-
- /**
- * Return an iterator over the hidden regions
- */
- 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 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, true);
- }
-
- /**
- * 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 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, 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 - not inclusive)
- */
- public Iterator<int[]> getVisContigsIterator(int start, int end)
- {
- 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 VisibleBlocksIterator
- // 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);
- }
- }
-
- /**
- * An iterator which iterates over hidden column regions in a range.
- */
- 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;
-
- // whether to make a local copy of hiddenColumns
- private final boolean useCopy;
-
- // local copy or reference to hiddenColumns
- private List<int[]> localHidden;
-
- /**
- * 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)
- */
- BoundedHiddenColsIterator(int lowerBound, int upperBound,
- boolean useCopyCols)
- {
- start = lowerBound;
- end = upperBound;
- useCopy = useCopyCols;
-
- try
- {
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- 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;
- 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);
- }
- i++;
- }
- }
- }
- finally
- {
- if (useCopy)
- {
- 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;
- }
- }
-
- private class VisibleColsIterator implements Iterator<Integer>
- {
- private int last;
-
- private int current;
-
- private int next;
-
- private List<int[]> localHidden = new ArrayList<>();
-
- private int lasthiddenregion;
-
- VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
- {
- last = lastcol;
- current = firstcol;
- next = firstcol;
- lasthiddenregion = -1;
-
- try
- {
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- 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;
- }
- }
-
- lasthiddenregion = 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 = lasthiddenregion + 1;
- 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++;
- }
- lasthiddenregion = -1;
- }
- } finally
- {
- if (useCopy)
- {
- 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)
- && (lasthiddenregion + 1 < localHidden.size()))
- {
- // still some more hidden regions
- if (next + 1 < localHidden.get(lasthiddenregion + 1)[0])
- {
- // next+1 is still before the next hidden region
- next++;
- }
- else if ((next + 1 >= localHidden.get(lasthiddenregion + 1)[0])
- && (next + 1 <= localHidden.get(lasthiddenregion + 1)[1]))
- {
- // next + 1 is in the next hidden region
- next = localHidden.get(lasthiddenregion + 1)[1] + 1;
- lasthiddenregion++;
- }
- }
- 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.
- */
- 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 as visible
- * column positions.
- */
- public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
- {
- private List<int[]> vcontigs = new ArrayList<>();
-
- private int currentPosition = 0;
-
- private boolean endsAtHidden = true;
-
- VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
- {
- try
- {
- if (usecopy)
- {
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- int blockStart = start;
- int blockEnd = end;
- int hiddenSoFar = 0;
- int visSoFar = 0;
- int maxVisible = end - start;
-
- // 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 too in
-
- // 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] <= blockEnd))
- {
- int[] region = hiddenColumns.get(i);
-
- blockEnd = Math.min(blockEnd, region[0] - 1);
-
- int[] contig = new int[] { blockStart, blockEnd };
- vcontigs.add(contig);
-
- visSoFar += blockEnd - blockStart + 1;
- blockStart = region[1] + 1;
- blockEnd = end + hiddenSoFar;
- hiddenSoFar += region[1] - region[0] + 1;
-
- i++;
- }
- if (visSoFar < maxVisible)
- {
- blockEnd = blockStart + maxVisible - visSoFar;
- int[] contig = new int[] { blockStart,
- blockEnd };
- vcontigs.add(contig);
-
- endsAtHidden = false;
- }
- }
- else
- {
- int[] contig = new int[] { start, end };
- vcontigs.add(contig);
- 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;
- }
- }
-