Merge branch 'develop' into ben/gecos_colour_schemes

[jalview.git] / src / jalview / ext / so / SequenceOntology.java

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 138aa58..436b0ef 100644 (file)
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -42,7 +42,7 @@ import org.biojava.nbio.ontology.Triple;
 import org.biojava.nbio.ontology.io.OboParser;
 import org.biojava.nbio.ontology.utils.Annotation;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.io.gff.SequenceOntologyI;
 
 /**
@@ -115,7 +115,7 @@ public class SequenceOntology implements SequenceOntologyI
         }
       }
       long elapsed = System.currentTimeMillis() - now;
-      Cache.log.info("Loaded Sequence Ontology from " + zipFile + " ("
+      Console.info("Loaded Sequence Ontology from " + zipFile + " ("
               + elapsed + "ms)");
     } catch (Exception e)
     {
@@ -184,21 +184,21 @@ public class SequenceOntology implements SequenceOntologyI
             boolean oldTermIsObsolete = isObsolete(replaced);
             if (newTermIsObsolete && !oldTermIsObsolete)
             {
-              Cache.log.debug("Ignoring " + term.getName()
+              Console.debug("Ignoring " + term.getName()
                       + " as obsolete and duplicated by "
                       + replaced.getName());
               term = replaced;
             }
             else if (!newTermIsObsolete && oldTermIsObsolete)
             {
-              Cache.log.debug("Ignoring " + replaced.getName()
+              Console.debug("Ignoring " + replaced.getName()
                       + " as obsolete and duplicated by " + term.getName());
             }
             else
             {
-              Cache.log.debug("Warning: " + term.getName()
-                      + " has replaced " + replaced.getName()
-                      + " for lookup of '" + description + "'");
+              Console.debug("Warning: " + term.getName() + " has replaced "
+                      + replaced.getName() + " for lookup of '"
+                      + description + "'");
             }
           }
           termsByDescription.put(description, term);
@@ -337,7 +337,7 @@ public class SequenceOntology implements SequenceOntologyI
     {
       if (!termsNotFound.contains(term))
       {
-        Cache.log.error("SO term " + term + " invalid");
+        Console.error("SO term " + term + " invalid");
         termsNotFound.add(term);
       }
     }