import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
-import java.util.NoSuchElementException;
import java.util.concurrent.locks.ReentrantReadWriteLock;
public class HiddenColumns
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+ private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+ private int numColumns = 0;
+
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
{
hiddenColumns.add(it.next());
}
+ cursor.resetCursor(hiddenColumns);
}
}
} finally
if (copy != null)
{
hiddenColumns = new ArrayList<>();
+ numColumns = 0;
Iterator<int[]> it = copy.getBoundedIterator(start, end);
while (it.hasNext())
{
hiddenColumns.add(
new int[]
{ region[0] - offset, region[1] - offset });
+ numColumns += region[1] - region[0] + 1;
}
}
+ cursor.resetCursor(hiddenColumns);
}
} finally
{
try
{
LOCK.readLock().lock();
- int size = 0;
- if (hiddenColumns != null)
+
+ if (numColumns == 0 && hiddenColumns != null)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ // numColumns is out of date, so recalculate
+ int size = 0;
+ if (hiddenColumns != null)
{
- int[] range = it.next();
- size += range[1] - range[0] + 1;
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
+ {
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
+ }
}
+ numColumns = size;
}
- return size;
+
+ return numColumns;
} finally
{
LOCK.readLock().unlock();
if (hiddenColumns != null)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
+ result += cursor.getHiddenOffset(column).getHiddenSoFar();
}
return result;
{
LOCK.readLock().lock();
int result = hiddenColumn;
- int[] region = null;
+
if (hiddenColumns != null)
{
- Iterator<int[]> it = new RegionsIterator(0,
- hiddenColumn);
- while (it.hasNext())
- {
- region = it.next();
- if (hiddenColumn > region[1])
- {
- result -= region[1] + 1 - region[0];
- }
- }
-
- if (region != null && hiddenColumn >= region[0]
- && hiddenColumn <= region[1])
+ HiddenCursorPosition cursorPos = cursor
+ .findRegionForColumn(hiddenColumn);
+ int index = cursorPos.getRegionIndex();
+ int hiddenBeforeCol = cursorPos.getHiddenSoFar();
+
+ // just subtract hidden cols count - this works fine if column is
+ // visible
+ result = hiddenColumn - hiddenBeforeCol;
+
+ // now check in case column is hidden - it will be in the returned
+ // hidden region
+ if (index < hiddenColumns.size())
{
- // Here the hidden column is within a region, so
- // we want to return the position of region[0]-1, adjusted for any
- // 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.
-
- // However, if the region begins at 0 we cannot return region[0]-1
- // just return 0
- if (region[0] == 0)
+ int[] region = hiddenColumns.get(index);
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
- return 0;
- }
- else
- {
- return result - (hiddenColumn - region[0] + 1);
+ // actually col is hidden, return region[0]-1
+ // unless region[0]==0 in which case return 0
+ if (region[0] == 0)
+ {
+ result = 0;
+ }
+ else
+ {
+ result = region[0] - 1 - hiddenBeforeCol;
+ }
}
}
}
+
return result; // return the shifted position after removing hidden
// columns.
} finally
// in case startColumn is in a hidden region, move it to the left
int start = adjustForHiddenColumns(findColumnPosition(startColumn));
- Iterator<int[]> it = new ReverseRegionsIterator(0, start);
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start,
+ hiddenColumns);
while (it.hasNext() && (distance > 0))
{
* hidden columns. In otherwords, the next hidden column.
*
* @param alPos
- * the (visible) alignmentPosition to find the next hidden column for
+ * the absolute (visible) alignmentPosition to find the next hidden
+ * column for
*/
public int getHiddenBoundaryRight(int alPos)
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+ if (index < hiddenColumns.size())
{
- int[] region = it.next();
+ int[] region = hiddenColumns.get(index);
if (alPos < region[0])
{
return region[0];
}
+ else if ((alPos <= region[1])
+ && (index + 1 < hiddenColumns.size()))
+ {
+ // alPos is within a hidden region, return the next one
+ // if there is one
+ region = hiddenColumns.get(index + 1);
+ return region[0];
+ }
}
}
return alPos;
* hidden columns. In otherwords, the previous hidden column.
*
* @param alPos
- * the (visible) alignmentPosition to find the previous hidden column
- * for
+ * the absolute (visible) alignmentPosition to find the previous
+ * hidden column for
*/
public int getHiddenBoundaryLeft(int alPos)
{
{
LOCK.readLock().lock();
- Iterator<int[]> it = new ReverseRegionsIterator(0, alPos);
- while (it.hasNext())
+ if (hiddenColumns != null)
{
- int[] region = it.next();
- if (alPos > region[1])
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+
+ if (index > 0)
{
+ int[] region = hiddenColumns.get(index - 1);
return region[1];
}
}
-
return alPos;
} finally
{
added = insertRangeAtRegion(i, start, end);
} // for
}
+ if (!wasAlreadyLocked)
+ {
+ cursor.resetCursor(hiddenColumns);
+
+ // reset the number of columns so they will be recounted
+ numColumns = 0;
+ }
} finally
{
if (!wasAlreadyLocked)
{
LOCK.readLock().lock();
- Iterator<int[]> it = new RegionsIterator(column, column);
- while (it.hasNext())
+ int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- int[] region = it.next();
+ int[] region = hiddenColumns.get(regionindex);
if (column >= region[0] && column <= region[1])
{
return false;
}
}
-
return true;
+
} finally
{
LOCK.readLock().unlock();
StringBuffer visibleSeq = new StringBuffer();
Iterator<int[]> blocks = new VisibleContigsIterator(start,
- end + 1, false);
+ end + 1, hiddenColumns);
while (blocks.hasNext())
{
int w = 0;
Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
- false);
+ hiddenColumns);
int copylength;
int annotationLength;
{
hideColumns(r[0], r[1]);
}
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
try
{
LOCK.writeLock().lock();
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ if (hiddenColumns != null)
{
- int[] region = it.next();
- for (int j = region[0]; j < region[1] + 1; j++)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- sel.addElement(j);
+ int[] region = it.next();
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
}
+ hiddenColumns = null;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
}
- hiddenColumns = null;
} finally
{
LOCK.writeLock().unlock();
try
{
LOCK.writeLock().lock();
- Iterator<int[]> it = new RegionsIterator(start, start);
- while (it.hasNext())
+
+ if (hiddenColumns != null)
{
- int[] region = it.next();
- if (start == region[0])
+ int regionIndex = cursor.findRegionForColumn(start)
+ .getRegionIndex();
+
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
{
- for (int j = region[0]; j < region[1] + 1; j++)
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
{
- sel.addElement(j);
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
+ int colsToRemove = region[1] - region[0] + 1;
+ hiddenColumns.remove(regionIndex);
+
+ if (hiddenColumns.isEmpty())
+ {
+ hiddenColumns = null;
+ numColumns = 0;
+ }
+ else
+ {
+ numColumns -= colsToRemove;
+ }
+ cursor.updateForDeletedRegion(hiddenColumns);
+
}
- it.remove();
- break;
- }
- else if (start < region[0])
- {
- break; // passed all possible matching regions
}
}
-
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
} finally
{
LOCK.writeLock().unlock();
}
hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
lastSet = inserts.nextClearBit(firstSet);
hideColumns(firstSet, lastSet - 1);
}
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
{
LOCK.readLock().unlock();
}
-
}
/**
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
- Iterator<int[]> it = new RegionsIterator(adjres - 2,
- adjres + 2);
- while (it.hasNext())
+
+ if (hiddenColumns != null)
{
- int[] region = it.next();
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
+ // look for a region ending just before adjres
+ int regionindex = cursor.findRegionForColumn(adjres - 1)
+ .getRegionIndex();
+ if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[1] == adjres - 1)
{
- reveal = region;
- break;
+ reveal = hiddenColumns.get(regionindex);
+ }
+ // check if the region ends just after adjres
+ else if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
+ {
+ reveal = hiddenColumns.get(regionindex);
+ }
+ // or try the next region
+ else
+ {
+ regionindex++;
+ if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
+ {
+ reveal = hiddenColumns.get(regionindex);
+ }
}
}
return reveal;
+
} finally
{
LOCK.readLock().unlock();
*/
public Iterator<int[]> iterator()
{
- return new BoundedHiddenColsIterator();
+ try
+ {
+ LOCK.readLock().lock();
+ return new BoundedHiddenColsIterator(hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
*/
public Iterator<int[]> getBoundedIterator(int start, int end)
{
- return new BoundedHiddenColsIterator(start, end);
+ try
+ {
+ LOCK.readLock().lock();
+ return new BoundedHiddenColsIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
*/
public Iterator<Integer> getBoundedStartIterator(int start, int end)
{
- return new BoundedStartRegionIterator(start, end, true);
+ try
+ {
+ LOCK.readLock().lock();
+ return new BoundedStartRegionIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
*/
public Iterator<Integer> getVisibleColsIterator(int start, int end)
{
- return new VisibleColsIterator(start, end);
+ try
+ {
+ LOCK.readLock().lock();
+ return new VisibleColsIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
*/
public Iterator<int[]> getVisContigsIterator(int start, int end)
{
- // return new VisibleBlocksIterator(start, end, true)
- return new VisibleContigsIterator(start, end, true);
+ try
+ {
+ LOCK.readLock().lock();
+ return new VisibleContigsIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
}
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<>();
- }
+ return new VisibleContigsIterator(start, end + 1, hiddenColumns);
} 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();
- }
+ LOCK.readLock().unlock();
}
}
-
- @Override
- public boolean hasNext()
- {
- return (currentPosition < vcontigs.size());
- }
-
- @Override
- public int[] next()
- {
- int[] result = vcontigs.get(currentPosition);
- currentPosition++;
- return result;
- }
}
/**
i++;
}
- if (visSoFar < end - start)
+ if (visSoFar < end - start + 1)
{
// the number of visible columns we've accounted for is less than
// the number specified by end-start; work out the end position of
git://source.jalview.org / jalview.git / blobdiff