X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=b251a8901387bd8d41357ab3bafeaf7605ba28f0;hb=5aba41507c4b7887ad4cf1fc19ed923e9a6bc7c7;hp=2289ac6314196fe08a62aa4797c8ef5897f0cc58;hpb=f80f1dd5762b7c035ca2502f35f059e9f5fe5a49;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2289ac6..b251a89 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,6 +30,7 @@ import jalview.util.MessageManager;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
@@ -661,7 +662,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
-  public int findIndex(SearchResults results)
+  public int findIndex(SearchResultsI results)
   {
     int i = 0;
 
@@ -1837,7 +1838,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**
@@ -1946,4 +1947,38 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  Map<Object, ContactMatrixI> contactmaps = new HashMap<Object, ContactMatrixI>();
+  @Override
+  public
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
+    if (cm == null)
+    {
+      return null;
+    }
+    return cm.getContactList(column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    Annotation _aa[] = new Annotation[getWidth()];
+    Annotation dummy = new Annotation(0.0f);
+    for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+    {
+      ;
+    }
+    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
+            "Contact Matrix", _aa);
+    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+    aa.graphMin = 0f;
+    aa.graphMax = 100f;
+    aa.editable = false;
+    // aa.autoCalculated = true;
+    contactmaps.put(aa.annotationId, cm);
+    addAnnotation(aa);
+    return aa;
+  }
 }