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removed some uncheck warnings
[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
39a778f
..
fa08ef2
100644
(file)
--- a/
forester/java/src/org/forester/go/GoUtils.java
+++ b/
forester/java/src/org/forester/go/GoUtils.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;
@@
-50,9
+50,9
@@
public final class GoUtils {
/**
* This is for counting the how many times each GO term in 'categories'
/**
* 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
* @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 )
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 ) );
}
}
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 )
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 ) );
}
}
my_go_term = map.get( my_go_term.getSuperGoIds().get( 0 ) );
}