- 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_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d";
- public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d";
- public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d";
- 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_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc";
- public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc";
- public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc";
- 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 DISPLAY_M_HISTOGRAMS_OPTION = "mhisto";
- // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false;
- 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 = "2.003";
- final static private String PRG_DATE = "2010.12.03";
- 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;
- final static private String DEFAULT_SEARCH_PARAMETER = "ls";
- final private static boolean VERBOSE_DEFAULT = true;
- 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 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 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";
+ 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 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_GENOMES_FILE_OPTION = "genomes";
+ final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
+ final static private String SEQ_EXTRACT_OPTION = "prot_extract";
+ final static private String PRG_VERSION = "2.302";
+ final static private String PRG_DATE = "130715";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
+ final static private boolean IGNORE_DUFS_DEFAULT = true;
+ 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";
+ final static private String OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION = "all_prot_e";
+ 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 String WRITE_TO_NEXUS_OPTION = "nexus";
+ private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE; //TODO look at me! change?
+ 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 final boolean CALC_SIMILARITY_SCORES = false;