final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
+ final static private String PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION = "dc_regain_stats";
+ final static private String DA_ANALYSIS_OPTION = "DA_analyis";
+ final static private String USE_LAST_IN_FITCH_OPTION = "last";
final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
final static private String OUTPUT_FILE_OPTION = "o";
+ ForesterConstants.PHYLO_XML_SUFFIX;
final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ ForesterConstants.PHYLO_XML_SUFFIX;
- final static private String JACKNIFE_OPTION = "jack";
- final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
- final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
- private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
- final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
- final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
final static private String FILTER_POSITIVE_OPTION = "pos_filter";
final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
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 PERFORM_DC_REGAIN_PROTEINS_STATS = true;
- private static final boolean DA_ANALYSIS = false;
private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
final String[][] input_file_properties,
allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
- allowed_options.add( JACKNIFE_OPTION );
- allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
- allowed_options.add( JACKNIFE_RATIO_OPTION );
+ //allowed_options.add( JACKNIFE_OPTION );
+ // allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
+ // allowed_options.add( JACKNIFE_RATIO_OPTION );
allowed_options.add( INPUT_SPECIES_TREE_OPTION );
allowed_options.add( FILTER_POSITIVE_OPTION );
allowed_options.add( FILTER_NEGATIVE_OPTION );
allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
allowed_options.add( WRITE_TO_NEXUS_OPTION );
+ allowed_options.add( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION );
+ allowed_options.add( DA_ANALYSIS_OPTION );
+ allowed_options.add( USE_LAST_IN_FITCH_OPTION );
boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
}
+ boolean use_last_in_fitch_parsimony = false;
+ if ( cla.isOptionSet( USE_LAST_IN_FITCH_OPTION ) ) {
+ use_last_in_fitch_parsimony = true;
+ }
boolean write_to_nexus = false;
if ( cla.isOptionSet( WRITE_TO_NEXUS_OPTION ) ) {
write_to_nexus = true;
}
+ boolean perform_dc_regain_proteins_stats = false;
+ if ( cla.isOptionSet( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION ) ) {
+ perform_dc_regain_proteins_stats = true;
+ }
+ boolean da_analysis = false;
+ if ( cla.isOptionSet( DA_ANALYSIS_OPTION ) ) {
+ da_analysis = true;
+ }
boolean output_binary_domain_combinationsfor_graph_analysis = false;
if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
output_binary_domain_combinationsfor_graph_analysis = true;
&& ( number_of_genomes > 2 ) ) {
domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
}
- boolean jacknifed_distances = false;
- int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
- double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
- long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
- if ( cla.isOptionSet( surfacing.JACKNIFE_OPTION ) ) {
- if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use jacknife resampling analysis (-"
- + surfacing.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
- + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
- + "=<suffix for pairwise comparison output files>)" );
- }
- jacknifed_distances = true;
- if ( cla.isOptionHasAValue( surfacing.JACKNIFE_OPTION ) ) {
- try {
- jacknife_resamplings = cla.getOptionValueAsInt( surfacing.JACKNIFE_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for number of resamplings" );
- }
- if ( jacknife_resamplings < 2 ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use less than 2 resamplings" );
- }
- }
- if ( cla.isOptionSet( surfacing.JACKNIFE_RATIO_OPTION )
- && cla.isOptionHasAValue( surfacing.JACKNIFE_RATIO_OPTION ) ) {
- try {
- jacknife_ratio = cla.getOptionValueAsDouble( surfacing.JACKNIFE_RATIO_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for jacknife ratio" );
- }
- if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use illegal value for jacknife ratio: "
- + jacknife_ratio );
- }
- }
- if ( cla.isOptionSet( surfacing.JACKNIFE_RANDOM_SEED_OPTION )
- && cla.isOptionHasAValue( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) ) {
- try {
- random_seed = cla.getOptionValueAsLong( surfacing.JACKNIFE_RANDOM_SEED_OPTION );
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for random generator seed" );
- }
- }
- }
File[] intree_files = null;
Phylogeny[] intrees = null;
if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
- // TODO FIXME if jacknife.... maybe not
if ( number_of_genomes < 3 ) {
ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
+ surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
+ ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
+ nl );
}
+ System.out.println( "Use last in Fitch parimony : " + use_last_in_fitch_parsimony );
+ html_desc.append( "<tr><td>Use last in Fitch parimon:</td><td>" + use_last_in_fitch_parsimony + "</td></tr>"
+ + nl );
System.out.println( "Write to Nexus files : " + write_to_nexus );
+ html_desc.append( "<tr><td>Write to Nexus files:</td><td>" + write_to_nexus + "</td></tr>" + nl );
+ System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats );
+ html_desc.append( "<tr><td>DC regain prot stats:</td><td>" + perform_dc_regain_proteins_stats + "</td></tr>"
+ + nl );
+ System.out.println( "DA analysis : " + da_analysis );
+ html_desc.append( "<tr><td>DA analysis :</td><td>" + da_analysis + "</td></tr>" + nl );
System.out.print( "Domain counts sort order : " );
+ html_desc.append( "<tr><td>Domain counts sort order:</td><td>" );
switch ( dc_sort_order ) {
case ALPHABETICAL_KEY_ID:
System.out.println( "alphabetical" );
+ html_desc.append( "alphabetical" + "</td></tr>" + nl );
break;
case KEY_DOMAIN_COUNT:
System.out.println( "domain count" );
+ html_desc.append( "domain count" + "</td></tr>" + nl );
break;
case KEY_DOMAIN_PROTEINS_COUNT:
System.out.println( "domain proteins count" );
+ html_desc.append( "domain proteins count" + "</td></tr>" + nl );
break;
case COMBINATIONS_COUNT:
System.out.println( "domain combinations count" );
+ html_desc.append( "domain combinations count" + "</td></tr>" + nl );
break;
default:
ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
}
System.out.println();
html_desc.append( "</td></tr>" + nl );
- if ( jacknifed_distances ) {
- html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
- html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
- + "</td></tr>" + nl );
- html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
- System.out.println( " Jacknife : " + jacknife_resamplings + " resamplings" );
- System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) );
- System.out.println( " Random number seed : " + random_seed );
- }
if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
for( final File intree_file : intree_files ) {
html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
Map<String, DescriptiveStatistics> protein_length_stats_by_dc = null;
Map<String, DescriptiveStatistics> domain_number_stats_by_dc = null;
final Map<String, DescriptiveStatistics> domain_length_stats_by_domain = new HashMap<String, DescriptiveStatistics>();
- if ( PERFORM_DC_REGAIN_PROTEINS_STATS ) {
+ if ( perform_dc_regain_proteins_stats ) {
protein_length_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
domain_number_stats_by_dc = new HashMap<String, DescriptiveStatistics>();
}
final double coverage = ( double ) protein_list.size() / parser.getProteinsEncountered();
protein_coverage_stats.addValue( coverage );
int distinct_das = -1;
- if ( DA_ANALYSIS ) {
+ if ( da_analysis ) {
final String genome = input_file_properties[ i ][ 0 ];
distinct_das = SurfacingUtil.storeDomainArchitectures( genome,
distinct_domain_architecutures_per_genome,
log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
log_writer );
}
- if ( DA_ANALYSIS ) {
+ if ( da_analysis ) {
System.out.println( "Distinct domain architectures stored : " + distinct_das );
log( "Distinct domain architectures stored : " + distinct_das, log_writer );
}
domains_which_never_single,
domains_per_potein_stats_writer );
domain_lengths_table.addLengths( protein_list );
- if ( !DA_ANALYSIS ) {
+ if ( !da_analysis ) {
gwcd_list.add( BasicGenomeWideCombinableDomains
.createInstance( protein_list,
ignore_combination_with_same,
ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ per_genome_domain_promiscuity_statistics_file );
//
- if ( DA_ANALYSIS ) {
+ if ( da_analysis ) {
SurfacingUtil.performDomainArchitectureAnalysis( distinct_domain_architecutures_per_genome,
distinct_domain_architecuture_counts,
10,
inferred_trees.add( nj_gd );
inferred_trees.add( nj_bc );
inferred_trees.add( nj_d );
- if ( jacknifed_distances ) {
- pwgc.performPairwiseComparisonsJacknifed( species,
- number_of_genomes,
- gwcd_list,
- true,
- jacknife_resamplings,
- jacknife_ratio,
- random_seed );
- SurfacingUtil
- .writeMatrixToFile( new File( matrix_output_file
- + "_"
- + ForesterUtil.round( jacknife_ratio, 2 )
- + "_"
- + jacknife_resamplings
- + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getSharedBinaryCombinationsBasedDistances() );
- SurfacingUtil
- .writeMatrixToFile( new File( matrix_output_file + "_" + ForesterUtil.round( jacknife_ratio, 2 )
- + "_" + jacknife_resamplings
- + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ),
- pwgc.getSharedDomainsBasedDistances() );
- // if ( infer_species_trees ) {
- // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
- // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
- // .getSharedBinaryCombinationsBasedDistances() );
- // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
- // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
- // }
- }
} // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
if ( ( out_dir != null ) && ( !perform_pwc ) ) {
output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
domain_number_stats_by_dc,
domain_length_stats_by_domain,
tax_code_to_id_map,
- write_to_nexus );
+ write_to_nexus,
+ use_last_in_fitch_parsimony );
// Listing of all domain combinations gained is only done if only one input tree is used.
if ( ( domain_id_to_secondary_features_maps != null )
&& ( domain_id_to_secondary_features_maps.length > 0 ) ) {
secondary_features_parsimony,
intree,
parameters_sb.toString(),
- mapping_results_map );
+ mapping_results_map,
+ use_last_in_fitch_parsimony );
if ( i == 0 ) {
System.out.println();
System.out.println( "Mapping to secondary features:" );
System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ ": species tree, to perform (Dollo, Fitch) parismony analyses" );
System.out
- .println( JACKNIFE_OPTION
- + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
- + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
- System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
- + JACKNIFE_RATIO_DEFAULT + "]" );
- System.out.println( JACKNIFE_RANDOM_SEED_OPTION
- + ": seed for random number generator for jacknife resampling [default: "
- + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
- // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
- // + ": to infer NJ species trees based on shared domains/binary domain combinations" );
- System.out
.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
System.out.println( surfacing.FILTER_POSITIVE_OPTION
System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION
+ ": e value max per domain for output of all proteins per domain" );
+ System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" );
System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" );
+ System.out.println( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" );
+ System.out.println( DA_ANALYSIS_OPTION + ": to DA 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"
}
};
public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" );
- private static final boolean USE_LAST = true;
private SurfacingUtil() {
// Hidden constructor.
/**
*
* @param all_binary_domains_combination_lost_fitch
+ * @param use_last_in_fitch_parsimony
* @param consider_directedness_and_adjacency_for_bin_combinations
* @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
* which were gained under unweighted (Fitch) parsimony.
final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
final Map<String, Integer> tax_code_to_id_map,
- final boolean write_to_nexus ) {
+ final boolean write_to_nexus,
+ final boolean use_last_in_fitch_parsimony ) {
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
all_pfams_lost_as_domains,
"_dollo_losses_d",
tax_code_to_id_map );
- writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
- go_id_to_term_map,
- go_namespace_limit,
- false,
- domain_parsimony.getGainLossMatrix(),
- null,
- outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- "Dollo Parsimony | Present | Domains",
- "",
- domain_id_to_secondary_features_maps,
- all_pfams_encountered,
- null,
- "_dollo_present_d",
- tax_code_to_id_map );
+ // writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
+ // go_id_to_term_map,
+ // go_namespace_limit,
+ // false,
+ // domain_parsimony.getGainLossMatrix(),
+ // null,
+ // outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
+ // sep,
+ // ForesterUtil.LINE_SEPARATOR,
+ // "Dollo Parsimony | Present | Domains",
+ // "",
+ // domain_id_to_secondary_features_maps,
+ // all_pfams_encountered,
+ // null,
+ // "_dollo_present_d",
+ // tax_code_to_id_map );
preparePhylogeny( local_phylogeny_l,
domain_parsimony,
date_time,
randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
}
else {
- domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
+ domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
}
SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
+ surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
all_pfams_lost_as_dom_combinations,
"_fitch_losses_dc",
tax_code_to_id_map );
- writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
- go_id_to_term_map,
- go_namespace_limit,
- true,
- domain_parsimony.getGainLossMatrix(),
- null,
- outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
- sep,
- ForesterUtil.LINE_SEPARATOR,
- "Fitch Parsimony | Present | Domain Combinations",
- "",
- null,
- all_pfams_encountered,
- null,
- "_fitch_present_dc",
- tax_code_to_id_map );
+ // writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
+ // go_id_to_term_map,
+ // go_namespace_limit,
+ // true,
+ // domain_parsimony.getGainLossMatrix(),
+ // null,
+ // outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
+ // sep,
+ // ForesterUtil.LINE_SEPARATOR,
+ // "Fitch Parsimony | Present | Domain Combinations",
+ // "",
+ // null,
+ // all_pfams_encountered,
+ // null,
+ // "_fitch_present_dc",
+ // tax_code_to_id_map );
writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
go_id_to_term_map,
outfile_name,
final DomainParsimonyCalculator secondary_features_parsimony,
final Phylogeny phylogeny,
final String parameters_str,
- final Map<Species, MappingResults> mapping_results_map ) {
+ final Map<Species, MappingResults> mapping_results_map,
+ final boolean use_last_in_fitch_parsimony ) {
final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
final String date_time = ForesterUtil.getCurrentDateTime();
System.out.println();
// -------------------------
local_phylogeny_copy = phylogeny.copy();
final String randomization = "no";
- secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
+ secondary_features_parsimony
+ .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
preparePhylogeny( local_phylogeny_copy,
secondary_features_parsimony,
date_time,
final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
final Set<String> dcs = dc_gain_counts.keySet();
final SortedSet<String> more_than_once = new TreeSet<String>();
- final DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
- final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
- final DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
+ DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
+ DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
+ DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
long gained_multiple_times_domain_length_sum = 0;
long gained_once_domain_length_sum = 0;
w.write( "Gained once, protein lengths:" );
w.write( "\n" );
w.write( gained_once_lengths_stats.toString() );
+ gained_once_lengths_stats = null;
w.write( "\n" );
w.write( "\n" );
w.write( "Gained once, domain counts:" );
w.write( "\n" );
w.write( gained_once_domain_count_stats.toString() );
+ gained_once_domain_count_stats = null;
w.write( "\n" );
w.write( "\n" );
w.write( "Gained multiple times, protein lengths:" );
w.write( "\n" );
w.write( gained_multiple_times_lengths_stats.toString() );
+ gained_multiple_times_lengths_stats = null;
w.write( "\n" );
w.write( "\n" );
w.write( "Gained multiple times, domain counts:" );
git://source.jalview.org / jalview.git / commitdiff