X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;fp=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;h=138aa58dc669abecd5d924339182387705145bfa;hb=f8691b979a068d0992608a51de66271f299dbb6b;hp=0d631e66ee3ed0c3124eb5f69f63d8a5f521f5f0;hpb=7c269dc87e6fda52db3d73d07bc5f3e879e1f681;p=jalview.git

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 0d631e6..138aa58 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -20,8 +20,6 @@
  */
 package jalview.ext.so;
 
-import jalview.io.gff.SequenceOntologyI;
-
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -44,6 +42,9 @@ 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.io.gff.SequenceOntologyI;
+
 /**
  * A wrapper class that parses the Sequence Ontology and exposes useful access
  * methods. This version uses the BioJava parser.
@@ -114,7 +115,7 @@ public class SequenceOntology implements SequenceOntologyI
         }
       }
       long elapsed = System.currentTimeMillis() - now;
-      System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+      Cache.log.info("Loaded Sequence Ontology from " + zipFile + " ("
               + elapsed + "ms)");
     } catch (Exception e)
     {
@@ -183,19 +184,19 @@ public class SequenceOntology implements SequenceOntologyI
             boolean oldTermIsObsolete = isObsolete(replaced);
             if (newTermIsObsolete && !oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + term.getName()
+              Cache.log.debug("Ignoring " + term.getName()
                       + " as obsolete and duplicated by "
                       + replaced.getName());
               term = replaced;
             }
             else if (!newTermIsObsolete && oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + replaced.getName()
+              Cache.log.debug("Ignoring " + replaced.getName()
                       + " as obsolete and duplicated by " + term.getName());
             }
             else
             {
-              System.err.println("Warning: " + term.getName()
+              Cache.log.debug("Warning: " + term.getName()
                       + " has replaced " + replaced.getName()
                       + " for lookup of '" + description + "'");
             }
@@ -336,7 +337,7 @@ public class SequenceOntology implements SequenceOntologyI
     {
       if (!termsNotFound.contains(term))
       {
-        System.err.println("SO term " + term + " invalid");
+        Cache.log.error("SO term " + term + " invalid");
         termsNotFound.add(term);
       }
     }