JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

[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 a4c195f..14969fe 100644 (file)
--- 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.
@@ -102,8 +103,8 @@ public class SequenceOntology implements SequenceOntologyI
     try
     {
       String zipFile = ontologyFile + ".zip";
-      InputStream inStream = this.getClass().getResourceAsStream(
-              "/" + zipFile);
+      InputStream inStream = this.getClass()
+              .getResourceAsStream("/" + zipFile);
       zipStream = new ZipInputStream(new BufferedInputStream(inStream));
       ZipEntry entry;
       while ((entry = zipStream.getNextEntry()) != null)
@@ -114,7 +115,7 @@ public class SequenceOntology implements SequenceOntologyI
         }
       }
       long elapsed = System.currentTimeMillis() - now;
-      System.out.println("Loaded Sequence Ontology from " + zipFile + " ("
+      Cache.info("Loaded Sequence Ontology from " + zipFile + " ("
               + elapsed + "ms)");
     } catch (Exception e)
     {
@@ -151,8 +152,8 @@ public class SequenceOntology implements SequenceOntologyI
    * @throws ParseException
    * @throws IOException
    */
-  protected void loadOboFile(InputStream is) throws ParseException,
-          IOException
+  protected void loadOboFile(InputStream is)
+          throws ParseException, IOException
   {
     BufferedReader oboFile = new BufferedReader(new InputStreamReader(is));
     OboParser parser = new OboParser();
@@ -183,19 +184,19 @@ public class SequenceOntology implements SequenceOntologyI
             boolean oldTermIsObsolete = isObsolete(replaced);
             if (newTermIsObsolete && !oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + term.getName()
+              Cache.debug("Ignoring " + term.getName()
                       + " as obsolete and duplicated by "
                       + replaced.getName());
               term = replaced;
             }
             else if (!newTermIsObsolete && oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + replaced.getName()
+              Cache.debug("Ignoring " + replaced.getName()
                       + " as obsolete and duplicated by " + term.getName());
             }
             else
             {
-              System.err.println("Warning: " + term.getName()
+              Cache.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.error("SO term " + term + " invalid");
         termsNotFound.add(term);
       }
     }