/**
*
- * Implements the SequenceI interface for a char[] based sequence object.
- *
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
*/
public class Sequence extends ASequence implements SequenceI
{
{
if (name == null)
{
- System.err
- .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ System.err.println(
+ "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
// Does sequence have the /start-end signature?
@Override
public AlignmentAnnotation[] getAnnotation()
{
- return annotation == null ? null : annotation
- .toArray(new AlignmentAnnotation[annotation.size()]);
+ return annotation == null ? null
+ : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
}
@Override
{
if (datasetSequence == null)
{
- Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, getSequenceAsString()),
+ Sequence dsseq = new Sequence(getName(),
+ AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ getSequenceAsString()),
getStart(), getEnd());
datasetSequence = dsseq;
List<SequenceFeature> sfs = entry.getSequenceFeatures();
for (SequenceFeature feature : sfs)
{
- SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
: new SequenceFeature[] { new SequenceFeature(feature) };
if (sf != null)
{
}
}
// whilst it looks like it is a primary ref, we also sanity check type
- if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
- DBRefUtils.getCanonicalName(ref.getSource())))
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
+ .equals(DBRefUtils.getCanonicalName(ref.getSource())))
{
// PDB dbrefs imply there should be a PDBEntry associated
// TODO: tighten PDB dbrefs
return count;
}
+
+ @Override
+ public List<SequenceFeature[]> adjustFeatures(int fromColumn, int toColumn)
+ {
+ List<SequenceFeature[]> amended = new ArrayList<>();
+
+ if (toColumn < fromColumn)
+ {
+ return amended;
+ }
+
+ synchronized (sequenceFeatureStore)
+ {
+ /*
+ * get features that overlap or span the cut region
+ */
+ List<SequenceFeature> overlaps = findFeatures(fromColumn, toColumn);
+ int cutWidth = toColumn - fromColumn + 1;
+
+ /*
+ * get features that strictly follow the cut region,
+ * and shift them left by the width of the cut
+ */
+ List<SequenceFeature> follow = findFeatures(toColumn + 1,
+ Integer.MAX_VALUE);
+ follow.removeAll(overlaps);
+ for (SequenceFeature sf : follow)
+ {
+ SequenceFeature copy = new SequenceFeature(sf, sf.getBegin()
+ - cutWidth, sf.getEnd() - cutWidth, sf.getFeatureGroup(),
+ sf.getScore());
+ deleteFeature(sf);
+ addSequenceFeature(copy);
+ }
+
+ /*
+ * adjust start-end of overlapping features, and delete if enclosed by
+ * the cut, or a partially overlapping contact feature
+ */
+ for (SequenceFeature sf : overlaps)
+ {
+ // TODO recode to compute newBegin, newEnd, isDelete
+ // then perform the action
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int startCol = findIndex(sfBegin);
+ int endCol = findIndex(sfEnd);
+ if (startCol >= fromColumn && endCol <= toColumn)
+ {
+ // within cut region - delete feature
+ deleteFeature(sf);
+ amended.add(new SequenceFeature[] { sf, null });
+ continue;
+ }
+ if (startCol < fromColumn && endCol > toColumn)
+ {
+ // feature spans cut region - shift end left
+ SequenceFeature copy = new SequenceFeature(sf, sf.getBegin(),
+ sf.getEnd() - cutWidth, sf.getFeatureGroup(),
+ sf.getScore());
+ deleteFeature(sf);
+ addSequenceFeature(copy);
+ amended.add(new SequenceFeature[] { sf, copy });
+ continue;
+ }
+ // todo partial overlap - delete if contact feature
+ }
+ }
+
+ return amended;
+ }
}