import jalview.util.MapList;
import jalview.ws.datamodel.alphafold.MappableContactMatrix;
-
/**
* Dummy contact matrix based on sequence distance
*
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix extends MappableContactMatrix<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 String getAnnotDescr()
{
{
return width;
}
- private List<BitSet> groups=null;
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- }
- @Override
- public boolean hasGroups()
- {
- return groups!=null;
- }
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- HashMap<BitSet,Color> colorMap = new HashMap<>();
- @Override
- public Color getColourForGroup(BitSet bs)
- {
- if (bs==null) {
- return Color.white;
- }
- Color groupCol=colorMap.get(bs);
- if (groupCol==null)
- {
- return Color.white;
- }
- return groupCol;
- }
- @Override
- public void setColorForGroup(BitSet bs,Color color)
- {
- colorMap.put(bs,color);
- }
@Override
protected double getElementAt(int _column, int i)
{
- return Math.abs(_column-i);
+ return Math.abs(_column - i);
}
-
@Override
protected SeqDistanceContactMatrix newMappableContactMatrix(
SequenceI newRefSeq, MapList newFromMapList)
{
-
+
return new SeqDistanceContactMatrix(width);
}
}