// =============================================================== // // // // File : GEN_gene.cxx // // Purpose : // // // // Coded by Ralf Westram (coder@reallysoft.de) in 2001 // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include "GEN_gene.hxx" #include "GEN_local.hxx" #include "GEN_nds.hxx" #include #include #include #include #include // Standard fields of a gb_gene entry: // ----------------------------------- // name = short name of gene (unique in one species) // type = type of gene (e.g. 'gene', 'CDS', 'tRNA', 'misc_feature') // pos_start = start-position(s) of gene(-parts); range is 1...genomeLength // pos_stop = end-position(s) of gene(-parts); range is 1...genomeLength // pos_certain = contains pairs of chars (1. for start-pos, 2. for end-pos) // // '=' means 'pos is exact' // '<' means 'pos may be lower' // '>' means 'pos may be higher' // '+' means 'pos is directly behind' // '-' means 'pos is directly before' // // if pos_certain is missing -> like '==' // // pos_complement = 1 -> CDS is on opposite strand // fields for split genes: // -------------------------- // pos_joined = xxx -> gene consists of abs(xxx) parts (if missing xxx == 1 is assumed) // // if abs(xxx)>1, the gene consists of several parts. // In that case the fields 'pos_start', 'pos_stop', 'pos_certain' and 'pos_complement' // contain multiple comma-separated values - one for each joined part. // // if xxx is < -1, then joining the parts does not make sense (or nothing is known about it) // // Note: Please do not access these fields manually - use GEN_read_position! // other fields added by importer: // ------------------------------- // // During import ARB tries to reproduce existing translations. // If it succeeds, it removes the translation. // // ARB_translation = written if ARB translation differs from original translation // (original translation is not deleted in this case) // ARB_translation_note = additional info about failed translation // ARB_translation_rm = 1 -> translation was reproduced and deleted // // if a gene with type 'gene' exists and another gene with different type, but // identical location exists as well, ARB sets ARB_display_hidden to 1 for // the 'gene'. For the other gene with diff. type ARB sets a reference to the // hidden 'gene': // // ARB_is_gene = shortname of related hidden gene // fields used for display: // ------------------------ // ARB_display_hidden = 1 -> do not display this gene (depends on AWAR_GENMAP_SHOW_HIDDEN too) // ARB_color = color group // Old format standard fields of a gb_gene entry: // ---------------------------------------------- // name = short name of gene (unique in one species) // pos_begin = start-position of gene // pos_end = end-position of gene // pos_uncertain = contains 2 chars (1. for start-pos, 2. for end-pos); = means 'pos is exact'; < means 'pos may be lower'; > means 'pos may be higher'; missing -> like == // complement = 1 -> encoding from right to left // // fields for split genes: // -------------------------- // pos_joined = xxx -> gene consists of xxx parts (may not exist if xxx == 1) // pos_beginxxx, pos_endxxx = start-/end-positions for parts 2...n // pos_uncertainxxx = like above for parts 2...n // using namespace std; static const GEN_position *loadPositions4gene(GBDATA *gb_gene) { static GEN_position *loaded_position = NULp; static GBDATA *positionLoaded4gene = NULp; if (positionLoaded4gene != gb_gene) { if (loaded_position) { GEN_free_position(loaded_position); loaded_position = NULp; positionLoaded4gene = NULp; } if (gb_gene) { loaded_position = GEN_read_position(gb_gene); if (loaded_position) positionLoaded4gene = gb_gene; } } return loaded_position; } void GEN_gene::init() { name = GBT_get_name_or_description(gb_gene); GBDATA *gbd = GB_entry(gb_gene, "complement"); complement = gbd ? GB_read_byte(gbd) == 1 : false; } void GEN_gene::load_location(int part, const GEN_position *location) { gen_assert(part >= 1); gen_assert(part <= location->parts); pos1 = location->start_pos[part-1]; pos2 = location->stop_pos[part-1]; complement = location->complement[part-1]; gen_assert(pos1 <= pos2); } GEN_gene::GEN_gene(GBDATA *gb_gene_, GEN_root *root_, const GEN_position *location) : gb_gene(gb_gene_), root(root_) { init(); load_location(1, location); nodeInfo = GEN_make_node_text_nds(gb_gene, 0); } GEN_gene::GEN_gene(GBDATA *gb_gene_, GEN_root *root_, const GEN_position *location, int partNumber) : gb_gene(gb_gene_), root(root_) { // partNumber 1..n which part of a split gene // maxParts 1..n of how many parts consists this gene? init(); load_location(partNumber, location); { char buffer[30]; sprintf(buffer, " (%i/%i)", partNumber, location->parts); nodeInfo = name+buffer; } } void GEN_gene::reinit_NDS() const { nodeInfo = GEN_make_node_text_nds(gb_gene, 0); } // ------------------ // GEN_root GEN_root::GEN_root(const char *organism_name_, const char *gene_name_, GBDATA *gb_main_, AW_root *aw_root, GEN_graphic *gen_graphic_) : gb_main(gb_main_), gen_graphic(gen_graphic_), organism_name(organism_name_), gene_name(gene_name_), error_reason(""), length(-1), gb_gene_data(NULp) { GB_transaction ta(gb_main); GBDATA *gb_organism = GBT_find_species(gb_main, organism_name.c_str()); if (!gb_organism) { error_reason = ARB_strdup("Please select a species."); } else { GBDATA *gb_data = GBT_find_sequence(gb_organism, GENOM_ALIGNMENT); if (!gb_data) { error_reason = GBS_global_string_copy("'%s' has no data in '%s'", organism_name.c_str(), GENOM_ALIGNMENT); } else { length = GB_read_count(gb_data); gb_gene_data = GEN_find_gene_data(gb_organism); GBDATA *gb_gene = gb_gene_data ? GEN_first_gene_rel_gene_data(gb_gene_data) : NULp; if (!gb_gene) { error_reason = GBS_global_string("Species '%s' has no gene-information", organism_name.c_str()); } else { bool show_hidden = aw_root->awar(AWAR_GENMAP_SHOW_HIDDEN)->read_int() != 0; while (gb_gene) { bool show_this = show_hidden; if (!show_this) { GBDATA *gbd = GB_entry(gb_gene, ARB_HIDDEN); if (!gbd || !GB_read_byte(gbd)) { // gene is not hidden show_this = true; } } if (show_this) { const GEN_position *location = loadPositions4gene(gb_gene); if (!location) { GB_ERROR warning = GB_await_error(); char *id = GEN_global_gene_identifier(gb_gene, gb_organism); aw_message(GBS_global_string("Can't load gene '%s':\nReason: %s", id, warning)); free(id); } else { int parts = location->parts; if (parts == 1) { gene_set.insert(GEN_gene(gb_gene, this, location)); } else { // joined gene for (int p = 1; p <= parts; ++p) { gene_set.insert(GEN_gene(gb_gene, this, location, p)); } } } } gb_gene = GEN_next_gene(gb_gene); } } } } } void GEN_root::reinit_NDS() const { GEN_iterator end = gene_set.end(); for (GEN_iterator gene = gene_set.begin(); gene != end; ++gene) { gene->reinit_NDS(); } }