package jalview.datamodel;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
- private List<int[]> hiddenColumns;
+ private List<int[]> hiddenColumns = new ArrayList<>();
/**
* Constructor
LOCK.writeLock().lock();
if (copy != null)
{
- hiddenColumns = new ArrayList<>();
numColumns = 0;
Iterator<int[]> it = copy.getBoundedIterator(start, end);
while (it.hasNext())
*/
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;
int regionindex = 0;
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<>();
- }
- else
+ if (!hiddenColumns.isEmpty())
{
// set up cursor reset values
HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
} finally
{
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
+ LOCK.writeLock().unlock();
}
}
}
/**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
+ * hide a list of ranges
*
- * @param sr
+ * @param ranges
*/
- public void hideInsertionsFor(SequenceI sr)
+ public void hideList(List<int[]> ranges)
{
try
{
LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
+ for (int[] r : ranges)
{
hideColumns(r[0], r[1]);
}
try
{
LOCK.writeLock().lock();
- if (hiddenColumns != null)
+
+ for (int[] region : hiddenColumns)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- int[] region = it.next();
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
+ sel.addElement(j);
}
- hiddenColumns = null;
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
}
+ hiddenColumns.clear();
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+
} finally
{
LOCK.writeLock().unlock();
{
LOCK.writeLock().lock();
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
int regionIndex = cursor.findRegionForColumn(start)
.getRegionIndex();
if (hiddenColumns.isEmpty())
{
- hiddenColumns = null;
+ 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 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.hideColumns(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();
- List<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);
- 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(StringBuffer 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.
{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- if (hiddenColumns != null)
+
+ boolean first = true;
+ for (int[] range : hiddenColumns)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ if (!first)
{
- int[] range = it.next();
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
- if (!it.hasNext())
- {
- regionBuilder.deleteCharAt(0);
- }
+ regionBuilder.append(delimiter);
}
+ else
+ {
+ first = false;
+ }
+ regionBuilder.append(range[0]).append(between).append(range[1]);
+
}
+
return regionBuilder.toString();
} finally
{
{
LOCK.readLock().lock();
- if (numColumns == 0 && hiddenColumns != null)
+ if (numColumns == 0)
{
// numColumns is out of date, so recalculate
int size = 0;
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ for (int[] range : hiddenColumns)
{
- int[] range = it.next();
size += range[1] - range[0] + 1;
}
try
{
LOCK.readLock().lock();
- int num = 0;
- if (hasHiddenColumns())
- {
- num = hiddenColumns.size();
- }
- return num;
+ return hiddenColumns.size();
} finally
{
LOCK.readLock().unlock();
/*
* check hidden columns are either both null, or match
*/
- if (this.hiddenColumns == null)
- {
- return (that.hiddenColumns == null);
- }
- if (that.hiddenColumns == null
- || that.hiddenColumns.size() != this.hiddenColumns.size())
+
+ if (that.hiddenColumns.size() != this.hiddenColumns.size())
{
return false;
}
- Iterator<int[]> it = hiddenColumns.iterator();
+ Iterator<int[]> it = this.iterator();
Iterator<int[]> thatit = that.iterator();
while (it.hasNext())
{
- int[] thisRange = it.next();
- 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();
LOCK.readLock().lock();
int result = column;
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
}
LOCK.readLock().lock();
int result = hiddenColumn;
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
HiddenCursorPosition cursorPos = cursor
.findRegionForColumn(hiddenColumn);
/**
* 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
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ 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 != null)
- {
- 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 != null && hiddenColumns.size() > 0)
- {
- for (int i = 0; i < iSize; i++)
- {
- StringBuffer visibleSeq = new StringBuffer();
-
- 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.
*
LOCK.readLock().lock();
int start = 0;
- if (hiddenColumns == null || hiddenColumns.size() == 0)
+ if (hiddenColumns.isEmpty())
{
return seq.findIndex(seq.getStart()) - 1;
}
}
}
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param alignmentAnnotation
- */
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
- {
- if (alignmentAnnotation != null
- && alignmentAnnotation.annotations != null)
- {
- makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
- alignmentAnnotation);
- }
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param start
- * remove any annotation to the right of this column
- * @param end
- * remove any annotation to the left of this column
- * @param alignmentAnnotation
- * the annotation to operate on
- */
- public void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
- {
- try
- {
- LOCK.readLock().lock();
-
- int startFrom = start;
- int endAt = end;
-
- if (alignmentAnnotation != null
- && alignmentAnnotation.annotations != null)
- {
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
- }
- else
- {
- alignmentAnnotation.restrict(startFrom, endAt);
- }
- }
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- private void removeHiddenAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
- {
- // mangle the alignmentAnnotation annotation array
- ArrayList<Annotation[]> annels = new ArrayList<>();
- Annotation[] els = null;
-
- int w = 0;
-
- Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
- hiddenColumns);
-
- int copylength;
- int annotationLength;
- while (blocks.hasNext())
- {
- int[] block = blocks.next();
- annotationLength = block[1] - block[0] + 1;
-
- if (blocks.hasNext())
- {
- // 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;
- }
- }
- }
/**
*
// we don't use getSize()>0 here because it has to iterate over
// the full hiddenColumns collection and so will be much slower
- return hiddenColumns != null && hiddenColumns.size() > 0;
+ return (!hiddenColumns.isEmpty());
} finally
{
LOCK.readLock().unlock();
try
{
LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 1;
+ return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1;
} finally
{
LOCK.readLock().unlock();
{
LOCK.readLock().lock();
int hashCode = 1;
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ for (int[] hidden : hiddenColumns)
{
- int[] hidden = it.next();
hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
* Hide columns corresponding to the marked bits
*
* @param inserts
- * - columns map to bits starting from zero
+ * - columns mapped to bits starting from zero
*/
public void hideColumns(BitSet inserts)
{
}
/**
+ * Hide columns corresponding to the marked bits, within the range
+ * [start,end]. Entries in tohide which are outside [start,end] are ignored.
*
- * @param inserts
- * BitSet where hidden columns will be marked
+ * @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
+ */
+ public void hideColumns(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);
+ }
+
+ /**
+ * Make all columns in the range [start,end] visible
+ *
+ * @param start
+ * start of range to show columns
+ * @param end
+ * end of range to show columns
*/
- public void markHiddenRegions(BitSet inserts)
+ private void clearHiddenColumnsInRange(int start, int end)
{
try
{
- LOCK.readLock().lock();
- if (hiddenColumns == null)
+ LOCK.writeLock().lock();
+
+ if (!hiddenColumns.isEmpty())
{
- return;
+ HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+ int index = pos.getRegionIndex();
+ int startindex = index; // first index in hiddenColumns to remove
+
+ if (index != -1 && index != hiddenColumns.size())
+ {
+ // 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)
+ {
+ // region contains end, truncate so that it starts just after end
+ region[0] = end + 1;
+ }
+ }
+
+ hiddenColumns.subList(startindex, endindex + 1).clear();
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
}
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
+ }
+
+ /**
+ *
+ * @param updates
+ * BitSet where hidden columns will be marked
+ */
+ protected void andNot(BitSet updates)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+
+ BitSet hiddenBitSet = new BitSet();
+ for (int[] range : hiddenColumns)
{
- int[] range = it.next();
- inserts.set(range[0], range[1] + 1);
+ hiddenBitSet.set(range[0], range[1] + 1);
}
+ hiddenBitSet.andNot(updates);
+ hiddenColumns.clear();
+ 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 };
+ int firstVisible = 0;
+ int lastVisible = width - 1;
- if (hiddenColumns == null)
+ if (!hiddenColumns.isEmpty())
{
- return new int[] { startPos, endPos };
- }
+ // first visible col with index 0, convert to absolute index
+ firstVisible = visibleToAbsoluteColumn(0);
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
- {
- int[] range = it.next();
- lowestRange = (range[0] <= startPos) ? range : lowestRange;
- higestRange = (range[1] >= endPos) ? range : higestRange;
- }
-
- 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();
int[] reveal = null;
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
// look for a region ending just before adjres
int regionindex = cursor.findRegionForColumn(adjres - 1)
* if true, start and end are visible column positions, not absolute
* positions*
*/
- public Iterator<int[]> getVisContigsIterator(int start, int end,
+ public VisibleContigsIterator getVisContigsIterator(int start,
+ int end,
boolean useVisibleCoords)
{
int adjstart = start;
git://source.jalview.org / jalview.git / blobdiff