import java.util.BitSet;
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
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
{
if (copy.hiddenColumns != null)
{
- hiddenColumns = copy.copyHiddenRegionsToArrayList(0);
+ hiddenColumns = new ArrayList<>();
+ Iterator<int[]> it = copy.iterator();
+ while (it.hasNext())
+ {
+ 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
{
{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
- while (it.hasNext())
+ if (hiddenColumns != null)
{
- int[] range = it.next();
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
- if (!it.hasNext())
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- regionBuilder.deleteCharAt(0);
+ int[] range = it.next();
+ regionBuilder.append(delimiter).append(range[0]).append(between)
+ .append(range[1]);
+ if (!it.hasNext())
+ {
+ regionBuilder.deleteCharAt(0);
+ }
}
}
return regionBuilder.toString();
try
{
LOCK.readLock().lock();
- int size = 0;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
- while (it.hasNext())
+
+ if (numColumns == 0 && hiddenColumns != null)
{
- int[] range = it.next();
- size += range[1] - range[0] + 1;
+ // numColumns is out of date, so recalculate
+ int size = 0;
+ if (hiddenColumns != null)
+ {
+ 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();
return false;
}
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = hiddenColumns.iterator();
Iterator<int[]> thatit = that.iterator();
while (it.hasNext())
{
LOCK.readLock().lock();
int result = column;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
- while (it.hasNext())
+ if (hiddenColumns != null)
{
- 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 LocalBoundedHiddenColsIterator(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)
- {
- return 0;
- }
- else
+ int[] region = hiddenColumns.get(index);
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
- 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
{
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,
+ hiddenColumns);
- 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 absolute (visible) alignmentPosition to find the next hidden
+ * column for
*/
public int getHiddenBoundaryRight(int alPos)
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
- int index = 0;
- do
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+ if (index < hiddenColumns.size())
{
int[] region = hiddenColumns.get(index);
if (alPos < region[0])
{
return region[0];
}
-
- index++;
- } while (index < hiddenColumns.size());
+ 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;
} 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 absolute (visible) alignmentPosition to find the previous
+ * hidden column for
*/
public int getHiddenBoundaryLeft(int alPos)
{
if (hiddenColumns != null)
{
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
- }
-
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * 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
- {
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
+ if (index > 0)
{
- int[] region = hiddenColumns.get(index);
- if (pos > region[1])
- {
- return index;
- }
-
- index--;
- } while (index > -1);
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
}
-
- return -1;
+ return alPos;
} 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
}
+ if (!wasAlreadyLocked)
+ {
+ cursor.resetCursor(hiddenColumns);
+
+ // reset the number of columns so they will be recounted
+ numColumns = 0;
+ }
} finally
{
if (!wasAlreadyLocked)
}
}
+ /**
+ * Insert [start, range] at the region at index i in hiddenColumns, if
+ * feasible
+ *
+ * @param i
+ * index to insert at
+ * @param start
+ * start of range to insert
+ * @param end
+ * end of range to insert
+ * @return true if range was successfully inserted
+ */
+ 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.subList(i + 1, i + 2).clear();
+ }
+ 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();
- 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();
}
}
- 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)
{
StringBuffer visibleSeq = new StringBuffer();
Iterator<int[]> blocks = new VisibleContigsIterator(start,
- end + 1, false);
+ end + 1, hiddenColumns);
while (blocks.hasNext())
{
// Simply walk along the sequence whilst watching for hidden column
// boundaries
- Iterator<int[]> regions = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> regions = hiddenColumns.iterator();
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;
Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
- false);
+ hiddenColumns);
int copylength;
int annotationLength;
}
els = new Annotation[annotationLength];
- annels.addElement(els);
+ annels.add(els);
System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
copylength);
w += annotationLength;
{
hideColumns(r[0], r[1]);
}
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
try
{
LOCK.writeLock().lock();
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
- 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 LocalBoundedHiddenColsIterator();
- 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);
- hiddenColumns.remove(region);
- break;
- }
- else if (start < region[0])
- {
- break; // passed all possible matching regions
- }
- }
+ if (hiddenColumns.isEmpty())
+ {
+ hiddenColumns = null;
+ numColumns = 0;
+ }
+ else
+ {
+ numColumns -= colsToRemove;
+ }
+ cursor.updateForDeletedRegion(hiddenColumns);
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
+ }
+ }
}
} finally
{
// of
// preceding visible gaps
// update hidden columns at the same time
- Iterator<int[]> regions = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> regions = hiddenColumns.iterator();
ArrayList<int[]> newhidden = new ArrayList<>();
int numGapsBefore = 0;
}
hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
{
LOCK.readLock().lock();
int hashCode = 1;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] hidden = it.next();
lastSet = inserts.nextClearBit(firstSet);
hideColumns(firstSet, lastSet - 1);
}
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
{
return;
}
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] range = it.next();
return new int[] { startPos, endPos };
}
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator();
+ Iterator<int[]> it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] range = it.next();
{
LOCK.readLock().unlock();
}
-
}
/**
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
- Iterator<int[]> it = new LocalBoundedHiddenColsIterator(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.
- * Works with the actual hidden columns collection (so locking before use may
- * be required).
- */
- private class LocalBoundedHiddenColsIterator 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[] nextRegion = null;
-
- LocalBoundedHiddenColsIterator(int lowerBound, int upperBound)
- {
- init(lowerBound, upperBound);
- }
-
- LocalBoundedHiddenColsIterator()
- {
- 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
- * @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)
- {
- 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()
- {
- int[] region = nextRegion;
- currentPosition++;
- if (currentPosition < hiddenColumns.size())
- {
- 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.
- */
- 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;
-
- // local copy or reference to hiddenColumns
- private List<int[]> localHidden;
-
- 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