* use an iterator obtained from one of:
*
* - getBoundedIterator: iterates over the hidden regions, within some bounds,
- * returning absolute positions
+ * returning *absolute* positions
*
* - getBoundedStartIterator: iterates over the start positions of hidden
- * regions, within some bounds, returning visible positions
+ * regions, within some bounds, returning *visible* positions
*
* - getVisContigsIterator: iterates over visible regions in a range, returning
- * absolute positions
+ * *absolute* positions
*
* - getVisibleColsIterator: iterates over the visible *columns*
*
* numbering begins at 0 throughout this class.
*
* @author kmourao
- *
+ */
+
+/* Implementation notes:
+ *
+ * Methods which change the hiddenColumns collection should use a writeLock to
+ * prevent other threads accessing the hiddenColumns collection while changes
+ * are being made. They should also reset the hidden columns cursor, and either
+ * update the hidden columns count, or set it to 0 (so that it will later be
+ * updated when needed).
+ *
+ *
+ * Methods which only need read access to the hidden columns collection should
+ * use a readLock to prevent other threads changing the hidden columns
+ * collection while it is in use.
*/
public class HiddenColumns
{
private static final int HASH_MULTIPLIER = 31;
+ private static final int NUMCOLUMNS_RESET = -1; // value of numColumns if it
+ // needs to be recalculated
+
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
/*
{
}
- /*
- * Methods which change the hiddenColumns collection. These methods should
- * use a writeLock to prevent other threads accessing the hiddenColumns
- * collection while changes are being made. They should also reset the hidden
- * columns cursor, and either update the hidden columns count, or set it to 0
- * (so that it will later be updated when needed).
- */
-
/**
* Copy constructor
*
numColumns += region[1] - region[0] + 1;
}
}
- cursor.resetCursor(hiddenColumns);
+ cursor = new HiddenColumnsCursor(hiddenColumns);
}
} finally
{
// reset the cursor to just before our insertion point: this saves
// a lot of reprocessing in large alignments
- cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount);
+ cursor = new HiddenColumnsCursor(hiddenColumns, previndex,
+ prevHiddenCount);
// reset the number of columns so they will be recounted
- numColumns = 0;
+ resetNumColumns();
} finally
{
}
region[1] = Math.max(nextRegion[1], end);
- // in theory this is faster than hiddenColumns.remove(i+1)
- // benchmarking results a bit ambivalent
- hiddenColumns.subList(i + 1, i + 2).clear();
+ // in theory hiddenColumns.subList(i + 1, i + 2).clear() is faster than
+ // hiddenColumns.remove(i+1) but benchmarking results a bit ambivalent
+ hiddenColumns.remove(i + 1);
}
added = true;
}
{
hideColumns(r[0], r[1]);
}
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ resetNumColumns();
} finally
{
LOCK.writeLock().unlock();
}
}
hiddenColumns.clear();
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ resetNumColumns();
} finally
{
if (hiddenColumns.isEmpty())
{
- hiddenColumns.clear();
- numColumns = 0;
+ resetNumColumns();
}
else
{
}
}
-
-
-
- /*
- * Methods which only need read access to the hidden columns collection.
- * These methods should use a readLock to prevent other threads changing
- * the hidden columns collection while it is in use.
- */
-
/**
* Output regions data as a string. String is in the format:
* reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
{
LOCK.readLock().lock();
- if (numColumns == 0)
+ if (numColumns == NUMCOLUMNS_RESET)
{
// numColumns is out of date, so recalculate
int size = 0;
}
/**
+ * Reset numColumns so that it gets recalculated. Currently the code does not
+ * recalculate numColumns on hide/reveal as it requires a full sweep of the
+ * hidden columns collection / smarter updating. Placeholder here if later on
+ * a recalculation is added.
+ */
+ private void resetNumColumns()
+ {
+ numColumns = NUMCOLUMNS_RESET;
+ }
+
+ /**
* Get the number of distinct hidden regions
*
* @return number of regions
* @return the index of the next hidden column, or alPos if there is no next
* hidden column
*/
- public int getHiddenBoundaryRight(int alPos)
+ public int getNextHiddenBoundary(boolean left, int alPos)
{
try
{
if (!hiddenColumns.isEmpty())
{
int index = cursor.findRegionForColumn(alPos).getRegionIndex();
- if (index < hiddenColumns.size())
+
+ if (left && index > 0)
+ {
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
+ else if (!left && index < hiddenColumns.size())
{
int[] region = hiddenColumns.get(index);
if (alPos < region[0])
}
/**
- * This method returns the leftmost limit of a region of an alignment with
- * hidden columns. In otherwords, the previous hidden column.
- *
- * @param alPos
- * the absolute (visible) alignmentPosition to find the previous
- * hidden column for
- */
- public int getHiddenBoundaryLeft(int alPos)
- {
- try
- {
- LOCK.readLock().lock();
-
- if (!hiddenColumns.isEmpty())
- {
- int index = cursor.findRegionForColumn(alPos).getRegionIndex();
-
- if (index > 0)
- {
- int[] region = hiddenColumns.get(index - 1);
- return region[1];
- }
- }
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
-
- /**
* Answers if a column in the alignment is visible
*
* @param column
}
/**
- * 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)
- {
- try
- {
- LOCK.readLock().lock();
- int iSize = seqs.length;
- String[] selections = new String[iSize];
- if (!hiddenColumns.isEmpty())
- {
- for (int i = 0; i < iSize; i++)
- {
- StringBuilder visibleSeq = new StringBuilder();
-
- Iterator<int[]> blocks = new VisibleContigsIterator(start,
- end + 1, hiddenColumns);
-
- while (blocks.hasNext())
- {
- int[] block = blocks.next();
- if (blocks.hasNext())
- {
- visibleSeq
- .append(seqs[i].getSequence(block[0], block[1] + 1));
- }
- else
- {
- visibleSeq
- .append(seqs[i].getSequence(block[0], block[1]));
- }
- }
-
- selections[i] = visibleSeq.toString();
- }
- }
- else
- {
- for (int i = 0; i < iSize; i++)
- {
- selections[i] = seqs[i].getSequenceAsString(start, end);
- }
- }
-
- return selections;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * Locate the first position visible for this sequence. If seq isn't visible
- * then return the position of the left side of the hidden boundary region.
- *
- * @param seq
- * sequence to find position for
- * @return visible start position
- */
- public int locateVisibleStartOfSequence(SequenceI seq)
- {
- try
- {
- LOCK.readLock().lock();
- int start = 0;
-
- if (hiddenColumns.isEmpty())
- {
- return seq.findIndex(seq.getStart()) - 1;
- }
-
- // Simply walk along the sequence whilst watching for hidden column
- // boundaries
- Iterator<int[]> regions = hiddenColumns.iterator();
- int hideStart = seq.getLength();
- int hideEnd = -1;
- int visPrev = 0;
- int visNext = 0;
- boolean foundStart = false;
-
- // step through the non-gapped positions of the sequence
- for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
- {
- // get alignment position of this residue in the sequence
- int p = seq.findIndex(i) - 1;
-
- // update hidden region start/end
- while (hideEnd < p && regions.hasNext())
- {
- int[] region = regions.next();
- visPrev = visNext;
- visNext += region[0] - visPrev;
- hideStart = region[0];
- hideEnd = region[1];
- }
- if (hideEnd < p)
- {
- hideStart = seq.getLength();
- }
- // update visible boundary for sequence
- if (p < hideStart)
- {
- start = p;
- foundStart = true;
- }
- }
-
- if (foundStart)
- {
- return absoluteToVisibleColumn(start);
- }
- // otherwise, sequence was completely hidden
- return visPrev;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
-
- /**
*
* @return true if there are columns hidden
*/
{
LOCK.readLock().lock();
int hashCode = 1;
+
for (int[] hidden : hiddenColumns)
{
hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
lastSet = inserts.nextClearBit(firstSet);
hideColumns(firstSet, lastSet - 1);
}
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ resetNumColumns();
} finally
{
LOCK.writeLock().unlock();
}
hiddenColumns.subList(startindex, endindex + 1).clear();
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ resetNumColumns();
}
} finally
{
git://source.jalview.org / jalview.git / blobdiff