
- {
- try
- {
- if (usecopy)
- {
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- int vstart = start;
- int hideStart;
- int hideEnd;
-
- for (int[] region : hiddenColumns)
- {
- hideStart = region[0];
- hideEnd = region[1];
-
- // navigate to start
- if (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- int[] contig = new int[] { vstart, hideStart - 1 };
- vcontigs.add(contig);
- }
- vstart = hideEnd + 1;
-
- // exit if we're past the end
- if (vstart >= end)
- {
- break;
- }
- }
-
- if (vstart < end)
- {
- int[] contig = new int[] { vstart, end - 1 };
- vcontigs.add(contig);
- }
- }
- else
- {
- int[] contig = new int[] { start, end - 1 };
- 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
- * column is adjacent to a hidden region.
- */
- public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
- {
- private List<int[]> vcontigs = new ArrayList<>();
-
- private int currentPosition = 0;
-
- private boolean endsAtHidden = false;
-
- /**
- * Constructor for iterator over visible regions in a range.
- *
- * @param start
- * start position in terms of visible column position
- * @param end
- * end position in terms of visible column position
- * @param usecopy
- * whether to use a local copy of hidden columns
- */
- VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
- {
- /* actually this implementation always uses a local copy but this may change in future */
- try
- {
- if (usecopy)
- {
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- int blockStart = start;
- int blockEnd = end;
- int hiddenSoFar = 0;
- int visSoFar = 0;
-
- // iterate until a region begins within (start,end]
- int i = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar))
- {
- hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0]
- + 1;
- i++;
- }
-
- blockStart += hiddenSoFar; // convert start to absolute position
- blockEnd += hiddenSoFar; // convert end to absolute position
-
- // iterate from start to end, adding each visible region. Positions
- // are
- // absolute, and all hidden regions which overlap [start,end] are
- // used.
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= blockEnd))
- {
- int[] region = hiddenColumns.get(i);
-
- // end position of this visible region is either just before the
- // start of the next hidden region, or the absolute position of
- // 'end', whichever is lowest
- blockEnd = Math.min(blockEnd, region[0] - 1);
-
- vcontigs.add(new int[] { blockStart, blockEnd });
-
- visSoFar += blockEnd - blockStart + 1;
-
- // next visible region starts after this hidden region
- blockStart = region[1] + 1;
-
- hiddenSoFar += region[1] - region[0] + 1;
-
- // reset blockEnd to absolute position of 'end', assuming we've now
- // passed all hidden regions before end
- blockEnd = end + hiddenSoFar;
-
- i++;
- }
- if (visSoFar < end - start)
- {
- // the number of visible columns we've accounted for is less than
- // the number specified by end-start; work out the end position of
- // the last visible region
- blockEnd = blockStart + end - start - visSoFar;
- vcontigs.add(new int[] { blockStart, blockEnd });
-
- // if the last visible region ends at the next hidden region, set
- // endsAtHidden=true
- if (i < hiddenColumns.size()
- && hiddenColumns.get(i)[0] - 1 == blockEnd)
- {
- endsAtHidden = true;
- }
- }
- }
- else
- {
- // there are no hidden columns, return a single visible contig
- vcontigs.add(new int[] { start, end });
- endsAtHidden = false;
- }
- } 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;
- }
-
- public boolean endsAtHidden()
- {
- return endsAtHidden;
- }
- }