import java.util.List;
import java.util.concurrent.locks.ReentrantReadWriteLock;
+/**
+ * This class manages the collection of hidden columns associated with an
+ * alignment. To iterate over the collection, or over visible columns/regions,
+ * use an iterator obtained from one of:
+ *
+ * - getBoundedIterator: iterates over the hidden regions, within some bounds,
+ * returning absolute positions
+ *
+ * - getBoundedStartIterator: iterates over the start positions of hidden
+ * regions, within some bounds, returning visible positions
+ *
+ * - getVisContigsIterator: iterates over visible regions in a range, returning
+ * absolute positions
+ *
+ * - getVisibleColsIterator: iterates over the visible *columns*
+ *
+ * For performance reasons, provide bounds where possible.
+ *
+ * @author kmourao
+ *
+ */
public class HiddenColumns
{
private static final int HASH_MULTIPLIER = 31;
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+ /*
+ * Cursor which tracks the last used hidden columns region, and the number
+ * of hidden columns up to (but not including) that region.
+ */
private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
/*
+ * cache of the number of hidden columns
+ */
+ private int numColumns = 0;
+
+ /*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
{
}
+ /*
+ * 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
*
* @param copy
+ * the HiddenColumns object to copy from
*/
public HiddenColumns(HiddenColumns copy)
{
try
{
LOCK.writeLock().lock();
+ numColumns = 0;
if (copy != null)
{
if (copy.hiddenColumns != null)
Iterator<int[]> it = copy.iterator();
while (it.hasNext())
{
- hiddenColumns.add(it.next());
+ int[] region = it.next();
+ hiddenColumns.add(region);
+ numColumns += region[1] - region[0] + 1;
+ }
+ cursor.resetCursor(hiddenColumns);
+ }
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Copy constructor within bounds and with offset. Copies hidden column
+ * regions fully contained between start and end, and offsets positions by
+ * subtracting offset.
+ *
+ * @param copy
+ * HiddenColumns instance to copy from
+ * @param start
+ * lower bound to copy from
+ * @param end
+ * upper bound to copy to
+ * @param offset
+ * offset to subtract from each region boundary position
+ *
+ */
+ public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+ if (copy != null)
+ {
+ hiddenColumns = new ArrayList<>();
+ numColumns = 0;
+ Iterator<int[]> it = copy.getBoundedIterator(start, end);
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+ // still need to check boundaries because iterator returns
+ // all overlapping regions and we need contained regions
+ if (region[0] >= start && region[1] <= end)
+ {
+ hiddenColumns.add(
+ new int[]
+ { region[0] - offset, region[1] - offset });
+ numColumns += region[1] - region[0] + 1;
+ }
+ }
+ cursor.resetCursor(hiddenColumns);
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * 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 wasAlreadyLocked = false;
+ try
+ {
+ // check if the write lock was already locked by this thread,
+ // as this method can be called internally in loops within HiddenColumns
+ if (!LOCK.isWriteLockedByCurrentThread())
+ {
+ LOCK.writeLock().lock();
+ }
+ else
+ {
+ wasAlreadyLocked = true;
+ }
+
+ int previndex = 0;
+ int prevHiddenCount = 0;
+ int regionindex = 0;
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList<>();
+ }
+ else
+ {
+ // set up cursor reset values
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+ regionindex = cursorPos.getRegionIndex();
+
+ if (regionindex > 0)
+ {
+ // get previous index and hidden count for updating the cursor later
+ previndex = regionindex - 1;
+ int[] prevRegion = hiddenColumns.get(previndex);
+ prevHiddenCount = cursorPos.getHiddenSoFar()
+ - (prevRegion[1] - prevRegion[0] + 1);
+ }
+ }
+
+ /*
+ * 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 });
+ }
+ else
+ {
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
+ boolean added = false;
+ if (regionindex > 0)
+ {
+ added = insertRangeAtRegion(regionindex - 1, start, end);
+ }
+ if (!added && regionindex < hiddenColumns.size())
+ {
+ insertRangeAtRegion(regionindex, start, end);
+ }
+ }
+
+ // 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;
+
+ } finally
+ {
+ if (!wasAlreadyLocked)
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+ }
+
+ /**
+ * 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);
+
+ // in theory this is faster than hiddenColumns.remove(i+1)
+ // benchmarking results a bit ambivalent
+ hiddenColumns.subList(i + 1, i + 2).clear();
+ }
+ added = true;
+ }
+ return added;
+ }
+
+ /**
+ * mark the columns corresponding to gap characters as hidden in the column
+ * selection
+ *
+ * @param sr
+ */
+ public void hideInsertionsFor(SequenceI sr)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+ List<int[]> inserts = sr.getInsertions();
+ for (int[] r : inserts)
+ {
+ hideColumns(r[0], r[1]);
+ }
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Unhides, and adds to the selection list, all hidden columns
+ */
+ public void revealAllHiddenColumns(ColumnSelection sel)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+ if (hiddenColumns != null)
+ {
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
+ }
+ hiddenColumns = null;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Reveals, and marks as selected, the hidden column range with the given
+ * start column
+ *
+ * @param start
+ * the start column to look for
+ * @param sel
+ * the column selection to add the hidden column range to
+ */
+ public void revealHiddenColumns(int start, ColumnSelection sel)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+
+ if (hiddenColumns != null)
+ {
+ int regionIndex = cursor.findRegionForColumn(start)
+ .getRegionIndex();
+
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
+ {
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
+ {
+ 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);
+ }
+ }
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * sequence in al which sequences are aligned to
+ * @param al
+ * alignment to have gaps inserted into it
+ * @param input
+ * alignment view where sequence corresponding to profileseq is first
+ * entry
+ * @return new HiddenColumns for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public static HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentI al, AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = al.getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ nview.propagateInsertions(profileseq, al, origseq);
+ return nview;
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ SequenceI origseq)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+
+ char gc = al.getGapCharacter();
+
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ BitSet gaps = origseq.gapBitset();
+
+ // now calculate hidden ^ not(gap)
+ BitSet hidden = new BitSet();
+ markHiddenRegions(hidden);
+ hidden.andNot(gaps);
+ hiddenColumns = null;
+ this.hideMarkedBits(hidden);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ Iterator<int[]> regions = hiddenColumns.iterator();
+ ArrayList<int[]> newhidden = new ArrayList<>();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ while (regions.hasNext())
+ {
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ int[] region = regions.next();
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
}
- cursor.resetCursor(hiddenColumns);
}
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+ newhidden.add(new int[] { left, right });
+
+ // make a string with number of gaps = length of hidden region
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0; s < right - left + 1; s++)
+ {
+ sb.append(gc);
+ }
+ padGaps(sb, left, profileseq, al);
+
}
+ hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
}
/**
- * Copy constructor within bounds and with offset. Copies hidden column
- * regions fully contained between start and end, and offsets positions by
- * subtracting offset.
- *
- * @param copy
- * HiddenColumns instance to copy from
- * @param start
- * lower bound to copy from
- * @param end
- * upper bound to copy to
- * @param offset
- * offset to subtract from each region boundary position
+ * Pad gaps in all sequences in alignment except profileseq
*
+ * @param sb
+ * gap string to insert
+ * @param left
+ * position to insert at
+ * @param profileseq
+ * sequence not to pad
+ * @param al
+ * alignment to pad sequences in
*/
- public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
+ private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+ AlignmentI al)
{
- try
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
{
- LOCK.writeLock().lock();
- if (copy != null)
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
{
- hiddenColumns = new ArrayList<>();
- Iterator<int[]> it = copy.getBoundedIterator(start, end);
- while (it.hasNext())
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= pos)
{
- int[] region = it.next();
- // still need to check boundaries because iterator returns
- // all overlapping regions and we need contained regions
- if (region[0] >= start && region[1] <= end)
+ // pad sequence
+ int diff = pos - sq.length() - 1;
+ if (diff > 0)
{
- hiddenColumns.add(
- new int[]
- { region[0] - offset, region[1] - offset });
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = pos - sq.length() - 1) > 0)
+ {
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ }
}
+ sq += sb.toString();
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, pos) + sb.toString() + sq.substring(pos));
}
- cursor.resetCursor(hiddenColumns);
}
- } finally
- {
- LOCK.writeLock().unlock();
}
}
+ /*
+ * 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]
try
{
LOCK.readLock().lock();
- int size = 0;
- if (hiddenColumns != null)
+
+ if (numColumns == 0 && hiddenColumns != null)
{
+ // numColumns is out of date, so recalculate
+ int size = 0;
+
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)
{
- result += cursor.getHiddenOffset(column);
+ result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
}
return result;
{
LOCK.readLock().lock();
int result = hiddenColumn;
- int[] region = null;
+
if (hiddenColumns != null)
{
- Iterator<int[]> it = new RegionsIterator(0,
- hiddenColumn, hiddenColumns, cursor);
- 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
// 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;
- }
- }
- }
-
- 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 alPos
- * the absolute (visible) alignmentPosition to find the next hidden
- * column for
- */
- public int getHiddenBoundaryRight(int alPos)
- {
- try
- {
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = cursor.findRegionForColumn(alPos);
- if (index < hiddenColumns.size())
- {
- 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;
- } 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 alPos
- * the absolute (visible) alignmentPosition to find the previous
- * hidden column for
- */
- public int getHiddenBoundaryLeft(int alPos)
- {
- try
- {
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
- {
- int index = cursor.findRegionForColumn(alPos);
-
- if (index > 0)
- {
- int[] region = hiddenColumns.get(index - 1);
- return region[1];
- }
- }
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * 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 wasAlreadyLocked = false;
- try
- {
- // check if the write lock was already locked by this thread,
- // as this method can be called internally in loops within HiddenColumns
- if (!LOCK.isWriteLockedByCurrentThread())
- {
- LOCK.writeLock().lock();
- }
- else
- {
- wasAlreadyLocked = true;
- }
-
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<>();
- }
-
- /*
- * 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 });
- }
- else
- {
- /*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
- */
- boolean added = false;
- for (int i = 0; !added && i < hiddenColumns.size(); i++)
- {
- added = insertRangeAtRegion(i, start, end);
- } // for
- }
- if (!wasAlreadyLocked)
- {
- cursor.resetCursor(hiddenColumns);
+ distance -= start - region[1];
+ start = region[0] - 1;
+ }
+ else
+ {
+ start = start - distance;
+ distance = 0;
+ }
+ }
}
+ return start - distance;
+
} finally
{
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
+ LOCK.readLock().unlock();
}
}
/**
- * Insert [start, range] at the region at index i in hiddenColumns, if
- * feasible
+ * This method returns the rightmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the next hidden column.
*
- * @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
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the next hidden
+ * column for
+ * @return the index of the next hidden column, or alPos if there is no next
+ * hidden column
*/
- private boolean insertRangeAtRegion(int i, int start, int end)
+ public int getHiddenBoundaryRight(int alPos)
{
- boolean added = false;
-
- int[] region = hiddenColumns.get(i);
- if (end < region[0] - 1)
+ try
{
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.add(i, new int[] { start, end });
- added = true;
- }
- else if (end <= region[1])
+ LOCK.readLock().lock();
+ if (hiddenColumns != null)
+ {
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+ if (index < hiddenColumns.size())
+ {
+ 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;
+ } finally
{
- /*
- * new range overlaps existing, or is contiguous preceding it - adjust
- * start column
- */
- region[0] = Math.min(region[0], start);
- added = true;
+ LOCK.readLock().unlock();
}
- else if (start <= region[1] + 1)
+ }
+
+ /**
+ * 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
{
- /*
- * 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);
+ LOCK.readLock().lock();
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
+ if (hiddenColumns != null)
{
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+
+ if (index > 0)
{
- /*
- * gap to next hidden range - no more to update
- */
- break;
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
}
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.subList(i + 1, i + 2).clear();
}
- added = true;
+ return alPos;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
- return added;
}
+
/**
* Answers if a column in the alignment is visible
*
{
LOCK.readLock().lock();
- Iterator<int[]> it = new RegionsIterator(column, column,
- hiddenColumns, cursor);
- while (it.hasNext())
+ int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- int[] region = it.next();
- if (column >= region[0] && column <= region[1])
+ 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();
*/
public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+ if (alignmentAnnotation != null
+ && alignmentAnnotation.annotations != null)
+ {
+ makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
alignmentAnnotation);
+ }
}
/**
int startFrom = start;
int endAt = end;
- if (alignmentAnnotation.annotations != null)
+ if (alignmentAnnotation != null
+ && alignmentAnnotation.annotations != null)
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
{
// copy just the visible segment of the annotation row
copylength = annotationLength;
- }
- else
- {
- if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
- {
- // copy just the visible segment of the annotation row
- copylength = annotationLength;
- }
- else
- {
- // copy to the end of the annotation row
- copylength = alignmentAnnotation.annotations.length - block[0];
- }
- }
-
- els = new Annotation[annotationLength];
- annels.add(els);
- System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
- copylength);
- w += annotationLength;
- }
-
- if (w != 0)
- {
- alignmentAnnotation.annotations = new Annotation[w];
-
- w = 0;
- for (Annotation[] chnk : annels)
- {
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
- chnk.length);
- w += chnk.length;
- }
- }
- }
-
- /**
- *
- * @return true if there are columns hidden
- */
- public boolean hasHiddenColumns()
- {
- try
- {
- LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 0;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- *
- * @return true if there are more than one set of columns hidden
- */
- public boolean hasManyHiddenColumns()
- {
- try
- {
- LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 1;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
- *
- * @param sr
- */
- public void hideInsertionsFor(SequenceI sr)
- {
- try
- {
- LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
- {
- hideColumns(r[0], r[1]);
- }
- cursor.resetCursor(hiddenColumns);
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Unhides, and adds to the selection list, all hidden columns
- */
- public void revealAllHiddenColumns(ColumnSelection sel)
- {
- try
- {
- LOCK.writeLock().lock();
- if (hiddenColumns != null)
- {
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
- }
- hiddenColumns = null;
- cursor.resetCursor(hiddenColumns);
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Reveals, and marks as selected, the hidden column range with the given
- * start column
- *
- * @param start
- */
- public void revealHiddenColumns(int start, ColumnSelection sel)
- {
- try
- {
- LOCK.writeLock().lock();
- Iterator<int[]> it = new RegionsIterator(start, start, hiddenColumns,
- cursor);
- while (it.hasNext())
+ }
+ else
{
- int[] region = it.next();
- if (start == region[0])
+ if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
{
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
- it.remove();
- break;
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
}
- else if (start < region[0])
+ else
{
- break; // passed all possible matching regions
+ // copy to the end of the annotation row
+ copylength = alignmentAnnotation.annotations.length - block[0];
}
}
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
+ copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
+ {
+ alignmentAnnotation.annotations = new Annotation[w];
- if (hiddenColumns.size() == 0)
+ w = 0;
+ for (Annotation[] chnk : annels)
{
- hiddenColumns = null;
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
}
- cursor.resetCursor(hiddenColumns);
- } finally
- {
- LOCK.writeLock().unlock();
}
}
/**
- * Add gaps into the sequences aligned to profileseq under the given
- * AlignmentView
- *
- * @param profileseq
- * @param al
- * - alignment to have gaps inserted into it
- * @param input
- * - alignment view where sequence corresponding to profileseq is
- * first entry
- * @return new HiddenColumns for new alignment view, with insertions into
- * profileseq marked as hidden.
- */
- public static HiddenColumns propagateInsertions(SequenceI profileseq,
- AlignmentI al, AlignmentView input)
- {
- int profsqpos = 0;
-
- char gc = al.getGapCharacter();
- Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
- HiddenColumns nview = (HiddenColumns) alandhidden[1];
- SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
- nview.propagateInsertions(profileseq, al, origseq);
- return nview;
- }
-
- /**
*
- * @param profileseq
- * - sequence in al which corresponds to origseq
- * @param al
- * - alignment which is to have gaps inserted into it
- * @param origseq
- * - sequence corresponding to profileseq which defines gap map for
- * modifying al
+ * @return true if there are columns hidden
*/
- private void propagateInsertions(SequenceI profileseq, AlignmentI al,
- SequenceI origseq)
+ public boolean hasHiddenColumns()
{
try
{
- LOCK.writeLock().lock();
-
- char gc = al.getGapCharacter();
-
- // take the set of hidden columns, and the set of gaps in origseq,
- // and remove all the hidden gaps from hiddenColumns
-
- // first get the gaps as a Bitset
- BitSet gaps = origseq.gapBitset();
-
- // now calculate hidden ^ not(gap)
- BitSet hidden = new BitSet();
- markHiddenRegions(hidden);
- hidden.andNot(gaps);
- hiddenColumns = null;
- this.hideMarkedBits(hidden);
-
- // for each sequence in the alignment, except the profile sequence,
- // insert gaps corresponding to each hidden region
- // but where each hidden column region is shifted backwards by the number
- // of
- // preceding visible gaps
- // update hidden columns at the same time
- Iterator<int[]> regions = hiddenColumns.iterator();
- ArrayList<int[]> newhidden = new ArrayList<>();
-
- int numGapsBefore = 0;
- int gapPosition = 0;
- while (regions.hasNext())
- {
- // get region coordinates accounting for gaps
- // we can rely on gaps not being *in* hidden regions because we already
- // removed those
- int[] region = regions.next();
- while (gapPosition < region[0])
- {
- gapPosition++;
- if (gaps.get(gapPosition))
- {
- numGapsBefore++;
- }
- }
-
- int left = region[0] - numGapsBefore;
- int right = region[1] - numGapsBefore;
- newhidden.add(new int[] { left, right });
-
- // make a string with number of gaps = length of hidden region
- StringBuffer sb = new StringBuffer();
- for (int s = 0; s < right - left + 1; s++)
- {
- sb.append(gc);
- }
- padGaps(sb, left, profileseq, al);
-
- }
- hiddenColumns = newhidden;
- cursor.resetCursor(hiddenColumns);
+ LOCK.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 0;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * Pad gaps in all sequences in alignment except profileseq
*
- * @param sb
- * gap string to insert
- * @param left
- * position to insert at
- * @param profileseq
- * sequence not to pad
- * @param al
- * alignment to pad sequences in
+ * @return true if there are more than one set of columns hidden
*/
- private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
- AlignmentI al)
+ public boolean hasManyHiddenColumns()
{
- // loop over the sequences and pad with gaps where required
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ try
{
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj != profileseq)
- {
- String sq = al.getSequenceAt(s).getSequenceAsString();
- if (sq.length() <= pos)
- {
- // pad sequence
- int diff = pos - sq.length() - 1;
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = pos - sq.length() - 1) > 0)
- {
- if (diff >= sb.length())
- {
- sq += sb.toString();
- }
- else
- {
- char[] buf = new char[diff];
- sb.getChars(0, diff, buf, 0);
- sq += buf.toString();
- }
- }
- }
- sq += sb.toString();
- }
- else
- {
- al.getSequenceAt(s).setSequence(
- sq.substring(0, pos) + sb.toString() + sq.substring(pos));
- }
- }
+ LOCK.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 1;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
}
+
/**
* Returns a hashCode built from hidden column ranges
*/
hideColumns(firstSet, lastSet - 1);
}
cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
higestRange = (range[1] >= endPos) ? range : higestRange;
}
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
{
startPos = alignmentStartEnd[0];
}
startPos = lowestRange[1] + 1;
}
- if (higestRange[0] == -1 && higestRange[1] == -1)
+ if (higestRange[0] == -1) // includes (higestRange[1] == -1)
{
endPos = alignmentStartEnd[1];
}
if (hiddenColumns != null)
{
- int regionindex = cursor.findRegionForColumn(adjres - 1);
- if (hiddenColumns.get(regionindex)[1] == adjres - 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 = hiddenColumns.get(regionindex);
}
- else
+ // check if the region ends just after adjres
+ else if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
{
- regionindex = cursor.findRegionForColumn(adjres + 1);
- if (hiddenColumns.get(regionindex)[0] == adjres + 1)
- {
- reveal = hiddenColumns.get(regionindex);
- }
+ reveal = hiddenColumns.get(regionindex);
}
}
return reveal;
try
{
LOCK.readLock().lock();
- return new BoundedStartRegionIterator(start, end, hiddenColumns);
+
+ // get absolute position of column in alignment
+ int absoluteStart = adjustForHiddenColumns(start);
+
+ // Get cursor position and supply it to the iterator:
+ // Since we want visible region start, we look for a cursor for the
+ // (absoluteStart-1), then if absoluteStart is the start of a visible
+ // region we'll get the cursor pointing to the region before, which is
+ // what we want
+ HiddenCursorPosition pos = cursor
+ .findRegionForColumn(absoluteStart - 1);
+
+ return new BoundedStartRegionIterator(pos, start, end,
+ hiddenColumns);
} finally
{
LOCK.readLock().unlock();
* boundaries
*
* @param start
- * (first column inclusive from 0)
- * @param end
- * (last column - not inclusive)
- */
- public Iterator<int[]> getVisContigsIterator(int start, int end)
- {
- try
- {
- LOCK.readLock().lock();
- return new VisibleContigsIterator(start, end, hiddenColumns);
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * return an iterator over visible segments between the given start and end
- * boundaries
- *
- * @param start
- * (first column - inclusive from 0)
+ * first column, inclusive from 0
* @param end
- * (last column - inclusive)
+ * last column - not inclusive
* @param useVisibleCoords
* if true, start and end are visible column positions, not absolute
- * positions
+ * positions*
*/
- public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
+ public Iterator<int[]> getVisContigsIterator(int start, int end,
boolean useVisibleCoords)
{
+ int adjstart = start;
+ int adjend = end;
if (useVisibleCoords)
{
- // TODO
- // we should really just convert start and end here with
- // adjustForHiddenColumns
- // and then create a VisibleContigsIterator
- // but without a cursor this will be horribly slow in some situations
- // ... so until then...
- return new VisibleBlocksVisBoundsIterator(start, end, true);
- }
- else
- {
- try
- {
- LOCK.readLock().lock();
- return new VisibleContigsIterator(start, end + 1, hiddenColumns);
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
- }
-
- /**
- * An iterator which iterates over visible regions in a range. The range is
- * specified in terms of visible column positions. Provides a special
- * "endsAtHidden" indicator to allow callers to determine if the final visible
- * column is adjacent to a hidden region.
- */
- public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
- {
- private List<int[]> vcontigs = new ArrayList<>();
-
- private int currentPosition = 0;
-
- private boolean endsAtHidden = false;
-
- /**
- * Constructor for iterator over visible regions in a range.
- *
- * @param start
- * start position in terms of visible column position
- * @param end
- * end position in terms of visible column position
- * @param usecopy
- * whether to use a local copy of hidden columns
- */
- VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
- {
- /* actually this implementation always uses a local copy but this may change in future */
- try
- {
- if (usecopy)
- {
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- int blockStart = start;
- int blockEnd = end;
- int hiddenSoFar = 0;
- int visSoFar = 0;
-
- // iterate until a region begins within (start,end]
- int i = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar))
- {
- hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0]
- + 1;
- i++;
- }
-
- blockStart += hiddenSoFar; // convert start to absolute position
- blockEnd += hiddenSoFar; // convert end to absolute position
-
- // iterate from start to end, adding each visible region. Positions
- // are
- // absolute, and all hidden regions which overlap [start,end] are
- // used.
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= blockEnd))
- {
- int[] region = hiddenColumns.get(i);
-
- // end position of this visible region is either just before the
- // start of the next hidden region, or the absolute position of
- // 'end', whichever is lowest
- blockEnd = Math.min(blockEnd, region[0] - 1);
-
- vcontigs.add(new int[] { blockStart, blockEnd });
-
- visSoFar += blockEnd - blockStart + 1;
-
- // next visible region starts after this hidden region
- blockStart = region[1] + 1;
-
- hiddenSoFar += region[1] - region[0] + 1;
-
- // reset blockEnd to absolute position of 'end', assuming we've now
- // passed all hidden regions before end
- blockEnd = end + hiddenSoFar;
-
- i++;
- }
- 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
- // the last visible region
- blockEnd = blockStart + end - start - visSoFar;
- vcontigs.add(new int[] { blockStart, blockEnd });
-
- // if the last visible region ends at the next hidden region, set
- // endsAtHidden=true
- if (i < hiddenColumns.size()
- && hiddenColumns.get(i)[0] - 1 == blockEnd)
- {
- endsAtHidden = true;
- }
- }
- }
- else
- {
- // there are no hidden columns, return a single visible contig
- vcontigs.add(new int[] { start, end });
- endsAtHidden = false;
- }
- } finally
- {
- if (usecopy)
- {
- LOCK.readLock().unlock();
- }
- }
- }
-
- @Override
- public boolean hasNext()
- {
- return (currentPosition < vcontigs.size());
+ adjstart = adjustForHiddenColumns(start);
+ adjend = adjustForHiddenColumns(end);
}
- @Override
- public int[] next()
+ try
{
- int[] result = vcontigs.get(currentPosition);
- currentPosition++;
- return result;
- }
-
- public boolean endsAtHidden()
+ LOCK.readLock().lock();
+ return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
+ } finally
{
- return endsAtHidden;
+ LOCK.readLock().unlock();
}
}
}
git://source.jalview.org / jalview.git / blobdiff