Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / ws / slivkaws / SlivkaAnnotationServiceInstance.java

diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
index 3c80fbc..999951a 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -2,6 +2,7 @@ package jalview.ws.slivkaws;
 
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
@@ -83,20 +84,20 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
     }
     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
     if (annotFile == null
-        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getContentUrl().toString(), DataSourceType.URL))
+        || !new AnnotationFile().readAnnotationFileWithCalcId(aln, service.getId(), annotFile.getContentUrl().toString(), DataSourceType.URL))
     {
-      Cache.log.debug("No annotation from slivka job\n" + annotFile);
+      Console.debug("No annotation from slivka job\n" + annotFile);
     }
     else {
-      Cache.log.debug("Annotation file loaded " + annotFile);
+      Console.debug("Annotation file loaded " + annotFile);
     }
     if (featFile == null
         || !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true))
     {
-      Cache.log.debug("No features from slivka job\n" + featFile);
+      Console.debug("No features from slivka job\n" + featFile);
     }
     else {
-      Cache.log.debug("Features feil loaded " + featFile);
+      Console.debug("Features feil loaded " + featFile);
     }
     return Arrays.asList(aln.getAlignmentAnnotation());
   }