X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;h=436b0ef2bb9c37960adfc2c6b72e597dddfa76c4;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=af80b7a0efbe2ae52d4c0c3ca269bd44d22fed30;hpb=d3d566fbf876a3511c06fecec695b2f59eb71169;p=jalview.git

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index af80b7a..436b0ef 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -1,7 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.so;
 
-import jalview.io.gff.SequenceOntologyI;
-
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -24,6 +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.Console;
+import jalview.io.gff.SequenceOntologyI;
+
 /**
  * A wrapper class that parses the Sequence Ontology and exposes useful access
  * methods. This version uses the BioJava parser.
@@ -77,13 +98,13 @@ public class SequenceOntology implements SequenceOntologyI
    */
   protected void loadOntologyZipFile(String ontologyFile)
   {
+    long now = System.currentTimeMillis();
     ZipInputStream zipStream = null;
     try
     {
       String zipFile = ontologyFile + ".zip";
-      System.out.println("Loading Sequence Ontology from " + zipFile);
-      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)
@@ -93,6 +114,9 @@ public class SequenceOntology implements SequenceOntologyI
           loadOboFile(zipStream);
         }
       }
+      long elapsed = System.currentTimeMillis() - now;
+      Console.info("Loaded Sequence Ontology from " + zipFile + " ("
+              + elapsed + "ms)");
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -128,8 +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();
@@ -160,21 +184,21 @@ public class SequenceOntology implements SequenceOntologyI
             boolean oldTermIsObsolete = isObsolete(replaced);
             if (newTermIsObsolete && !oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + term.getName()
+              Console.debug("Ignoring " + term.getName()
                       + " as obsolete and duplicated by "
                       + replaced.getName());
               term = replaced;
             }
             else if (!newTermIsObsolete && oldTermIsObsolete)
             {
-              System.err.println("Ignoring " + replaced.getName()
+              Console.debug("Ignoring " + replaced.getName()
                       + " as obsolete and duplicated by " + term.getName());
             }
             else
             {
-            System.err.println("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);
@@ -197,8 +221,8 @@ public class SequenceOntology implements SequenceOntologyI
     {
       try
       {
-      if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
-      {
+        if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
+        {
           return true;
         }
       } catch (NoSuchElementException e)
@@ -313,7 +337,7 @@ public class SequenceOntology implements SequenceOntologyI
     {
       if (!termsNotFound.contains(term))
       {
-        System.err.println("SO term " + term + " invalid");
+        Console.error("SO term " + term + " invalid");
         termsNotFound.add(term);
       }
     }