JAL-629 Adding PAE and TFType at structure loading time. Display PAE automatically

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index d0538c1..8044717 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -314,6 +314,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     if (isStruct)
     {
+      // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+      // different params.
       StructureSelectionManager ssm = StructureSelectionManager
               .getStructureSelectionManager(Desktop.instance);
       if (ssm != null)
@@ -474,6 +476,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return paeDict;
   }
 
+  // ###### TEST THIS
   public static boolean importPaeJSONAsContactMatrixToStructure(
           StructureMapping[] smArray, InputStream paeInput, String label)
           throws IOException, ParseException
@@ -505,9 +508,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             (Map<String, Object>) pae_obj);
     ((PAEContactMatrix) matrix).makeGroups(5f, true);
     AlignmentAnnotation cmannot = seq.addContactList(matrix);
-    seq.addAlignmentAnnotation(cmannot);
-    // seq.addAlignmentAnnotation(cmannot);
-
+    /* this already happens in Sequence.addContactList()
+     seq.addAlignmentAnnotation(cmannot);
+     */
     return true;
   }