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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git]
/
src
/
jalview
/
datamodel
/
SeqDistanceContactMatrix.java
diff --git
a/src/jalview/datamodel/SeqDistanceContactMatrix.java
b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index
a915bb0
..
f8fd750
100644
(file)
--- a/
src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/
src/jalview/datamodel/SeqDistanceContactMatrix.java
@@
-5,16
+5,19
@@
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
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
*
*/
/**
* 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 static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
-
private int width = 0;
public SeqDistanceContactMatrix(int width)
private int width = 0;
public SeqDistanceContactMatrix(int width)
@@
-82,20
+85,6
@@
public class SeqDistanceContactMatrix implements ContactMatrixI
}
@Override
}
@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";
public String getAnnotDescr()
{
return "Sequence distance matrix";
@@
-124,47
+113,16
@@
public class SeqDistanceContactMatrix implements ContactMatrixI
{
return width;
}
{
return width;
}
-
- private List<BitSet> groups = null;
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- }
-
@Override
@Override
- public boolean hasGroups()
+ protected double getElementAt(int _column, int i)
{
{
- return groups != null;
+ return Math.abs(_column - i);
}
}
-
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
@Override
@Override
- public Color getColourForGroup(BitSet bs)
+ protected SeqDistanceContactMatrix newMappableContactMatrix(
+ SequenceI newRefSeq, MapList newFromMapList)
{
{
- 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);
+ return new SeqDistanceContactMatrix(width);
}
}
}
}