import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
+import java.util.ListIterator;
import java.util.Vector;
import com.stevesoft.pat.Regex;
}
/**
- * {@inheritDoc}
- */
- @Override
- public Range findPositions(int fromCol, int toCol)
- {
- /*
- * count residues before fromCol
- */
- int j = 0;
- int count = 0;
- int seqlen = sequence.length;
- while (j < fromCol && j < seqlen)
- {
- if (!Comparison.isGap(sequence[j]))
- {
- count++;
- }
- j++;
- }
-
- /*
- * find first and last residues between fromCol and toCol
- */
- int firstPos = 0;
- int lastPos = 0;
- int firstPosCol = 0;
- boolean foundFirst = false;
-
- while (j <= toCol && j < seqlen)
- {
- if (!Comparison.isGap(sequence[j]))
- {
- count++;
- if (!foundFirst)
- {
- firstPos = count;
- firstPosCol = j;
- foundFirst = true;
- }
- lastPos = count;
- }
- j++;
- }
-
- if (firstPos == 0)
- {
- /*
- * no residues in this range
- */
- return null;
- }
-
- /*
- * adjust for sequence start coordinate
- */
- firstPos += start - 1;
- lastPos += start - 1;
-
- return new Range(firstPos, lastPos);
- }
-
- /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
* {@inheritDoc}
*/
@Override
- public List<SequenceFeature> findFeatures(int from, int to,
+ public List<SequenceFeature> findFeatures(int fromColumn, int toColumn,
String... types)
{
+ int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
+ int endPos = findPosition(toColumn - 1);
+
+ List<SequenceFeature> result = new ArrayList<>();
if (datasetSequence != null)
{
- return datasetSequence.findFeatures(from, to, types);
+ result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+ types);
}
- return sequenceFeatureStore.findFeatures(from, to, types);
+ else
+ {
+ result = sequenceFeatureStore.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;
+ * remove any that are not enclosing, non-contact features
+ */
+ if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
+ || 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)
+ {
+ noOverlap = true;
+ }
+ if (noOverlap)
+ {
+ it.remove();
+ }
+ }
+ }
+
+ return result;
}
}