JAL-629 implementation of --tempfac options

[jalview.git] / src / jalview / ws / datamodel / alphafold / PAEContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 8b6771e..3298a96 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -30,7 +30,6 @@ public class PAEContactMatrix implements ContactMatrixI
 
   @SuppressWarnings("unchecked")
   public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
-          throws Exception
   {
     refSeq = _refSeq;
     while (refSeq.getDatasetSequence() != null)
@@ -75,6 +74,8 @@ public class PAEContactMatrix implements ContactMatrixI
       row++;
       col = 0;
     }
+    maxcol = length;
+    maxrow = length;
   }
 
   /**
@@ -124,6 +125,12 @@ public class PAEContactMatrix implements ContactMatrixI
     return new ContactListImpl(new ContactListProviderI()
     {
       @Override
+      public int getPosition()
+      {
+        return _column;
+      }
+
+      @Override
       public int getContactHeight()
       {
         return maxcol - 1;
@@ -166,4 +173,15 @@ public class PAEContactMatrix implements ContactMatrixI
     return refSeq;
   }
 
+  @Override
+  public String getAnnotDescr()
+  {
+    return "Predicted Alignment Error for " + refSeq.getName();
+  }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "pAE Matrix";
+  }
 }