From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 8 Mar 2023 13:45:11 +0000 (+0000)
Subject: Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-4134_treeviewerfo... 
X-Git-Tag: Release_2_11_3_0~15^2^2~19
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fea1abc4a4d2c45a1ba6e6127bac5d2466de18fc;p=jalview.git

Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-4134_treeviewerforcolumns
---

fea1abc4a4d2c45a1ba6e6127bac5d2466de18fc
diff --cc src/jalview/ws/dbsources/EBIAlfaFold.java
index dd71ec3,8592bd3..d9cbbd9
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@@ -469,15 -495,9 +496,9 @@@ public class EBIAlfaFold extends EbiFil
  
      ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
              (Map<String, Object>) pae_obj);
 -
 +    ((PAEContactMatrix) matrix).makeGroups(5f, true);
      AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
-     // sm.getSequence().addAlignmentAnnotation(cmannot);
-     sm.transfer(cmannot);
-     // return true;
- 
-     StructureSelectionManager ssm = StructureSelectionManager
-             .getStructureSelectionManager(Desktop.instance);
-     List<AlignedCodonFrame> acfList = ssm.getSequenceMappings();
+     sm.getSequence().addAlignmentAnnotation(cmannot);
  
      return true;
    }