import java.util.HashMap;
import java.util.List;
+import jalview.util.MapList;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
+
/**
* Dummy contact matrix based on sequence distance
*
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix implements ContactMatrixI
+public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceContactMatrix> implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
private int width = 0;
}
});
}
-
- @Override
- public boolean hasReferenceSeq()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
@Override
public String getAnnotDescr()
{
{
colorMap.put(bs,color);
}
+ @Override
+ protected double getElementAt(int _column, int i)
+ {
+ return Math.abs(_column-i);
+ }
+
+ @Override
+ protected SeqDistanceContactMatrix newMappableContactMatrix(
+ SequenceI newRefSeq, MapList newFromMapList)
+ {
+
+ return new SeqDistanceContactMatrix(width);
+ }
}