From: cmzmasek@gmail.com Date: Mon, 23 Apr 2012 18:03:22 +0000 (+0000) Subject: cleanup X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7bd2b51cf167a38ef4e11fa45d8877706f40e4a2;p=jalview.git cleanup --- diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index ed54586..c19902f 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -99,192 +99,192 @@ import org.forester.util.ForesterUtil; public class surfacing { - private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000; - public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; - public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot"; - public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc"; + private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000; + public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; + public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot"; + public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc"; // gain/loss: - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d"; - public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d"; + public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc"; // gain/loss counts: - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d"; - public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d"; + public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc"; // tables: - public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc"; - public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html"; - public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc"; - public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc"; - public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html"; - public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html"; - public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html"; - public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d"; - public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html"; - public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex"; - public final static String BDC_PRESENT_NEXUS = "_dc.nex"; + public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html"; + public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc"; + public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html"; + public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d"; + public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html"; + public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex"; + public final static String BDC_PRESENT_NEXUS = "_dc.nex"; // --- - public final static String PRG_NAME = "surfacing"; - public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex"; - public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex"; - public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex"; - public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features"; - public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features"; - public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features"; - public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features"; - public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features"; - public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d"; - public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String OUTPUT_DIR_OPTION = "out_dir"; - final static private String SCORING_OPTION = "scoring"; - private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS; - final static private String SCORING_DOMAIN_COUNT_BASED = "domains"; - final static private String SCORING_PROTEIN_COUNT_BASED = "proteins"; - final static private String SCORING_COMBINATION_BASED = "combinations"; - final static private String DETAILEDNESS_OPTION = "detail"; - private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; - final static private String SPECIES_MATRIX_OPTION = "smatrix"; - final static private String DETAILEDNESS_BASIC = "basic"; - final static private String DETAILEDNESS_LIST_IDS = "list_ids"; - final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious"; - final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort"; - private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; - final static private String DOMAIN_SIMILARITY_SORT_MIN = "min"; - final static private String DOMAIN_SIMILARITY_SORT_MAX = "max"; - final static private String DOMAIN_SIMILARITY_SORT_SD = "sd"; - final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean"; - final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff"; - final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff"; - final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff"; - final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species"; - final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha"; - final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first"; - final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort"; - private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID; - final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha"; - final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom"; - final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot"; - final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb"; - final static private String CUTOFF_SCORE_FILE_OPTION = "cos"; - final static private String NOT_IGNORE_DUFS_OPTION = "dufs"; - final static private String MAX_E_VALUE_OPTION = "e"; - 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 PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_"; - final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc"; - final static private String OUTPUT_FILE_OPTION = "o"; - final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g"; - final static private String GO_OBO_FILE_USE_OPTION = "obo"; - final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace"; - final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function"; - final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process"; - final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component"; - final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html"; - final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output"; - private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML; - final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains"; - final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids"; - final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false; - final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains"; - final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false; - final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd"; - final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd"; - final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd"; - final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; - final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ" - + 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; + public final static String PRG_NAME = "surfacing"; + public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex"; + public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex"; + public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex"; + public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features"; + public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features"; + public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features"; + public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features"; + public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features"; + public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d"; + public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String OUTPUT_DIR_OPTION = "out_dir"; + final static private String SCORING_OPTION = "scoring"; + private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS; + final static private String SCORING_DOMAIN_COUNT_BASED = "domains"; + final static private String SCORING_PROTEIN_COUNT_BASED = "proteins"; + final static private String SCORING_COMBINATION_BASED = "combinations"; + final static private String DETAILEDNESS_OPTION = "detail"; + private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS; + final static private String SPECIES_MATRIX_OPTION = "smatrix"; + final static private String DETAILEDNESS_BASIC = "basic"; + final static private String DETAILEDNESS_LIST_IDS = "list_ids"; + final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious"; + final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort"; + private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID; + final static private String DOMAIN_SIMILARITY_SORT_MIN = "min"; + final static private String DOMAIN_SIMILARITY_SORT_MAX = "max"; + final static private String DOMAIN_SIMILARITY_SORT_SD = "sd"; + final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean"; + final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff"; + final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff"; + final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff"; + final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species"; + final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha"; + final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first"; + final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort"; + private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID; + final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha"; + final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom"; + final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot"; + final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb"; + final static private String CUTOFF_SCORE_FILE_OPTION = "cos"; + final static private String NOT_IGNORE_DUFS_OPTION = "dufs"; + final static private String MAX_E_VALUE_OPTION = "e"; + 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 PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_"; + final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc"; + final static private String OUTPUT_FILE_OPTION = "o"; + final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g"; + final static private String GO_OBO_FILE_USE_OPTION = "obo"; + final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace"; + final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function"; + final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process"; + final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component"; + final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html"; + final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output"; + private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML; + final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains"; + final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids"; + final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false; + final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains"; + final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false; + final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd"; + final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd"; + final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd"; + final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ" + + ForesterConstants.PHYLO_XML_SUFFIX; + final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ" + + 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 INFER_SPECIES_TREES_OPTION = "species_tree_inference"; - final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh"; - final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh"; - 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"; - final static private String INPUT_FILES_FROM_FILE_OPTION = "input"; - final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; - final static private String SEQ_EXTRACT_OPTION = "prot_extract"; - final static private char SEPARATOR_FOR_INPUT_VALUES = '#'; - final static private String PRG_VERSION = "2.230"; - final static private String PRG_DATE = "2012.04.22"; - final static private String E_MAIL = "czmasek@burnham.org"; - final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; - final static private boolean IGNORE_DUFS_DEFAULT = true; - final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false; - final static private double MAX_E_VALUE_DEFAULT = -1; - final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1; - private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed"; - private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction"; - private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj"; - private static final String SEQ_EXTRACT_SUFFIX = ".prot"; - private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus"; - private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt"; - private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html"; - private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html"; - private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0; - private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0; - private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt"; - private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt"; - private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot"; - private static final boolean VERBOSE = false; - private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts"; - private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts"; - private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis"; - private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true; - public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams"; - public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation"; - public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary"; - public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains"; - public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains"; - public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc"; - public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc"; - public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS"; - public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS"; - public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities"; - private static final String LOG_FILE_SUFFIX = "_log.txt"; - private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt"; - private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN"; - private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt"; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt"; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt"; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"; - public static final String LIMIT_SPEC_FOR_PROT_EX = null; // e.g. "HUMAN"; set to null for not using this feature (default). - public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED = "_dc_MAPPED_secondary_features_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; - public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts_MAPPED.txt"; - 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"; + final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh"; + final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh"; + 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"; + final static private String INPUT_FILES_FROM_FILE_OPTION = "input"; + final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; + final static private String SEQ_EXTRACT_OPTION = "prot_extract"; + final static private char SEPARATOR_FOR_INPUT_VALUES = '#'; + final static private String PRG_VERSION = "2.230"; + final static private String PRG_DATE = "2012.04.22"; + final static private String E_MAIL = "czmasek@burnham.org"; + final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; + final static private boolean IGNORE_DUFS_DEFAULT = true; + final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false; + final static private double MAX_E_VALUE_DEFAULT = -1; + final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1; + private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed"; + private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction"; + private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj"; + private static final String SEQ_EXTRACT_SUFFIX = ".prot"; + private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus"; + private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt"; + private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html"; + private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html"; + private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0; + private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0; + private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt"; + private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt"; + private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot"; + private static final boolean VERBOSE = false; + private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts"; + private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts"; + private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis"; + private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true; + public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams"; + public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation"; + public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary"; + public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains"; + public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains"; + public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc"; + public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc"; + public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS"; + public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS"; + public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities"; + private static final String LOG_FILE_SUFFIX = "_log.txt"; + private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt"; + private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN"; + private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping.txt"; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"; + public static final String LIMIT_SPEC_FOR_PROT_EX = null; // e.g. "HUMAN"; set to null for not using this feature (default). + public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED = "_dc_MAPPED_secondary_features_fitch" + + ForesterConstants.PHYLO_XML_SUFFIX; + public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts_MAPPED.txt"; + 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 void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option, final String[][] input_file_properties, @@ -2370,14 +2370,13 @@ public class surfacing { final Runtime rt = java.lang.Runtime.getRuntime(); final long free_memory = rt.freeMemory() / 1000000; final long total_memory = rt.totalMemory() / 1000000; - - ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" ); + ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + + "ms" ); ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); - ForesterUtil.programMessage( PRG_NAME, "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" ); - - ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" ); - ForesterUtil.programMessage( PRG_NAME, surfacing.WWW ); - + ForesterUtil.programMessage( PRG_NAME, "Free memory : " + free_memory + "MB, total memory: " + + total_memory + "MB" ); + ForesterUtil.programMessage( PRG_NAME, "If this application is useful to you, please cite:" ); + ForesterUtil.programMessage( PRG_NAME, surfacing.WWW ); ForesterUtil.programMessage( PRG_NAME, "OK" ); System.out.println(); } diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java index 4658371..ee9524c 100644 --- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java @@ -212,11 +212,10 @@ public final class DomainParsimonyCalculator { setTotalLosses( fitch.getTotalLosses() ); setTotalUnchanged( fitch.getTotalUnchanged() ); } - - private void executeFitchParsimonyOnSecondaryFeatures( - final boolean use_last, - final boolean randomize, - final long random_number_seed ) { + + private void executeFitchParsimonyOnSecondaryFeatures( final boolean use_last, + final boolean randomize, + final long random_number_seed ) { reset(); if ( use_last ) { System.out.println( " Fitch parsimony: use_last = true" ); @@ -229,21 +228,19 @@ public final class DomainParsimonyCalculator { fitch.setUseLast( use_last ); fitch.setReturnGainLossMatrix( true ); fitch.setReturnInternalStates( true ); - final Map> map = getDomainIdToSecondaryFeaturesMap(); final Map newmap = new HashMap(); final Iterator>> it = map.entrySet().iterator(); - while (it.hasNext()) { - final Map.Entry> pair = (Map.Entry>)it.next(); + while ( it.hasNext() ) { + final Map.Entry> pair = it.next(); if ( pair.getValue().size() != 1 ) { - throw new IllegalArgumentException( pair.getKey().getId() + " mapps to " + pair.getValue().size() + " items" ); + throw new IllegalArgumentException( pair.getKey().getId() + " mapps to " + pair.getValue().size() + + " items" ); } newmap.put( pair.getKey(), ( String ) pair.getValue().toArray()[ 0 ] ); } - - CharacterStateMatrix states =createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(), - newmap ); - + final CharacterStateMatrix states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(), + newmap ); fitch.execute( getPhylogeny(), states ); setGainLossMatrix( fitch.getGainLossMatrix() ); setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() ); @@ -256,7 +253,7 @@ public final class DomainParsimonyCalculator { public void executeFitchParsimonyOnBinaryDomainCombintion( final boolean use_last ) { executeFitchParsimony( false, use_last, false, 0 ); } - + public void executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( final boolean use_last ) { executeFitchParsimonyOnSecondaryFeatures( use_last, false, 0 ); } @@ -546,7 +543,6 @@ public final class DomainParsimonyCalculator { return new DomainParsimonyCalculator( phylogeny, gwcd_list, domain_id_to_secondary_features_map ); } - /** * For folds instead of Pfam-domains, for example * @@ -619,10 +615,9 @@ public final class DomainParsimonyCalculator { } return matrix; } - - + public static CharacterStateMatrix createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List gwcd_list, - final Map domain_id_to_second_features_map) { + final Map domain_id_to_second_features_map ) { if ( gwcd_list.isEmpty() ) { throw new IllegalArgumentException( "genome wide combinable domains list is empty" ); } @@ -633,12 +628,10 @@ public final class DomainParsimonyCalculator { final SortedSet all_binary_combinations_mapped = new TreeSet(); final Set[] binary_combinations_per_genome_mapped = new HashSet[ number_of_identifiers ]; int identifier_index = 0; - final SortedSet no_mappings = new TreeSet(); for( final GenomeWideCombinableDomains gwcd : gwcd_list ) { binary_combinations_per_genome_mapped[ identifier_index ] = new HashSet(); for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) { - final BinaryDomainCombination mapped_bc = mapBinaryDomainCombination( domain_id_to_second_features_map, bc, no_mappings ); @@ -647,14 +640,13 @@ public final class DomainParsimonyCalculator { } ++identifier_index; } - if ( !no_mappings.isEmpty() ) { - ForesterUtil.programMessage( surfacing.PRG_NAME, "No mappings for the following (" + no_mappings.size() + "):" ); + ForesterUtil.programMessage( surfacing.PRG_NAME, "No mappings for the following (" + no_mappings.size() + + "):" ); for( final String id : no_mappings ) { - ForesterUtil.programMessage( surfacing.PRG_NAME, id); + ForesterUtil.programMessage( surfacing.PRG_NAME, id ); } } - final int number_of_characters = all_binary_combinations_mapped.size(); final CharacterStateMatrix matrix = new BasicCharacterStateMatrix( number_of_identifiers, number_of_characters ); @@ -699,30 +691,23 @@ public final class DomainParsimonyCalculator { final SortedSet no_mappings ) { String id0 = ""; String id1 = ""; - if ( !domain_id_to_second_features_map.containsKey( bc.getId0() ) ) { - - no_mappings.add(bc.getId0().getId() ); + no_mappings.add( bc.getId0().getId() ); id0 = bc.getId0().getId(); } else { - id0 = domain_id_to_second_features_map.get( bc.getId0()); + id0 = domain_id_to_second_features_map.get( bc.getId0() ); } if ( !domain_id_to_second_features_map.containsKey( bc.getId1() ) ) { - - no_mappings.add(bc.getId1().getId() ); + no_mappings.add( bc.getId1().getId() ); id1 = bc.getId1().getId(); } else { - id1 = domain_id_to_second_features_map.get( bc.getId1()); + id1 = domain_id_to_second_features_map.get( bc.getId1() ); } - return new BasicBinaryDomainCombination( id0, id1 ); } - - - - + public static CharacterStateMatrix createMatrixOfBinaryDomainCombinationPresenceOrAbsence( final List gwcd_list ) { if ( gwcd_list.isEmpty() ) { throw new IllegalArgumentException( "genome wide combinable domains list is empty" ); @@ -846,8 +831,6 @@ public final class DomainParsimonyCalculator { return matrix; } - - private static int getStateSumDeltaOnNode( final String node_identifier, final CharacterStateMatrix gain_loss_matrix, final GainLossStates state ) { diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 24823a4..8f5bf5e 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -105,12 +105,12 @@ public final class SurfacingUtil { } }; public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" ); - private static final boolean USE_LAST = true; + private static final boolean USE_LAST = true; private SurfacingUtil() { // Hidden constructor. } - + public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome, final SortedSet binary_domain_combinations ) { final SortedMap all_cd = genome.getAllCombinableDomainsIds(); @@ -841,18 +841,11 @@ public final class SurfacingUtil { parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); - - // FITCH DOMAIN COMBINATIONS // ------------------------- - local_phylogeny_copy = phylogeny.copy(); - String randomization = "no"; - + local_phylogeny_copy = phylogeny.copy(); + final String randomization = "no"; secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST ); - - - - preparePhylogeny( local_phylogeny_copy, secondary_features_parsimony, date_time, @@ -867,9 +860,8 @@ public final class SurfacingUtil { + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name - + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt" ); - - + + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt" ); } public static void extractProteinNames( final List proteins,