in progress

[jalview.git] / forester / java / src / org / forester / go / GoUtils.java

diff --git a/forester/java/src/org/forester/go/GoUtils.java b/forester/java/src/org/forester/go/GoUtils.java
index 680489a..fa08ef2 100644 (file)
--- a/forester/java/src/org/forester/go/GoUtils.java
+++ b/forester/java/src/org/forester/go/GoUtils.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.go;
 
@@ -50,9 +50,9 @@ public final class GoUtils {
 
     /**
      * This is for counting the how many times each GO term in 'categories'
-     * is a (direct or indirect) super term of the GO terms in 'experiment_set'. 
-     * 
-     * 
+     * is a (direct or indirect) super term of the GO terms in 'experiment_set'.
+     *
+     *
      * @param categories the set of super terms to be counted
      * @param experiment_set the list of GO terms to be analyzed
      * @param all_go_terms all terms in the ontology
@@ -160,7 +160,7 @@ public final class GoUtils {
             penultimate = my_go_term;
             if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) {
                 throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 )
-                        + "] not found in map" );
+                                                    + "] not found in map" );
             }
             my_go_term = map.get( my_go_term.getSuperGoIds().get( 0 ) );
         }
@@ -172,7 +172,7 @@ public final class GoUtils {
         while ( ( my_go_term.getSuperGoIds() != null ) && ( my_go_term.getSuperGoIds().size() > 0 ) ) {
             if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) {
                 throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 )
-                        + "] not found in map" );
+                                                    + "] not found in map" );
             }
             my_go_term = map.get( my_go_term.getSuperGoIds().get( 0 ) );
         }