X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqDistanceContactMatrix.java;h=f8fd750955d0861ca20606d3b4b6a7ea85ff7812;hb=d622d93ba5a3e596a4ea29bc1ba75bf2acacfdf0;hp=ee7de5ed66531d3a66dbf841224ecf3ec50a4529;hpb=3e88ca066c0cc12f1f1f4c63e9cd49e19586b2bd;p=jalview.git

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index ee7de5e..f8fd750 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,48 +1,68 @@
 package jalview.datamodel;
 
 import java.awt.Color;
+import java.util.BitSet;
+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;
 
   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)
   {
-    if (column<0 || column >= width)
+    if (column < 0 || column >= width)
     {
       return null;
     }
-    return new ContactListI() {
+    return new ContactListImpl(new ContactListProviderI()
+    {
+
       int p = column;
-      @Override
-      public Color getColorForScore(int column)
-      {
-        return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p), 0, Color.white, width, Color.magenta);
-      }
-      @Override
-      public Color getColorForRange(int from_column, int to_column)
-      {
-        return jalview.util.ColorUtils.getGraduatedColour(
-                Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
-                Color.magenta);
-      }
 
-      @Override
-      public int getColumnWidth()
-      {
-        return 1;
-      }
+      // @Override
+      // public Color getColorForScore(int column)
+      // {
+      // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
+      // 0, Color.white, width, Color.magenta);
+      // }
+      // @Override
+      // public Color getColorForRange(int from_column, int to_column)
+      // {
+      // return jalview.util.ColorUtils.getGraduatedColour(
+      // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
+      // Color.magenta);
+      // }
+
       @Override
       public int getContactHeight()
       {
@@ -51,11 +71,58 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
       }
 
       @Override
+      public int getPosition()
+      {
+        return p;
+      }
+
+      @Override
       public double getContactAt(int column)
       {
         return Math.abs(column - p);
       }
-    };
+    });
   }
 
+  @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;
+  }
+  @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);
+  }
 }