refactoring

[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..82015fb 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
@@ -15,7 +15,7 @@
 // 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
@@ -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;
         }
@@ -55,6 +58,15 @@ public class BasicGoSubset implements GoSubset {
         else if ( my_s.equals( GOSLIM_POMBE_STR ) ) {
             _type = Type.GOSLIM_POMBE;
         }
+        else if ( my_s.equals( HIGH_LEVEL_ANNOTATION_QC_STR ) ) {
+            _type = Type.HIGH_LEVEL_ANNOTATION_QC;
+        }
+        else if ( my_s.equals( UNVETTED_STR ) ) {
+            _type = Type.UNVETTED;
+        }
+        else if ( my_s.equals( MF_NEEDS_REVIEW_STR ) ) {
+            _type = Type.MF_NEEDS_REVIEW;
+        }
         else {
             throw new IllegalArgumentException( "unknown GO subset type: " + my_s );
         }
@@ -64,6 +76,7 @@ public class BasicGoSubset implements GoSubset {
         _type = type;
     }
 
+    @Override
     public int compareTo( final GoSubset sub ) {
         return getType().compareTo( sub.getType() );
     }
@@ -85,6 +98,7 @@ public class BasicGoSubset implements GoSubset {
         }
     }
 
+    @Override
     public Type getType() {
         return _type;
     }
@@ -108,6 +122,9 @@ 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;
@@ -117,6 +134,15 @@ public class BasicGoSubset implements GoSubset {
             case GOSLIM_POMBE:
                 sb.append( GOSLIM_POMBE_STR );
                 break;
+            case MF_NEEDS_REVIEW:
+                sb.append( MF_NEEDS_REVIEW_STR );
+                break;
+            case HIGH_LEVEL_ANNOTATION_QC:
+                sb.append( HIGH_LEVEL_ANNOTATION_QC_STR );
+                break;
+            case UNVETTED:
+                sb.append( UNVETTED_STR );
+                break;
             default:
                 new AssertionError( "unknown type: " + getType() );
         }