X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fpfam2go_extractor.java;h=f086af3013d7cda02f556731be4b66c0ef9bf60f;hb=b528989f688291ba7615867e5322090ec42096d8;hp=d9f4cd3c89c35929a5fb1bfacecf7fb43f103ac9;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/application/pfam2go_extractor.java b/forester/java/src/org/forester/application/pfam2go_extractor.java
index d9f4cd3..f086af3 100644
--- a/forester/java/src/org/forester/application/pfam2go_extractor.java
+++ b/forester/java/src/org/forester/application/pfam2go_extractor.java
@@ -39,7 +39,6 @@ import org.forester.go.GoUtils;
 import org.forester.go.OBOparser;
 import org.forester.go.PfamToGoMapping;
 import org.forester.go.PfamToGoParser;
-import org.forester.protein.DomainId;
 
 public class pfam2go_extractor {
 
@@ -79,7 +78,7 @@ public class pfam2go_extractor {
         }
         final SortedSet<String> pfams = new TreeSet<String>();
         for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
-            final DomainId domain_id = pfam_to_go_mapping.getKey();
+            final String domain_id = pfam_to_go_mapping.getKey();
             final GoId go_id = pfam_to_go_mapping.getValue();
             final Set<GoId> supers = GoUtils.getAllSuperGoIds( go_id, goid_to_term_map );
             supers.add( go_id );
@@ -97,7 +96,7 @@ public class pfam2go_extractor {
     private static void printHelp() {
         System.out.println();
         System.out.println( PRG_NAME
-                + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
+                            + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
         System.out.println();
     }
 }