JAL-1551 spotlessApply

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

diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java
index ac1b267..af083dd 100644 (file)
--- a/src/jalview/datamodel/ContactMapHolder.java
+++ b/src/jalview/datamodel/ContactMapHolder.java
@@ -5,6 +5,8 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 
+import jalview.ws.datamodel.MappableContactMatrixI;
+
 public class ContactMapHolder implements ContactMapHolderI
 {
 
@@ -28,25 +30,38 @@ public class ContactMapHolder implements ContactMapHolderI
     {
       return null;
     }
+    if (cm instanceof MappableContactMatrixI)
+    {
+      if (_aa.sequenceRef != null)
+      {
+        return ((MappableContactMatrixI) cm)
+                .getMappableContactList(_aa.sequenceRef, column);
+      }
+    }
+    // TODO: could resolve sequence position to column position here
+    // TODO: what about for complexes - where contactMatrix may involve two or
+    // more sequences
     return cm.getContactList(column);
   }
 
   @Override
   public AlignmentAnnotation addContactList(ContactMatrixI cm)
   {
-    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
-            "Contact Matrix", new Annotation[0]);
-    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+
+    AlignmentAnnotation aa = new AlignmentAnnotation(cm.getAnnotLabel(),
+            cm.getAnnotDescr(), new Annotation[0]);
+    aa.graph = AlignmentAnnotation.CONTACT_MAP;
     aa.graphMin = cm.getMin();
     aa.graphMax = cm.getMax();
     aa.editable = false;
-    // aa.autoCalculated = true;
+    aa.calcId = cm.getType();
+
     contactmaps.put(aa.annotationId, cm);
     // TODO: contact matrices could be intra or inter - more than one refseq
     // possible!
-    if (cm.hasReferenceSeq())
+    if (cm instanceof MappableContactMatrixI)
     {
-      aa.setSequenceRef(cm.getReferenceSeq());
+      aa.setSequenceRef(((MappableContactMatrixI) cm).getReferenceSeq());
     }
     return aa;
   }
@@ -61,6 +76,21 @@ public class ContactMapHolder implements ContactMapHolderI
   public void addContactListFor(AlignmentAnnotation annotation,
           ContactMatrixI cm)
   {
+    // update annotation with data from contact map
+    annotation.graphMin = cm.getMin();
+    annotation.graphMax = cm.getMax();
+    annotation.editable = false;
+    annotation.graph = AlignmentAnnotation.CONTACT_MAP;
+    annotation.calcId = cm.getType();
+    if (annotation.label == null || "".equals(annotation.label))
+    {
+      annotation.label = cm.getAnnotLabel();
+
+    }
+    if (annotation.description == null || "".equals(annotation.description))
+    {
+      annotation.description = cm.getAnnotDescr();
+    }
     contactmaps.put(annotation.annotationId, cm);
   }
 }