X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fpfam2go_extractor.java;h=6852d055d788bfe8568d4a0b286afdcb87b7ad78;hb=51045a46f54b0cdd39f1e30a06993148e61abde7;hp=164a1701e8aec70b05b7ca2342f9561bca2e3387;hpb=493e40b0c936b65da342134da37e8b856b9b80af;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 164a170..6852d05 100644
--- a/forester/java/src/org/forester/application/pfam2go_extractor.java
+++ b/forester/java/src/org/forester/application/pfam2go_extractor.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2009 Christian M. Zmasek
 // Copyright (C) 2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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.surfacing.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() );
                 }
             }