final static private String INPUT_GENOMES_FILE_OPTION = "genomes";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
- final static private String PRG_VERSION = "2.300";
- final static private String PRG_DATE = "130711";
+ final static private String PRG_VERSION = "2.302";
+ final static private String PRG_DATE = "130715";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_MAPPED.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
+ private static final boolean CALC_SIMILARITY_SCORES = false;
private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final String[][] input_file_properties,
all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
}
- final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
+ DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
+ output_file + D_PROMISCUITY_FILE_SUFFIX );
BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
System.out.println();
}
+ domain_lengths_table = null;
final long analysis_start_time = new Date().getTime();
PairwiseDomainSimilarityCalculator pw_calc = null;
- // double[] values_for_all_scores_histogram = null;
final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
sort_by_species_count_first,
- number_of_genomes == 2 );
+ number_of_genomes == 2,
+ CALC_SIMILARITY_SCORES );
switch ( scoring ) {
case COMBINATIONS:
pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
+ new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
+ "</td></tr>" + nl );
html_desc.append( "</table>" + nl );
- final DescriptiveStatistics pw_stats = SurfacingUtil
- .writeDomainSimilaritiesToFile( html_desc,
- new StringBuilder( number_of_genomes + " genomes" ),
- writer,
- split_writers,
- similarities,
- number_of_genomes == 2,
- species_order,
- domain_similarity_print_option,
- scoring,
- true,
- tax_code_to_id_map,
- false );
+ final Writer simple_tab_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR
+ + my_outfile + ".tsv" ) );
+ SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
+ new StringBuilder( number_of_genomes + " genomes" ),
+ simple_tab_writer,
+ writer,
+ split_writers,
+ similarities,
+ number_of_genomes == 2,
+ species_order,
+ domain_similarity_print_option,
+ scoring,
+ true,
+ tax_code_to_id_map );
+ simple_tab_writer.close();
ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
}
surfacing.PRG_NAME,
out_dir,
write_pwc_files,
- tax_code_to_id_map );
+ tax_code_to_id_map,
+ CALC_SIMILARITY_SCORES );
String matrix_output_file = new String( output_file.toString() );
if ( matrix_output_file.indexOf( '.' ) > 1 ) {
matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );