*/
protected void updateCursor(int residuePos, int column, int startColumn)
{
- int endColumn = cursor == null ? 0 : cursor.lastColumnPosition;
+ /*
+ * preserve end residue column provided cursor was valid
+ */
+ int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
if (residuePos == this.end)
{
endColumn = column;
}
/**
+ * {@inheritDoc}
+ */
+ @Override
+ public Range findPositions(int fromColumn, int toColumn)
+ {
+ if (toColumn < fromColumn || fromColumn < 1)
+ {
+ return null;
+ }
+
+ /*
+ * find the first non-gapped position, if any
+ */
+ int firstPosition = 0;
+ int col = fromColumn - 1;
+ int length = sequence.length;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col]))
+ {
+ firstPosition = findPosition(col++);
+ break;
+ }
+ col++;
+ }
+
+ if (firstPosition == 0)
+ {
+ return null;
+ }
+
+ /*
+ * find the last non-gapped position
+ */
+ int lastPosition = firstPosition;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col++]))
+ {
+ lastPosition++;
+ }
+ }
+
+ return new Range(firstPosition, lastPosition);
+ }
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
String... types)
{
int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
- int endPos = findPosition(toColumn - 1);
- // to trace / debug behaviour:
- // System.out
- // .println(String
- // .format("%s.findFeatures columns [%d-%d] positions [%d-%d] leaves cursor %s",
- // getName(), fromColumn, toColumn, startPos,
- // endPos, cursor));
- List<SequenceFeature> result = new ArrayList<>();
- if (datasetSequence != null)
- {
- result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
- types);
- }
- else
- {
- result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
- }
+ int endPos = fromColumn == toColumn ? startPos
+ : findPosition(toColumn - 1);
+
+ List<SequenceFeature> result = getFeatures().findFeatures(startPos,
+ endPos, types);
/*
- * if the start or end column is gapped, startPos or endPos may be to the
- * left or right, and we may have included adjacent or enclosing features;
+ * if end column is gapped, endPos may be to the right,
+ * 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[fromColumn - 1])
- || Comparison.isGap(sequence[toColumn - 1]))
+ if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
{
ListIterator<SequenceFeature> it = result.listIterator();
while (it.hasNext())
{
SequenceFeature sf = it.next();
- int featureStartColumn = findIndex(sf.getBegin());
- int featureEndColumn = findIndex(sf.getEnd());
- boolean noOverlap = featureStartColumn > toColumn
- || featureEndColumn < fromColumn;
-
- /*
- * reject an 'enclosing' feature if it is actually a contact feature
- */
- if (sf.isContactFeature() && featureStartColumn < fromColumn
- && featureEndColumn > toColumn)
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int featureStartColumn = findIndex(sfBegin);
+ if (featureStartColumn > toColumn)
{
- noOverlap = true;
+ it.remove();
}
- if (noOverlap)
+ else if (featureStartColumn < fromColumn)
{
- it.remove();
+ int featureEndColumn = sfEnd == sfBegin ? featureStartColumn
+ : findIndex(sfEnd);
+ if (featureEndColumn < fromColumn)
+ {
+ it.remove();
+ }
+ else if (featureEndColumn > toColumn && sf.isContactFeature())
+ {
+ /*
+ * remove an enclosing feature if it is a contact feature
+ */
+ it.remove();
+ }
}
}
}