in progress

[jalview.git] / forester / java / src / org / forester / application / pfam2go_extractor.java

diff --git a/forester/java/src/org/forester/application/pfam2go_extractor.java b/forester/java/src/org/forester/application/pfam2go_extractor.java
index 63b4320..f086af3 100644 (file)
--- a/forester/java/src/org/forester/application/pfam2go_extractor.java
+++ b/forester/java/src/org/forester/application/pfam2go_extractor.java
@@ -21,7 +21,7 @@
 // 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.application;
 
@@ -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 {
 
@@ -79,12 +78,12 @@ 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 );
-            for( int i = 0; i < queries.length; ++i ) {
-                if ( supers.contains( queries[ i ] ) ) {
+            for( final GoId querie : queries ) {
+                if ( supers.contains( querie ) ) {
                     pfams.add( domain_id.toString() );
                 }
             }
@@ -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();
     }
 }