package jalview.datamodel;
import jalview.util.Comparison;
-import jalview.util.ShiftList;
import java.util.ArrayList;
import java.util.BitSet;
}
/**
- * removes intersection of position,length ranges in deletions from the
- * start,end regions marked in intervals.
- *
- * @param shifts
- * @param intervals
- * @return
- */
- private boolean pruneIntervalList(final List<int[]> shifts,
- ArrayList<int[]> intervals)
- {
- boolean pruned = false;
- int i = 0;
- int j = intervals.size() - 1;
- int s = 0;
- int t = shifts.size() - 1;
- int[] hr = intervals.get(i);
- int[] sr = shifts.get(s);
- while (i <= j && s <= t)
- {
- boolean trailinghn = hr[1] >= sr[0];
- if (!trailinghn)
- {
- if (i < j)
- {
- hr = intervals.get(++i);
- }
- else
- {
- i++;
- }
- continue;
- }
- int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
- if (endshift < hr[0] || endshift < sr[0])
- { // leadinghc disjoint or not a deletion
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- boolean leadinghn = hr[0] >= sr[0];
- boolean leadinghc = hr[0] < endshift;
- boolean trailinghc = hr[1] < endshift;
- if (leadinghn)
- {
- if (trailinghc)
- { // deleted hidden region.
- intervals.remove(i);
- pruned = true;
- j--;
- if (i <= j)
- {
- hr = intervals.get(i);
- }
- continue;
- }
- if (leadinghc)
- {
- hr[0] = endshift; // clip c terminal region
- leadinghn = !leadinghn;
- pruned = true;
- }
- }
- if (!leadinghn)
- {
- if (trailinghc)
- {
- if (trailinghn)
- {
- hr[1] = sr[0] - 1;
- pruned = true;
- }
- }
- else
- {
- // sr contained in hr
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- }
- }
- return pruned; // true if any interval was removed or modified by
- // operations.
- }
-
- /**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
- *
- * @param deletions
- */
- public void pruneDeletions(List<int[]> shifts)
- {
- try
- {
- LOCK.writeLock().lock();
- // delete any intervals intersecting.
- if (hiddenColumns != null)
- {
- pruneIntervalList(shifts, hiddenColumns);
- if (hiddenColumns != null && hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
* Add gaps into the sequences aligned to profileseq under the given
* AlignmentView
*
SequenceI origseq)
{
char gc = al.getGapCharacter();
- // recover mapping between sequence's non-gap positions and positions
- // mapping to view.
- pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
- int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
- int spos = 0;
- int offset = 0;
- // add profile to visible contigs
- for (int v = 0; v < viscontigs.length; v += 2)
- {
- if (viscontigs[v] > spos)
+ // 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
+ ArrayList<int[]> regions = getHiddenColumnsCopy();
+ ArrayList<int[]> newhidden = new ArrayList<>();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ for (int[] region : regions)
+ {
+ // 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])
{
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ gapPosition++;
+ if (gaps.get(gapPosition))
{
- sb.append(gc);
+ numGapsBefore++;
}
- 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() <= spos + offset)
- {
- // pad sequence
- int diff = spos + offset - sq.length() - 1;
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = spos + offset - sq.length() - 1) > 0)
- {
- // sq = sq
- // + ((diff >= sb.length()) ? sb.toString() : sb
- // .substring(0, diff));
- 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, spos + offset)
- + sb.toString() + sq.substring(spos + offset));
- }
- }
- }
- // offset+=sb.length();
}
- spos = viscontigs[v + 1] + 1;
- }
- if ((offset + spos) < profileseq.getLength())
- {
- // pad the final region with gaps.
+
+ 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, ns = profileseq.getLength() - spos
- - offset; s < ns; s++)
+ for (int s = 0; s < right - left + 1; s++)
{
sb.append(gc);
}
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
- {
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj == profileseq)
- {
- continue;
- }
- String sq = sqobj.getSequenceAsString();
- // pad sequence
- int diff = origseq.getLength() - sq.length();
- while (diff > 0)
- {
- // sq = sq
- // + ((diff >= sb.length()) ? sb.toString() : sb
- // .substring(0, diff));
- if (diff >= sb.length())
- {
- sq += sb.toString();
- }
- else
- {
- char[] buf = new char[diff];
- sb.getChars(0, diff, buf, 0);
- sq += buf.toString();
- }
- diff = origseq.getLength() - sq.length();
- }
- }
- }
- }
-
- /**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
- *
- * @param deletions
- */
- private void pruneDeletions(ShiftList deletions)
- {
- if (deletions != null)
- {
- final List<int[]> shifts = deletions.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- pruneDeletions(shifts);
+ padGaps(sb, left, profileseq, al);
- // and shift the rest.
- this.compensateForEdits(deletions);
- }
}
+ hiddenColumns = newhidden;
}
/**
- * Adjust hidden column boundaries based on a series of column additions or
- * deletions in visible regions.
+ * Pad gaps in all sequences in alignment except profileseq
*
- * @param shiftrecord
- * @return
+ * @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 ShiftList compensateForEdits(ShiftList shiftrecord)
+ private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+ AlignmentI al)
{
- if (shiftrecord != null)
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
{
- final List<int[]> shifts = shiftrecord.getShifts();
- if (shifts != null && shifts.size() > 0)
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
{
- int shifted = 0;
- for (int i = 0, j = shifts.size(); i < j; i++)
+ 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
{
- int[] sh = shifts.get(i);
- compensateForDelEdits(shifted + sh[0], sh[1]);
- shifted -= sh[1];
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, pos) + sb.toString() + sq.substring(pos));
}
}
- return shiftrecord.getInverse();
}
- return null;
}
/**
{
if (pdbIds == null)
{
- pdbIds = new Vector<PDBEntry>();
+ pdbIds = new Vector<>();
pdbIds.add(entry);
return true;
}
return map;
}
+ /**
+ * Build a bitset corresponding to sequence gaps
+ *
+ * @return a BitSet where set values correspond to gaps in the sequence
+ */
+ @Override
+ public BitSet gapBitset()
+ {
+ BitSet gaps = new BitSet(sequence.length);
+ int j = 0;
+ while (j < sequence.length)
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ gaps.set(j);
+ }
+ j++;
+ }
+ return gaps;
+ }
+
@Override
public int[] findPositionMap()
{
@Override
public List<int[]> getInsertions()
{
- ArrayList<int[]> map = new ArrayList<int[]>();
+ ArrayList<int[]> map = new ArrayList<>();
int lastj = -1, j = 0;
int pos = start;
int seqlen = sequence.length;
{
if (this.annotation == null)
{
- this.annotation = new Vector<AlignmentAnnotation>();
+ this.annotation = new Vector<>();
}
if (!this.annotation.contains(annotation))
{
return null;
}
- Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+ Vector<AlignmentAnnotation> subset = new Vector<>();
Enumeration<AlignmentAnnotation> e = annotation.elements();
while (e.hasMoreElements())
{
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
- List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
}
synchronized (dbrefs)
{
- List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> primaries = new ArrayList<>();
DBRefEntry[] tmp = new DBRefEntry[1];
for (DBRefEntry ref : dbrefs)
{
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