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,
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();
}
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" );
fitch.setUseLast( use_last );
fitch.setReturnGainLossMatrix( true );
fitch.setReturnInternalStates( true );
-
final Map<DomainId, Set<String>> map = getDomainIdToSecondaryFeaturesMap();
final Map<DomainId, String> newmap = new HashMap<DomainId, String>();
final Iterator<Entry<DomainId, Set<String>>> it = map.entrySet().iterator();
- while (it.hasNext()) {
- final Map.Entry<DomainId, Set<String>> pair = (Map.Entry<DomainId, Set<String>>)it.next();
+ while ( it.hasNext() ) {
+ final Map.Entry<DomainId, Set<String>> 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<BinaryStates> states =createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
- newmap );
-
+ final CharacterStateMatrix<BinaryStates> states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
+ newmap );
fitch.execute( getPhylogeny(), states );
setGainLossMatrix( fitch.getGainLossMatrix() );
setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
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 );
}
return new DomainParsimonyCalculator( phylogeny, gwcd_list, domain_id_to_secondary_features_map );
}
-
/**
* For folds instead of Pfam-domains, for example
*
}
return matrix;
}
-
-
+
public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, String> domain_id_to_second_features_map) {
+ final Map<DomainId, String> domain_id_to_second_features_map ) {
if ( gwcd_list.isEmpty() ) {
throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
}
final SortedSet<BinaryDomainCombination> all_binary_combinations_mapped = new TreeSet<BinaryDomainCombination>();
final Set<BinaryDomainCombination>[] binary_combinations_per_genome_mapped = new HashSet[ number_of_identifiers ];
int identifier_index = 0;
-
final SortedSet<String> no_mappings = new TreeSet<String>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
binary_combinations_per_genome_mapped[ identifier_index ] = new HashSet<BinaryDomainCombination>();
for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) {
-
final BinaryDomainCombination mapped_bc = mapBinaryDomainCombination( domain_id_to_second_features_map,
bc,
no_mappings );
}
++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<CharacterStateMatrix.BinaryStates> matrix = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( number_of_identifiers,
number_of_characters );
final SortedSet<String> 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<BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list ) {
if ( gwcd_list.isEmpty() ) {
throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
return matrix;
}
-
-
private static int getStateSumDeltaOnNode( final String node_identifier,
final CharacterStateMatrix<GainLossStates> gain_loss_matrix,
final GainLossStates state ) {
git://source.jalview.org / jalview.git / commitdiff