X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqDistanceContactMatrix.java;h=987ea36ed6f1f32f34352f245ac3ca813eab734f;hb=164fb77632cc3c9a3b5f5ac5290eadec920ffbc6;hp=7dd9778b2ca2aeb6cf93fc71b8b8c22202a11fba;hpb=059c891e783721341341b71ef222559c9f68fe31;p=jalview.git
diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 7dd9778..987ea36 100644
--- 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 .
+ * 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
+ 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);
}
}