// 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;
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;
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;
}
}
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 );
}