package jalview.datamodel;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
* 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
{
{
}
- /*
- * 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
{
*/
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;
- }
+ LOCK.writeLock().lock();
int previndex = 0;
int prevHiddenCount = 0;
// 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;
} finally
{
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
+ LOCK.writeLock().unlock();
}
}
}
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);
+ cursor = new HiddenColumnsCursor(hiddenColumns);
numColumns = 0;
} finally
{
}
}
hiddenColumns.clear();
- cursor.resetCursor(hiddenColumns);
+ cursor = new HiddenColumnsCursor(hiddenColumns);
numColumns = 0;
} finally
if (hiddenColumns.isEmpty())
{
- hiddenColumns.clear();
numColumns = 0;
}
else
}
/**
- * 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 non-gaps as a Bitset
- // then calculate hidden ^ not(gap)
- BitSet gaps = origseq.gapBitset();
- this.andNot(gaps);
-
- // 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
- List<int[]> newhidden = new ArrayList<>();
-
- int numGapsBefore = 0;
- int gapPosition = 0;
- for (int[] region : hiddenColumns)
- {
- // get region coordinates accounting for gaps
- // we can rely on gaps not being *in* hidden regions because we already
- // removed those
- 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
- StringBuilder sb = new StringBuilder();
- 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();
- }
- }
-
- /**
- * 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
- */
- private void padGaps(StringBuilder sb, int pos, SequenceI profileseq,
- AlignmentI al)
- {
- // loop over the sequences and pad with gaps where required
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
- {
- 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));
- }
- }
- }
- }
-
- /*
- * 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 num = 0;
- if (hasHiddenColumns())
- {
- num = hiddenColumns.size();
- }
- return num;
+ return hiddenColumns.size();
} finally
{
LOCK.readLock().unlock();
return false;
}
+ Iterator<int[]> it = this.iterator();
Iterator<int[]> thatit = that.iterator();
- for (int[] thisRange : hiddenColumns)
+ while (it.hasNext())
{
- int[] thatRange = thatit.next();
- if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ if (!(Arrays.equals(it.next(), thatit.next())))
{
return false;
}
}
return true;
+
} finally
{
LOCK.readLock().unlock();
/**
* Find the visible column which is a given visible number of columns to the
- * left of another visible column. i.e. for a startColumn x, the column which
- * is distance 1 away will be column x-1.
+ * left (negative visibleDistance) or right (positive visibleDistance) of
+ * startColumn. If startColumn is not visible, we use the visible column at
+ * the left boundary of the hidden region containing startColumn.
*
* @param visibleDistance
- * the number of visible columns to offset by
+ * the number of visible columns to offset by (left offset = negative
+ * value; right offset = positive value)
* @param startColumn
- * the column to start from
- * @return the position of the column in the visible alignment
+ * the position of the column to start from (absolute position)
+ * @return the position of the column which is <visibleDistance> away
+ * (absolute position)
*/
- public int subtractVisibleColumns(int visibleDistance, int startColumn)
+ public int offsetByVisibleColumns(int visibleDistance, int startColumn)
{
try
{
LOCK.readLock().lock();
- int distance = visibleDistance;
-
- // in case startColumn is in a hidden region, move it to the left
- int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn));
-
- Iterator<int[]> it = new ReverseRegionsIterator(0, start,
- hiddenColumns);
-
- while (it.hasNext() && (distance > 0))
- {
- int[] region = it.next();
-
- 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;
- }
- }
- }
- return start - distance;
+ int start = absoluteToVisibleColumn(startColumn);
+ return visibleToAbsoluteColumn(start + visibleDistance);
} finally
{
* @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);
+ cursor = new HiddenColumnsCursor(hiddenColumns);
numColumns = 0;
} finally
{
// make sure only bits between start and end are set
if (!tohide.isEmpty())
{
- tohide.clear(0, start - 1);
- tohide.clear(Math.min(end + 1, tohide.length() - 1),
- tohide.length() - 1);
+ tohide.clear(0, start);
+ tohide.clear(Math.min(end + 1, tohide.length() + 1),
+ tohide.length() + 1);
}
hideColumns(tohide);
{
LOCK.writeLock().lock();
- HiddenCursorPosition pos = cursor.findRegionForColumn(start);
- int index = pos.getRegionIndex();
- int startindex = index; // first index in hiddenColumns to remove
-
- if (index != -1 && index != hiddenColumns.size())
+ if (!hiddenColumns.isEmpty())
{
- // regionIndex is the region which either contains start
- // or lies to the right of start
- int[] region = hiddenColumns.get(index);
- if (region[0] < start && region[1] >= start)
+ HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+ int index = pos.getRegionIndex();
+ int startindex = index; // first index in hiddenColumns to remove
+
+ if (index != -1 && index != hiddenColumns.size())
{
- // region contains start, truncate so that it ends just before start
- region[1] = start - 1;
- startindex++;
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(index);
+ if (region[0] < start && region[1] >= start)
+ {
+ // region contains start, truncate so that it ends just before start
+ region[1] = start - 1;
+ startindex++;
+ }
}
- }
-
- 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)
+ pos = cursor.findRegionForColumn(end);
+ index = pos.getRegionIndex();
+ int endindex = index - 1; // last index in hiddenColumns to remove
+
+ if (index != -1 && index != hiddenColumns.size())
{
- // region contains end, truncate so that it starts just after end
- region[0] = end + 1;
+ // 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)
+ {
+ // region contains end, truncate so that it starts just after end
+ region[0] = end + 1;
+ }
}
+
+ hiddenColumns.subList(startindex, endindex + 1).clear();
+ cursor = new HiddenColumnsCursor(hiddenColumns);
+ numColumns = 0;
}
-
- hiddenColumns.subList(startindex, endindex + 1).clear();
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
/**
*
- * @param inserts
+ * @param updates
* BitSet where hidden columns will be marked
*/
- private void andNot(BitSet updates)
+ protected void andNot(BitSet updates)
{
try
{
- LOCK.readLock().lock();
+ LOCK.writeLock().lock();
BitSet hiddenBitSet = new BitSet();
for (int[] range : hiddenColumns)
hideColumns(hiddenBitSet);
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
try
{
LOCK.readLock().lock();
- int[] alignmentStartEnd = new int[] { 0, width - 1 };
- int startPos = alignmentStartEnd[0];
- int endPos = alignmentStartEnd[1];
- int[] lowestRange = new int[] { -1, -1 };
- int[] higestRange = new int[] { -1, -1 };
-
- if (hiddenColumns.isEmpty())
- {
- return new int[] { startPos, endPos };
- }
+ int firstVisible = 0;
+ int lastVisible = width - 1;
- for (int[] range : hiddenColumns)
+ if (!hiddenColumns.isEmpty())
{
- lowestRange = (range[0] <= startPos) ? range : lowestRange;
- higestRange = (range[1] >= endPos) ? range : higestRange;
- }
+ // first visible col with index 0, convert to absolute index
+ firstVisible = visibleToAbsoluteColumn(0);
- if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
- {
- startPos = alignmentStartEnd[0];
- }
- else
- {
- startPos = lowestRange[1] + 1;
+ // last visible column is either immediately to left of
+ // last hidden region, or is just the last column in the alignment
+ int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1);
+ if (lastregion[1] == width - 1)
+ {
+ // last region is at very end of alignment
+ // last visible column immediately precedes it
+ lastVisible = lastregion[0] - 1;
+ }
}
+ return new int[] { firstVisible, lastVisible };
- if (higestRange[0] == -1) // includes (higestRange[1] == -1)
- {
- endPos = alignmentStartEnd[1];
- }
- else
- {
- endPos = higestRange[0] - 1;
- }
- return new int[] { startPos, endPos };
} finally
{
LOCK.readLock().unlock();