JAL-4090 JAL-1551 source license

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

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 7dd9778..987ea36 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,13 +1,45 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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)
@@ -75,28 +107,46 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
+  public String getAnnotDescr()
   {
-    // TODO Auto-generated method stub
-    return false;
+    return "Sequence distance matrix";
   }
 
   @Override
-  public SequenceI getReferenceSeq()
+  public String getAnnotLabel()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return "Sequence Distance";
   }
 
   @Override
-  public String getAnnotDescr()
+  public String getType()
   {
-    return "Sequence distance matrix";
+    return SEQUENCE_DISTANCE;
   }
 
   @Override
-  public String getAnnotLabel()
+  public int getWidth()
   {
-    return "Sequence Distance";
+    return width;
+  }
+
+  @Override
+  public int getHeight()
+  {
+    return width;
+  }
+
+  @Override
+  public double getElementAt(int _column, int i)
+  {
+    return Math.abs(_column - i);
+  }
+
+  @Override
+  protected SeqDistanceContactMatrix newMappableContactMatrix(
+          SequenceI newRefSeq, MapList newFromMapList)
+  {
+
+    return new SeqDistanceContactMatrix(width);
   }
 }