X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fgo%2FBasicGoRelationship.java;h=3a41d6df0012a9f92ea959831201fd004eca5b7f;hb=4d7228400f44ee88136f3d70d9455b1b1d95de27;hp=6f8dd32a227061c08a3429fe8be8586d774ff12a;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/go/BasicGoRelationship.java b/forester/java/src/org/forester/go/BasicGoRelationship.java
index 6f8dd32..3a41d6d 100644
--- a/forester/java/src/org/forester/go/BasicGoRelationship.java
+++ b/forester/java/src/org/forester/go/BasicGoRelationship.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;
 
@@ -49,6 +49,9 @@ public class BasicGoRelationship implements GoRelationship {
         else if ( type.toLowerCase().equals( POSITIVELY_REGULATES_STR ) ) {
             _type = Type.POSITIVELY_REGULATES;
         }
+        else if ( type.toLowerCase().equals( HAS_PART_STR ) ) {
+            _type = Type.HAS_PART;
+        }
         else {
             throw new IllegalArgumentException( "unknown GO relationship type: " + type );
         }
@@ -70,6 +73,7 @@ public class BasicGoRelationship implements GoRelationship {
         _go_id = go_id;
     }
 
+    @Override
     public int compareTo( final GoRelationship rel ) {
         return getGoId().compareTo( rel.getGoId() );
     }
@@ -97,10 +101,12 @@ public class BasicGoRelationship implements GoRelationship {
         }
     }
 
+    @Override
     public GoId getGoId() {
         return _go_id;
     }
 
+    @Override
     public Type getType() {
         return _type;
     }
@@ -121,8 +127,11 @@ public class BasicGoRelationship implements GoRelationship {
             case REGULATES:
                 sb.append( REGULATES_STR );
                 break;
+            case HAS_PART:
+                sb.append( HAS_PART_STR );
+                break;
             default:
-                new AssertionError( "unknown type: " + getType() );
+                new IllegalStateException( "unknown type: " + getType() );
         }
         sb.append( ": " );
         sb.append( getGoId().toString() );