* 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 HiddenColumnsCursor cursor = new HiddenColumnsCursor();
/*
- * cache of the number of hidden columns
+ * cache of the number of hidden columns: must be kept up to date by methods
+ * which add or remove hidden columns
*/
private int numColumns = 0;
{
}
- /*
- * 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
{
if (!hiddenColumns.isEmpty())
{
// set up cursor reset values
- HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start, false);
regionindex = cursorPos.getRegionIndex();
if (regionindex > 0)
}
}
- /*
- * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
- */
+ // new range follows everything else; check first to avoid looping over
+ // whole hiddenColumns collection
if (hiddenColumns.isEmpty()
|| start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
{
hiddenColumns.add(new int[] { start, end });
+ numColumns += end - start + 1;
}
else
{
// reset the cursor to just before our insertion point: this saves
// a lot of reprocessing in large alignments
- cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount);
-
- // reset the number of columns so they will be recounted
- numColumns = 0;
-
+ cursor = new HiddenColumnsCursor(hiddenColumns, previndex,
+ prevHiddenCount);
} finally
{
LOCK.writeLock().unlock();
* insert discontiguous preceding range
*/
hiddenColumns.add(i, new int[] { start, end });
+ numColumns += end - start + 1;
added = true;
}
else if (end <= region[1])
* new range overlaps existing, or is contiguous preceding it - adjust
* start column
*/
+ int oldstart = region[0];
region[0] = Math.min(region[0], start);
+ numColumns += oldstart - region[0]; // new columns are between old and
+ // adjusted starts
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);
+ insertRangeAtOverlap(i, start, end, region);
+ added = true;
+ }
+ return added;
+ }
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
+ /**
+ * Insert a range whose start position overlaps an existing region and/or is
+ * contiguous to the right of the region
+ *
+ * @param i
+ * index to insert at
+ * @param start
+ * start of range to insert
+ * @param end
+ * end of range to insert
+ * @param region
+ * the overlapped/continued region
+ */
+ private void insertRangeAtOverlap(int i, int start, int end, int[] region)
+ {
+ int oldstart = region[0];
+ int oldend = region[1];
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
+
+ numColumns += oldstart - region[0];
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ int endi = i;
+ while (endi < hiddenColumns.size() - 1)
+ {
+ int[] nextRegion = hiddenColumns.get(endi + 1);
+ if (nextRegion[0] > end + 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);
-
- // in theory this is faster than hiddenColumns.remove(i+1)
- // benchmarking results a bit ambivalent
- hiddenColumns.subList(i + 1, i + 2).clear();
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
}
- added = true;
+ numColumns -= nextRegion[1] - nextRegion[0] + 1;
+ region[1] = Math.max(nextRegion[1], end);
+ endi++;
}
- return added;
+ numColumns += region[1] - oldend;
+ hiddenColumns.subList(i + 1, endi + 1).clear();
}
/**
{
hideColumns(r[0], r[1]);
}
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+
} finally
{
LOCK.writeLock().unlock();
}
}
hiddenColumns.clear();
- cursor.resetCursor(hiddenColumns);
+ cursor = new HiddenColumnsCursor(hiddenColumns);
numColumns = 0;
} finally
if (!hiddenColumns.isEmpty())
{
- int regionIndex = cursor.findRegionForColumn(start)
+ int regionIndex = cursor.findRegionForColumn(start, false)
.getRegionIndex();
if (regionIndex != -1 && regionIndex != hiddenColumns.size())
}
int colsToRemove = region[1] - region[0] + 1;
hiddenColumns.remove(regionIndex);
-
- if (hiddenColumns.isEmpty())
- {
- hiddenColumns.clear();
- numColumns = 0;
- }
- else
- {
- numColumns -= colsToRemove;
- }
- cursor.updateForDeletedRegion(hiddenColumns);
+ numColumns -= colsToRemove;
}
}
}
}
}
-
-
-
- /*
- * 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]
*/
public int getSize()
{
- try
- {
- LOCK.readLock().lock();
-
- if (numColumns == 0)
- {
- // numColumns is out of date, so recalculate
- int size = 0;
-
- for (int[] range : hiddenColumns)
- {
- size += range[1] - range[0] + 1;
- }
-
- numColumns = size;
- }
-
- return numColumns;
- } finally
- {
- LOCK.readLock().unlock();
- }
+ return numColumns;
}
/**
}
}
+ /**
+ * Answers true if obj is an instance of HiddenColumns, and holds the same
+ * array of start-end column ranges as this, else answers false
+ */
@Override
public boolean equals(Object obj)
{
if (!hiddenColumns.isEmpty())
{
- result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
+ result += cursor.findRegionForColumn(column, true)
+ .getHiddenSoFar();
}
return result;
if (!hiddenColumns.isEmpty())
{
HiddenCursorPosition cursorPos = cursor
- .findRegionForColumn(hiddenColumn);
+ .findRegionForColumn(hiddenColumn, false);
int index = cursorPos.getRegionIndex();
int hiddenBeforeCol = cursorPos.getHiddenSoFar();
* @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
{
LOCK.readLock().lock();
if (!hiddenColumns.isEmpty())
{
- int index = cursor.findRegionForColumn(alPos).getRegionIndex();
- if (index < hiddenColumns.size())
+ int index = cursor.findRegionForColumn(alPos, false)
+ .getRegionIndex();
+
+ 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
{
LOCK.readLock().lock();
- int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
- if (regionindex > -1 && regionindex < hiddenColumns.size())
- {
- int[] region = hiddenColumns.get(regionindex);
- // already know that column <= region[1] as cursor returns containing
- // region or region to right
- if (column >= region[0])
- {
- return false;
- }
- }
- return true;
-
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * 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++)
+ int regionindex = cursor.findRegionForColumn(column, false)
+ .getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- StringBuilder visibleSeq = new StringBuilder();
-
- Iterator<int[]> blocks = new VisibleContigsIterator(start,
- end + 1, hiddenColumns);
-
- while (blocks.hasNext())
+ int[] region = hiddenColumns.get(regionindex);
+ // already know that column <= region[1] as cursor returns containing
+ // region or region to right
+ if (column >= region[0])
{
- 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]));
- }
+ return false;
}
-
- 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;
}
}
+ return 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];
*/
public void hideColumns(BitSet inserts)
{
+ hideColumns(inserts, 0, inserts.length() - 1);
+ }
+
+ /**
+ * Hide columns corresponding to the marked bits, within the range
+ * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+ *
+ * @param tohide
+ * columns mapped to bits starting from zero
+ * @param start
+ * start of range to hide columns within
+ * @param end
+ * end of range to hide columns within
+ */
+ private void hideColumns(BitSet tohide, int start, int end)
+ {
try
{
LOCK.writeLock().lock();
- for (int firstSet = inserts
- .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
+ for (int firstSet = tohide
+ .nextSetBit(start), lastSet = start; firstSet >= start
+ && lastSet <= end; firstSet = tohide
.nextSetBit(lastSet))
{
- lastSet = inserts.nextClearBit(firstSet);
- hideColumns(firstSet, lastSet - 1);
+ lastSet = tohide.nextClearBit(firstSet);
+ if (lastSet <= end)
+ {
+ hideColumns(firstSet, lastSet - 1);
+ }
+ else if (firstSet <= end)
+ {
+ hideColumns(firstSet, end);
+ }
}
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
} finally
{
LOCK.writeLock().unlock();
/**
* Hide columns corresponding to the marked bits, within the range
* [start,end]. Entries in tohide which are outside [start,end] are ignored.
+ * NB Existing entries in [start,end] are cleared.
*
* @param tohide
* columns mapped to bits starting from zero
* @param end
* end of range to hide columns within
*/
- public void hideColumns(BitSet tohide, int start, int end)
+ public void clearAndHideColumns(BitSet tohide, int start, int end)
{
clearHiddenColumnsInRange(start, end);
-
- // make sure only bits between start and end are set
- if (!tohide.isEmpty())
- {
- tohide.clear(0, start);
- tohide.clear(Math.min(end + 1, tohide.length() + 1),
- tohide.length() + 1);
- }
-
- hideColumns(tohide);
+ hideColumns(tohide, start, end);
}
/**
if (!hiddenColumns.isEmpty())
{
- HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+ HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
int index = pos.getRegionIndex();
- int startindex = index; // first index in hiddenColumns to remove
if (index != -1 && index != hiddenColumns.size())
{
if (region[0] < start && region[1] >= start)
{
// region contains start, truncate so that it ends just before start
+ numColumns -= region[1] - start + 1;
region[1] = start - 1;
- startindex++;
+ index++;
}
- }
-
- pos = cursor.findRegionForColumn(end);
- index = pos.getRegionIndex();
- int endindex = index - 1; // last index in hiddenColumns to remove
- if (index != -1 && index != hiddenColumns.size())
- {
- // regionIndex is the region which either contains end
- // or lies to the right of end
- int[] region = hiddenColumns.get(index);
- if (region[0] <= end && region[1] > end)
+ int endi = index;
+ while (endi < hiddenColumns.size())
{
- // region contains end, truncate so that it starts just after end
- region[0] = end + 1;
+ region = hiddenColumns.get(endi);
+
+ if (region[1] > end)
+ {
+ if (region[0] <= end)
+ {
+ // region contains end, truncate so it starts just after end
+ numColumns -= end - region[0] + 1;
+ region[0] = end + 1;
+ }
+ break;
+ }
+
+ numColumns -= region[1] - region[0] + 1;
+ endi++;
}
+ hiddenColumns.subList(index, endi).clear();
+
}
- hiddenColumns.subList(startindex, endindex + 1).clear();
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ cursor = new HiddenColumnsCursor(hiddenColumns);
}
} finally
{
if (!hiddenColumns.isEmpty())
{
// look for a region ending just before adjres
- int regionindex = cursor.findRegionForColumn(adjres - 1)
+ int regionindex = cursor.findRegionForColumn(adjres - 1, false)
.getRegionIndex();
if (regionindex < hiddenColumns.size()
&& hiddenColumns.get(regionindex)[1] == adjres - 1)
try
{
LOCK.readLock().lock();
- return new HiddenColsIterator(hiddenColumns);
+ return new RangeIterator(hiddenColumns);
} finally
{
LOCK.readLock().unlock();
try
{
LOCK.readLock().lock();
- return new HiddenColsIterator(start, end, hiddenColumns);
+ return new RangeIterator(start, end, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
* @param end
* position to end at (inclusive, visible column position)
*/
- public Iterator<Integer> getBoundedStartIterator(int start, int end)
+ public Iterator<Integer> getStartRegionIterator(int start, int end)
{
try
{
// region we'll get the cursor pointing to the region before, which is
// what we want
HiddenCursorPosition pos = cursor
- .findRegionForColumn(absoluteStart - 1);
+ .findRegionForColumn(absoluteStart - 1, false);
- return new BoundedStartRegionIterator(pos, start, end,
+ return new StartRegionIterator(pos, start, end,
hiddenColumns);
} finally
{
try
{
LOCK.readLock().lock();
- return new VisibleColsIterator(start, end, hiddenColumns);
+ return new RangeElementsIterator(
+ new VisibleContigsIterator(start, end + 1, hiddenColumns));
} finally
{
LOCK.readLock().unlock();
git://source.jalview.org / jalview.git / blobdiff