+ catch ( IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ int counter = 1;
+ for( final File gf : gene_trees_files ) {
+ String outname = gf.getName();
+ System.out
+ .print( "\r " );
+ System.out.print( "\r" + counter + "/" + gene_trees_files.length + ": " + outname );
+ counter++;
+ if ( outname.indexOf( "." ) > 0 ) {
+ outname = outname.substring( 0, outname.lastIndexOf( "." ) );
+ }
+ try {
+ RIOUtil.executeAnalysis( gf,
+ species_tree_file,
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHO_OUTTABLE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.LOGFILE_SUFFIX ),
+ outgroup,
+ rerooting,
+ gt_first,
+ gt_last,
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ),
+ new File( outdir.getCanonicalFile() + "/" + outname
+ + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ),
+ true,
+ algorithm,
+ true,
+ log,
+ ortholog_group_cutoff,
+ perform_id_mapping,
+ id_mapping_dir,
+ id_mapping_suffix,
+ perform_gsdir_on_best_tree,
+ outdir,
+ best_trees_indir,
+ best_trees_suffix );
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ System.out
+ .print( "\r " );
+ System.out.println();
+ }
+ else {
+ String outname = ForesterUtil.removeFileExtension( orthology_outtable.toString() );
+ RIOUtil.executeAnalysis( gene_trees_file,
+ species_tree_file,
+ orthology_outtable,
+ null,
+ new File( outname + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ),
+ logfile,
+ outgroup,
+ rerooting,
+ gt_first,
+ gt_last,
+ new File( outname + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ),
+ new File( outname + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ),
+ new File( outname + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ),
+ algorithm == ALGORITHM.GSDIR,
+ algorithm,
+ false,
+ null,
+ ortholog_group_cutoff,
+ false,
+ null,
+ null,
+ false,
+ null,
+ null,
+ null );
+ }
+ if ( !use_dir ) {
+ time = System.currentTimeMillis() - time;
+ System.out.println( "Time :\t" + time + "ms" );
+ }
+ else {
+ try {
+ log.close();
+ }
+ catch ( IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ time = System.currentTimeMillis() - time;
+ System.out.println( "Time :\t" + time + "ms" );