*/
Vector<AlignmentAnnotation> annotation;
- /**
- * The index of the sequence in a MSA
- */
- int index = -1;
-
- private SequenceFeatures sequenceFeatureStore;
+ private SequenceFeaturesI sequenceFeatureStore;
/*
* A cursor holding the approximate current view position to the sequence,
}
}
- /**
- * @return The index (zero-based) on this sequence in the MSA. It returns
- * {@code -1} if this information is not available.
- */
- @Override
- public int getIndex()
- {
- return index;
- }
-
- /**
- * Defines the position of this sequence in the MSA. Use the value {@code -1}
- * if this information is undefined.
- *
- * @param The
- * position for this sequence. This value is zero-based (zero for
- * this first sequence)
- */
- @Override
- public void setIndex(int value)
- {
- index = value;
- }
-
@Override
public void setRNA(RNA r)
{
* and we may have included adjacent or enclosing features;
* remove any that are not enclosing, non-contact features
*/
- if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
+ boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+ && Comparison.isGap(sequence[toColumn - 1]);
+ if (endPos > this.end || endColumnIsGapped)
{
ListIterator<SequenceFeature> it = result.listIterator();
while (it.hasNext())