if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
output_binary_domain_combinationsfor_graph_analysis = true;
}
- final boolean output_binary_domain_combinationsfor_counts = false;
+ boolean output_binary_domain_combinationsfor_counts = false;
if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) {
- output_binary_domain_combinationsfor_graph_analysis = true;
+ output_binary_domain_combinationsfor_counts = true;
}
if ( cla.isOptionSet( surfacing.MAX_FS_E_VALUE_OPTION ) ) {
try {
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
sort_by_species_count_first,
number_of_genomes == 2,
- CALC_SIMILARITY_SCORES );
+ CALC_SIMILARITY_SCORES,
+ true );
switch ( scoring ) {
case COMBINATIONS:
pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
SurfacingUtil.writeProteinListsForAllSpecies( out_dir,
protein_lists_per_species,
gwcd_list,
- output_list_of_all_proteins_per_domain_e_value_max );
+ output_list_of_all_proteins_per_domain_e_value_max,
+ positive_filter_file != null ? filter : null );
}
gwcd_list = null;
if ( all_bin_domain_combinations_gained_fitch != null ) {
System.out.println( DA_ANALYSIS_OPTION + ": to perform DA analysis" );
System.out.println( PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION + ": to perform domain length analysis" );
System.out.println();
- System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
- + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
- + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o "
- + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" );
System.out.println();
- System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar"
- + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
- + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
- + "-dc_sort=dom -ignore_with_self -no_singles -ie=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
- + "-ds_output=detailed_html -scoring=domains -sort=alpha " );
+ System.out
+ .println( "Example: surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_155.xml -last -detail=punctilious -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" );
System.out.println();
}
}