package jalview.datamodel;
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
/**
* Dummy contact matrix based on sequence distance
*
*/
public class SeqDistanceContactMatrix implements ContactMatrixI
{
+ private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
{
this.width = width;
}
+
+ @Override
+ public float getMin()
+ {
+ return 0f;
+ }
+
+ @Override
+ public float getMax()
+ {
+ return width;
+ }
+
@Override
public ContactListI getContactList(final int column)
{
}
@Override
+ public int getPosition()
+ {
+ return p;
+ }
+
+ @Override
public double getContactAt(int column)
{
return Math.abs(column - p);
});
}
+ @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()
+ {
+ return "Sequence distance matrix";
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ return "Sequence Distance";
+ }
+
+ @Override
+ public String getType()
+ {
+ return SEQUENCE_DISTANCE;
+ }
+
+ @Override
+ public int getWidth()
+ {
+ return width;
+ }
+
+ @Override
+ public int getHeight()
+ {
+ 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);
+ }
}