JAL-3855 report download errors as errors!

[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 0e148ff..ba78199 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -197,7 +197,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                 "exception.no_pdb_records_for_chain", new String[]
                 { id, ((chain == null) ? "' '" : chain) }));
       }
-      retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
+      // done during structure retrieval
+      // retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
 
     } catch (Exception ex) // Problem parsing PDB file
     {
@@ -247,7 +248,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       }
     } catch (Exception pae_ex)
     {
-      Console.debug("Couldn't download PAE", pae_ex);
+      Console.error("Couldn't download PAE", pae_ex);
     }
 
   }
@@ -274,11 +275,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             pdbAlignment.getSequenceAt(0),
             (Map<String, Object>) pae_obj.get(0));
 
-    // THIS IS NOT GOING TO WORK !!!
-    // ?? StructureFile assumes sequenceI holds all data, so AlignmentAnnotation
-    // needs to hold the contact matrix data.
-    pdbAlignment.getSequenceAt(0)
-            .addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+    AlignmentAnnotation cmannot = pdbAlignment.getSequenceAt(0)
+            .addContactList(matrix);
+    pdbAlignment.addAnnotation(cmannot);
     return true;
   }