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Thank you, Oracle!
[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
dc63b52
..
8dd8f64
100644
(file)
--- a/
forester/java/src/org/forester/go/BasicGoSubset.java
+++ b/
forester/java/src/org/forester/go/BasicGoSubset.java
@@
-21,7
+21,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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;
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_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;
}
else if ( my_s.equals( GOSLIM_PLANT_STR ) ) {
_type = Type.GOSLIM_PLANT;
}
@@
-55,14
+58,8
@@
public class BasicGoSubset implements GoSubset {
else if ( my_s.equals( GOSLIM_POMBE_STR ) ) {
_type = Type.GOSLIM_POMBE;
}
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 {
else {
- throw new IllegalArgumentException( "unknown GO subset type: " + my_s );
+ _type = Type.OTHER;
}
}
}
}
@@
-85,7
+82,7
@@
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 if ( o.getClass() != this.getClass() ) {
throw new IllegalArgumentException( "attempt to check go subset equality to " + o + " [" + o.getClass()
- + "]" );
+ + "]" );
}
else {
return ( getType() == ( ( GoSubset ) o ).getType() );
}
else {
return ( getType() == ( ( GoSubset ) o ).getType() );
@@
-116,6
+113,9
@@
public class BasicGoSubset implements GoSubset {
case GOSLIM_PLANT:
sb.append( GOSLIM_PLANT_STR );
break;
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;
case GOSLIM_YEAST:
sb.append( GOSLIM_YEAST_STR );
break;
@@
-125,8
+125,9
@@
public class BasicGoSubset implements GoSubset {
case GOSLIM_POMBE:
sb.append( GOSLIM_POMBE_STR );
break;
case GOSLIM_POMBE:
sb.append( GOSLIM_POMBE_STR );
break;
- default:
- new AssertionError( "unknown type: " + getType() );
+ case OTHER:
+ sb.append( "other" );
+ break;
}
return sb.toString();
}
}
return sb.toString();
}