import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.InferenceManager;
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
final Configuration config,
final String title,
final File current_dir ) {
+ super();
_configuration = config;
if ( _configuration == null ) {
throw new IllegalArgumentException( "configuration is null" );
void buildPhylogeneticInferenceMenu() {
final InferenceManager inference_manager = InferenceManager.getInstance();
_inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
- _inference_menu
- .add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
customizeJMenuItem( _inference_from_msa_item );
_inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
- _inference_menu
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
customizeJMenuItem( _inference_from_seqs_item );
_inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
_jmenubar.add( _inference_menu );