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more tests for isDuplication() and isSpecation() added
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
pfam_go.java
diff --git
a/forester/java/src/org/forester/application/pfam_go.java
b/forester/java/src/org/forester/application/pfam_go.java
index
475b5d4
..
df679e1
100644
(file)
--- a/
forester/java/src/org/forester/application/pfam_go.java
+++ b/
forester/java/src/org/forester/application/pfam_go.java
@@
-78,7
+78,7
@@
public class pfam_go {
encountered_domains.add( line );
boolean found = false;
for( final PfamToGoMapping mapping : mappings ) {
encountered_domains.add( line );
boolean found = false;
for( final PfamToGoMapping mapping : mappings ) {
- if ( mapping.getKey().getId().equals( line ) ) {
+ if ( mapping.getKey().equals( line ) ) {
System.out.println( mapping.getValue() );
found = true;
}
System.out.println( mapping.getValue() );
found = true;
}
@@
-150,7
+150,7
@@
public class pfam_go {
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION
- + " to allow duplicates] <pfam2go file> <file with pfams>" );
+ + " to allow duplicates] <pfam2go file> <file with pfams>" );
System.out.println();
System.out.println();
}
System.out.println();
System.out.println();
}