Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-4134_treeviewerfo...

[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 8609046..d9cbbd9 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -154,20 +154,12 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    // used by the SequenceFetcher. Put forSequencesOnly to true (don't open
-    // structure viewer later)
-    return getSequenceRecords(queries, null, true);
+    return getSequenceRecords(queries, null);
   }
 
   public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
           throws Exception
   {
-    return getSequenceRecords(queries, retrievalUrl, false);
-  }
-
-  public AlignmentI getSequenceRecords(String queries, String retrievalUrl,
-          boolean forSequencesOnly) throws Exception
-  {
     AlignmentI pdbAlignment = null;
     String chain = null;
     String id = null;
@@ -226,8 +218,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       stopQuery();
       throw (ex);
     }
-    // distinguish between AlphaFold cif/pdb opened as structure file or fetched
-    // as sequence/alignment
     return pdbAlignment;
   }
 
@@ -452,6 +442,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
     ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) paeDict);
+    ((PAEContactMatrix) matrix).makeGroups(5f, true);
 
     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
     pdbAlignment.addAnnotation(cmannot);
@@ -505,7 +496,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     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);