Merge branch 'develop' into releases/Release_2_11_3_Branch

[jalview.git] / src / jalview / datamodel / SeqDistanceContactMatrix.java

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index ec19b25..b04ac13 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -7,14 +7,15 @@ 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 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;
@@ -82,6 +83,7 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
       }
     });
   }
+
   @Override
   public String getAnnotDescr()
   {
@@ -112,16 +114,15 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
     return width;
   }
   @Override
-  protected double getElementAt(int _column, int i)
+  public 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);
   }
 }