in progress...

[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 07e22bb..df679e1 100644 (file)
--- a/forester/java/src/org/forester/application/pfam_go.java
+++ b/forester/java/src/org/forester/application/pfam_go.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;
 
@@ -49,8 +49,9 @@ public class pfam_go {
     final static private String E_MAIL                  = "czmasek@burnham.org";
     final static private String WWW                     = "www.phylosoft.org";
 
-    private static void process( final File pfams_file, final List<PfamToGoMapping> mappings, boolean allow_duplicates )
-            throws IOException {
+    private static void process( final File pfams_file,
+                                 final List<PfamToGoMapping> mappings,
+                                 final boolean allow_duplicates ) throws IOException {
         final BufferedReader reader = ForesterUtil.obtainReader( pfams_file );
         String line = "";
         int found_count = 0;
@@ -77,7 +78,7 @@ public class pfam_go {
                     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;
                         }
@@ -113,7 +114,7 @@ public class pfam_go {
         }
         final List<String> allowed_options = new ArrayList<String>();
         allowed_options.add( ALLOW_DUPLICATES_OPTION );
-        if ( cla.getNumberOfNames() != 2 && cla.getNumberOfNames() != 3 ) {
+        if ( ( cla.getNumberOfNames() != 2 ) && ( cla.getNumberOfNames() != 3 ) ) {
             printHelp();
             System.exit( -1 );
         }
@@ -149,7 +150,7 @@ public class pfam_go {
         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();
     }