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();
+
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
{
hiddenColumns.add(it.next());
}
+ cursor.resetCursor(hiddenColumns);
}
}
} finally
{ region[0] - offset, region[1] - offset });
}
}
+ cursor.resetCursor(hiddenColumns);
}
} finally
{
if (hiddenColumns != null)
{
+ result += cursor.getHiddenOffset(column);
+
+ /*
Iterator<int[]> it = hiddenColumns.iterator();
while (it.hasNext())
{
{
result += region[1] - region[0] + 1;
}
- }
+ }*/
}
return result;
if (hiddenColumns != null)
{
Iterator<int[]> it = new RegionsIterator(0,
- hiddenColumn);
+ hiddenColumn, hiddenColumns, cursor);
while (it.hasNext())
{
region = it.next();
// 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))
{
{
LOCK.readLock().lock();
- Iterator<int[]> it = new ReverseRegionsIterator(0, alPos);
+ Iterator<int[]> it = new ReverseRegionsIterator(0, alPos,
+ hiddenColumns);
while (it.hasNext())
{
int[] region = it.next();
added = insertRangeAtRegion(i, start, end);
} // for
}
+ if (!wasAlreadyLocked)
+ {
+ cursor.resetCursor(hiddenColumns);
+ }
} finally
{
if (!wasAlreadyLocked)
{
LOCK.readLock().lock();
- Iterator<int[]> it = new RegionsIterator(column, column);
+ Iterator<int[]> it = new RegionsIterator(column, column,
+ hiddenColumns, cursor);
while (it.hasNext())
{
int[] region = it.next();
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);
} finally
{
LOCK.writeLock().unlock();
}
}
hiddenColumns = null;
+ cursor.resetCursor(hiddenColumns);
} finally
{
LOCK.writeLock().unlock();
try
{
LOCK.writeLock().lock();
- Iterator<int[]> it = new RegionsIterator(start, start);
+ Iterator<int[]> it = new RegionsIterator(start, start, hiddenColumns,
+ cursor);
while (it.hasNext())
{
int[] region = it.next();
{
hiddenColumns = null;
}
+ cursor.resetCursor(hiddenColumns);
} finally
{
LOCK.writeLock().unlock();
}
hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
} finally
{
LOCK.writeLock().unlock();
lastSet = inserts.nextClearBit(firstSet);
hideColumns(firstSet, lastSet - 1);
}
+ cursor.resetCursor(hiddenColumns);
} finally
{
LOCK.writeLock().unlock();
{
LOCK.readLock().unlock();
}
-
}
/**
int[] reveal = null;
Iterator<int[]> it = new RegionsIterator(adjres - 2,
- adjres + 2);
+ adjres + 2, hiddenColumns, cursor);
while (it.hasNext())
{
int[] region = it.next();
*/
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;
- }
}
/**
--- /dev/null
+package jalview.datamodel;
+
+import java.util.List;
+
+public class HiddenColumnsCursor
+{
+ // absolute position of first hidden column
+ private int firstColumn;
+
+ // absolute position of last hidden column
+ private int lastColumn;
+
+ // index of last visited region
+ private int regionIndex;
+
+ // number of hidden columns before last visited region
+ private int hiddenSoFar;
+
+ // flag to indicate if current cursor settings are valid
+ private boolean isValid;
+
+ private List<int[]> hiddenColumns;
+
+ protected HiddenColumnsCursor()
+ {
+ isValid = false;
+ }
+
+ /**
+ * Set the cursor to a position
+ *
+ * @param first
+ * absolute position of first hidden column
+ * @param last
+ * absolute position of last hidden column
+ * @param index
+ * index of last visited region
+ * @param hiddenCount
+ * number of hidden columns before last visited region
+ */
+ protected void resetCursor(// int first, int last, int index, int hiddenCount,
+ List<int[]> hiddenCols)
+ {
+ isValid = true;
+ if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
+ {
+ hiddenColumns = hiddenCols;
+ firstColumn = hiddenColumns.get(0)[0];
+ lastColumn = hiddenColumns.get(hiddenColumns.size() - 1)[1];
+ regionIndex = 0;
+ hiddenSoFar = 0;
+ }
+ }
+
+ protected void updateCursor(int index, int hiddenCount)
+ {
+ regionIndex = index;
+ hiddenSoFar = hiddenCount;
+ }
+
+ /**
+ * Get the index of the region that column is within (if column is hidden) or
+ * which is to the right of column (if column is visible). If no hidden
+ * columns are to the right, will return size of hiddenColumns. If hidden
+ * columns is empty returns -1.
+ *
+ * @param column
+ * absolute position of a column in the alignment
+ * @return region index
+ */
+ protected int findRegionForColumn(int column)
+ {
+ if (hiddenColumns == null)
+ {
+ return -1;
+ }
+
+ if ((hiddenColumns.get(regionIndex)[0] <= column)
+ && (hiddenColumns.get(regionIndex)[1] >= column))
+ {
+ // we hit the jackpot
+ return regionIndex;
+ }
+ else if (column < firstColumn)
+ {
+ return 0;
+ }
+ else if (column > lastColumn)
+ {
+ return hiddenColumns.size();
+ }
+ else if (column > hiddenColumns.get(regionIndex)[1])
+ {
+ // iterate from where we are now, if we're lucky we'll be close by
+ // (but still better than iterating from 0)
+ while ((regionIndex < hiddenColumns.size())
+ && (hiddenColumns.get(regionIndex)[0] <= column))
+ {
+ int[] region = hiddenColumns.get(regionIndex);
+ hiddenSoFar += region[1] - region[0] + 1;
+ regionIndex++;
+ }
+
+ }
+ else // (column < hiddenColumns.get(regionIndex)[0])
+ {
+ int lastHidden = 0;
+ while ((regionIndex >= 0)
+ && (hiddenColumns.get(regionIndex)[0] > column))
+ {
+ int[] region = hiddenColumns.get(regionIndex);
+ hiddenSoFar -= lastHidden;
+ lastHidden = region[1] - region[0] + 1;
+ regionIndex--;
+ }
+ hiddenSoFar -= lastHidden;
+ }
+ return regionIndex;
+ }
+
+ protected int getHiddenOffset(int column)
+ {
+ if (hiddenColumns == null)
+ {
+ return -1;
+ }
+
+ if (column < firstColumn)
+ {
+ return 0;
+ }
+ else if ((regionIndex < hiddenColumns.size())
+ && (hiddenColumns.get(regionIndex)[0] <= column
+ + hiddenSoFar))
+ {
+
+ // iterate from where we are now, if we're lucky we'll be close by
+ // (but still better than iterating from 0)
+ while ((regionIndex < hiddenColumns.size())
+ && (hiddenColumns.get(regionIndex)[0] <= column
+ + hiddenSoFar))
+ {
+ int[] region = hiddenColumns.get(regionIndex);
+ hiddenSoFar += region[1] - region[0] + 1;
+ regionIndex++;
+ }
+ }
+ else if (regionIndex < hiddenColumns.size())
+ {
+ int lastHidden = hiddenColumns.get(regionIndex)[1]
+ - hiddenColumns.get(regionIndex)[0] + 1;
+
+ while ((regionIndex >= 0)
+ && (hiddenColumns.get(regionIndex)[0] <= column + hiddenSoFar
+ - lastHidden))
+ {
+ int[] region = hiddenColumns.get(regionIndex);
+ hiddenSoFar -= lastHidden;
+ lastHidden = region[1] - region[0] + 1;
+ regionIndex--;
+ }
+
+ }
+
+ int result = hiddenSoFar;
+ if ((regionIndex >= 0) && (regionIndex < hiddenColumns.size())
+ && (hiddenColumns.get(regionIndex)[0] <= column + hiddenSoFar)
+ && (hiddenColumns.get(regionIndex)[1] >= column + hiddenSoFar))
+ {
+ int[] region = hiddenColumns.get(regionIndex);
+ result += region[1] - region[0] + 1;
+ }
+
+ return result;
+ }
+
+ /* public int findVisiblePositionFromAbsolute(int column)
+ {
+
+ }
+
+ public int findAbsolutePositionFromVisible(int column)
+ {
+
+ }*/
+}
git://source.jalview.org / jalview.git / commitdiff