*
* - getVisibleColsIterator: iterates over the visible *columns*
*
- * For performance reasons, provide bounds where possible.
+ * For performance reasons, provide bounds where possible. Note that column
+ * numbering begins at 0 throughout this class.
*
* @author kmourao
*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
- private ArrayList<int[]> hiddenColumns;
+ private List<int[]> hiddenColumns = new ArrayList<>();
/**
* Constructor
*/
public HiddenColumns(HiddenColumns copy)
{
- try
- {
- LOCK.writeLock().lock();
- numColumns = 0;
- if (copy != null)
- {
- if (copy.hiddenColumns != null)
- {
- hiddenColumns = new ArrayList<>();
- Iterator<int[]> it = copy.iterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- hiddenColumns.add(region);
- numColumns += region[1] - region[0] + 1;
- }
- cursor.resetCursor(hiddenColumns);
- }
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
+ this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
}
/**
LOCK.writeLock().lock();
if (copy != null)
{
- hiddenColumns = new ArrayList<>();
numColumns = 0;
Iterator<int[]> it = copy.getBoundedIterator(start, end);
while (it.hasNext())
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);
}
/**
- * 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
BitSet hidden = new BitSet();
markHiddenRegions(hidden);
hidden.andNot(gaps);
- hiddenColumns = null;
- this.hideMarkedBits(hidden);
+ hiddenColumns.clear();
+ 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();
- ArrayList<int[]> newhidden = new ArrayList<>();
+ List<int[]> newhidden = new ArrayList<>();
int numGapsBefore = 0;
int gapPosition = 0;
- while (regions.hasNext())
+ 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
- int[] region = regions.next();
while (gapPosition < region[0])
{
gapPosition++;
newhidden.add(new int[] { left, right });
// make a string with number of gaps = length of hidden region
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
for (int s = 0; s < right - left + 1; s++)
{
sb.append(gc);
* @param al
* alignment to pad sequences in
*/
- private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+ private void padGaps(StringBuilder sb, int pos, SequenceI profileseq,
AlignmentI al)
{
// loop over the sequences and pad with gaps where required
{
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;
}
/*
* 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[]> thatit = that.iterator();
- while (it.hasNext())
+ for (int[] thisRange : hiddenColumns)
{
- int[] thisRange = it.next();
int[] thatRange = thatit.next();
if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
{
* int column index in alignment view (count from zero)
* @return alignment column index for column
*/
- public int adjustForHiddenColumns(int column)
+ public int visibleToAbsoluteColumn(int column)
{
try
{
LOCK.readLock().lock();
int result = column;
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
}
/**
* Use this method to find out where a column will appear in the visible
* alignment when hidden columns exist. If the column is not visible, then the
- * left-most visible column will always be returned.
+ * index of the next visible column on the left will be returned (or 0 if
+ * there is no visible column on the left)
*
* @param hiddenColumn
* the column index in the full alignment including hidden columns
* @return the position of the column in the visible alignment
*/
- public int findColumnPosition(int hiddenColumn)
+ public int absoluteToVisibleColumn(int hiddenColumn)
{
try
{
LOCK.readLock().lock();
int result = hiddenColumn;
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
HiddenCursorPosition cursorPos = cursor
.findRegionForColumn(hiddenColumn);
int distance = visibleDistance;
// in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+ int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn));
Iterator<int[]> it = new ReverseRegionsIterator(0, start,
hiddenColumns);
try
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
int index = cursor.findRegionForColumn(alPos).getRegionIndex();
if (index < hiddenColumns.size())
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
int index = cursor.findRegionForColumn(alPos).getRegionIndex();
LOCK.readLock().lock();
int iSize = seqs.length;
String[] selections = new String[iSize];
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ if (!hiddenColumns.isEmpty())
{
for (int i = 0; i < iSize; i++)
{
- StringBuffer visibleSeq = new StringBuffer();
+ StringBuilder visibleSeq = new StringBuilder();
Iterator<int[]> blocks = new VisibleContigsIterator(start,
end + 1, hiddenColumns);
LOCK.readLock().lock();
int start = 0;
- if (hiddenColumns == null || hiddenColumns.size() == 0)
+ if (hiddenColumns.isEmpty())
{
return seq.findIndex(seq.getStart()) - 1;
}
if (foundStart)
{
- return findColumnPosition(start);
+ return absoluteToVisibleColumn(start);
}
// otherwise, sequence was completely hidden
return visPrev;
}
}
- /**
- * 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];
}
* @param inserts
* - columns map to bits starting from zero
*/
- public void hideMarkedBits(BitSet inserts)
+ public void hideColumns(BitSet inserts)
{
try
{
try
{
LOCK.readLock().lock();
- if (hiddenColumns == null)
- {
- return;
- }
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+
+ for (int[] range : hiddenColumns)
{
- int[] range = it.next();
inserts.set(range[0], range[1] + 1);
}
} finally
int[] lowestRange = new int[] { -1, -1 };
int[] higestRange = new int[] { -1, -1 };
- if (hiddenColumns == null)
+ if (hiddenColumns.isEmpty())
{
return new int[] { startPos, endPos };
}
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ for (int[] range : hiddenColumns)
{
- int[] range = it.next();
lowestRange = (range[0] <= startPos) ? range : lowestRange;
higestRange = (range[1] >= endPos) ? range : higestRange;
}
*
* @param res
* visible residue position, unadjusted for hidden columns
- * @return region as [start,end] or null if no matching region is found
+ * @return region as [start,end] or null if no matching region is found. If
+ * res is adjacent to two regions, returns the left region.
*/
public int[] getRegionWithEdgeAtRes(int res)
{
try
{
LOCK.readLock().lock();
- int adjres = adjustForHiddenColumns(res);
+ int adjres = visibleToAbsoluteColumn(res);
int[] reveal = null;
- if (hiddenColumns != null)
+ if (!hiddenColumns.isEmpty())
{
// look for a region ending just before adjres
int regionindex = cursor.findRegionForColumn(adjres - 1)
try
{
LOCK.readLock().lock();
- return new BoundedHiddenColsIterator(hiddenColumns);
+ return new HiddenColsIterator(hiddenColumns);
} finally
{
LOCK.readLock().unlock();
try
{
LOCK.readLock().lock();
- return new BoundedHiddenColsIterator(start, end, hiddenColumns);
+ return new HiddenColsIterator(start, end, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
LOCK.readLock().lock();
// get absolute position of column in alignment
- int absoluteStart = adjustForHiddenColumns(start);
+ int absoluteStart = visibleToAbsoluteColumn(start);
// Get cursor position and supply it to the iterator:
// Since we want visible region start, we look for a cursor for the
* 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;
int adjend = end;
if (useVisibleCoords)
{
- adjstart = adjustForHiddenColumns(start);
- adjend = adjustForHiddenColumns(end);
+ adjstart = visibleToAbsoluteColumn(start);
+ adjend = visibleToAbsoluteColumn(end);
}
try
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