JAL-2844 partitioning code made slightly clearer

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

diff --git a/forester/java/src/org/forester/go/BasicGoSubset.java b/forester/java/src/org/forester/go/BasicGoSubset.java
index 19d20ed..8dd8f64 100644 (file)
--- a/forester/java/src/org/forester/go/BasicGoSubset.java
+++ b/forester/java/src/org/forester/go/BasicGoSubset.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;
 
@@ -46,6 +46,9 @@ public class BasicGoSubset implements GoSubset {
         else if ( my_s.equals( GOSLIM_CANDIDA_STR ) ) {
             _type = Type.GOSLIM_CANDIDA;
         }
+        else if ( my_s.equals( GOSLIM_ASPERGILLUS_STR ) ) {
+            _type = Type.GOSLIM_ASPERGILLUS;
+        }
         else if ( my_s.equals( GOSLIM_PLANT_STR ) ) {
             _type = Type.GOSLIM_PLANT;
         }
@@ -56,7 +59,7 @@ public class BasicGoSubset implements GoSubset {
             _type = Type.GOSLIM_POMBE;
         }
         else {
-            throw new IllegalArgumentException( "unknown GO subset type: " + my_s );
+            _type = Type.OTHER;
         }
     }
 
@@ -64,6 +67,7 @@ public class BasicGoSubset implements GoSubset {
         _type = type;
     }
 
+    @Override
     public int compareTo( final GoSubset sub ) {
         return getType().compareTo( sub.getType() );
     }
@@ -78,13 +82,14 @@ public class BasicGoSubset implements GoSubset {
         }
         else if ( o.getClass() != this.getClass() ) {
             throw new IllegalArgumentException( "attempt to check go subset equality to " + o + " [" + o.getClass()
-                    + "]" );
+                                                + "]" );
         }
         else {
             return ( getType() == ( ( GoSubset ) o ).getType() );
         }
     }
 
+    @Override
     public Type getType() {
         return _type;
     }
@@ -108,6 +113,9 @@ public class BasicGoSubset implements GoSubset {
             case GOSLIM_PLANT:
                 sb.append( GOSLIM_PLANT_STR );
                 break;
+            case GOSLIM_ASPERGILLUS:
+                sb.append( GOSLIM_ASPERGILLUS_STR );
+                break;
             case GOSLIM_YEAST:
                 sb.append( GOSLIM_YEAST_STR );
                 break;
@@ -117,8 +125,9 @@ public class BasicGoSubset implements GoSubset {
             case GOSLIM_POMBE:
                 sb.append( GOSLIM_POMBE_STR );
                 break;
-            default:
-                new AssertionError( "unknown type: " + getType() );
+            case OTHER:
+                sb.append( "other" );
+                break;
         }
         return sb.toString();
     }