// =============================================================== // // // // File : primer_design.cxx // // Purpose : // // // // Coded by Wolfram Foerster in February 2001 // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include "primer_design.hxx" #include "PRD_Design.hxx" #include "PRD_SequenceIterator.hxx" #include #include #include #include #include #include #include #include #include #include #include #include #include using std::string; static AW_window_simple *pdrw = NULp; static AW_selection_list *resultList = NULp; static double get_estimated_memory(AW_root *root) { int bases = root->awar(AWAR_PRIMER_DESIGN_LEFT_LENGTH)->read_int() + root->awar(AWAR_PRIMER_DESIGN_RIGHT_LENGTH)->read_int(); int length = root->awar(AWAR_PRIMER_DESIGN_LENGTH_MAX)->read_int(); double mem = bases*length*0.9*(sizeof(Node)+16); return mem; } static void primer_design_event_update_memory(AW_root *root) { double mem = get_estimated_memory(root); const char *display = NULp; if (mem > 1073741824) { mem = mem / 1073741824; display = GBS_global_string("%.1f TB", mem); } else if (mem > 1048576) { mem = mem / 1048576; display = GBS_global_string("%.1f MB", mem); } else if (mem > 1024) { mem = mem / 1024; display = GBS_global_string("%.1f KB", mem); } else { display = GBS_global_string("%.0f bytes", mem); } root->awar(AWAR_PRIMER_DESIGN_APROX_MEM)->write_string(display); } static void primer_design_event_check_primer_length(AW_root *root, bool max_changed) { static bool avoid_recursion = false; if (!avoid_recursion) { avoid_recursion = true; int min_length = root->awar(AWAR_PRIMER_DESIGN_LENGTH_MIN)->read_int(); int max_length = root->awar(AWAR_PRIMER_DESIGN_LENGTH_MAX)->read_int(); if (max_length<1) max_length = 1; if (min_length<1) min_length = 1; if (min_length > max_length) { if (max_changed) min_length = max_length; else max_length = min_length; } prd_assert(min_length>0); root->awar(AWAR_PRIMER_DESIGN_LENGTH_MIN)->write_int(min_length); root->awar(AWAR_PRIMER_DESIGN_LENGTH_MAX)->write_int(max_length); avoid_recursion = false; } } void create_primer_design_variables(AW_root *aw_root, AW_default aw_def, AW_default global) { aw_root->awar_int(AWAR_PRIMER_DESIGN_LEFT_POS, 0, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_LEFT_LENGTH, 100, aw_def)->add_callback(primer_design_event_update_memory); aw_root->awar_int(AWAR_PRIMER_DESIGN_RIGHT_POS, 1000, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_RIGHT_LENGTH, 100, aw_def)->add_callback(primer_design_event_update_memory); aw_root->awar_int(AWAR_PRIMER_DESIGN_LENGTH_MIN, 10, aw_def)->add_callback(makeRootCallback(primer_design_event_check_primer_length, false)); aw_root->awar_int(AWAR_PRIMER_DESIGN_LENGTH_MAX, 20, aw_def)->add_callback(makeRootCallback(primer_design_event_check_primer_length, true)); aw_root->awar_int(AWAR_PRIMER_DESIGN_DIST_MIN, 1050, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_DIST_MAX, 1200, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_GCRATIO_MIN, 10, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_GCRATIO_MAX, 50, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_TEMPERATURE_MIN, 30, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_TEMPERATURE_MAX, 80, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, 0, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_EXPAND_IUPAC, 1, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_MAX_PAIRS, 25, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_GC_FACTOR, 50, aw_def); aw_root->awar_int(AWAR_PRIMER_DESIGN_TEMP_FACTOR, 50, aw_def); aw_root->awar_string(AWAR_PRIMER_DESIGN_APROX_MEM, "", aw_def); aw_root->awar_string(AWAR_PRIMER_TARGET_STRING, NULp, global); primer_design_event_update_memory(aw_root); } static void create_primer_design_result_window(AW_window *aww) { if (!pdrw) { pdrw = new AW_window_simple; pdrw->init(aww->get_root(), "PRD_RESULT", "Primer Design RESULT"); pdrw->load_xfig("pd_reslt.fig"); pdrw->button_length(6); pdrw->auto_space(10, 10); pdrw->at("help"); pdrw->callback(makeHelpCallback("primer_result.hlp")); pdrw->create_button("HELP", "HELP", "H"); pdrw->at("result"); resultList = pdrw->create_selection_list(AWAR_PRIMER_TARGET_STRING, 40, 5); const StorableSelectionList *storable_primer_list = new StorableSelectionList(TypedSelectionList("prim", resultList, "primers", "primer")); // never freed pdrw->at("buttons"); pdrw->callback(AW_POPDOWN); pdrw->create_button("CLOSE", "CLOSE", "C"); pdrw->callback(makeWindowCallback(awt_clear_selection_list_cb, resultList)); pdrw->create_button("CLEAR", "CLEAR", "R"); pdrw->callback(makeCreateWindowCallback(create_load_box_for_selection_lists, storable_primer_list)); pdrw->create_button("LOAD", "LOAD", "L"); pdrw->callback(makeCreateWindowCallback(create_save_box_for_selection_lists, storable_primer_list)); pdrw->create_button("SAVE", "SAVE", "S"); pdrw->callback(makeWindowCallback(create_print_box_for_selection_lists, &storable_primer_list->get_typedsellist())); pdrw->create_button("PRINT", "PRINT", "P"); } pdrw->show(); } static void primer_design_event_go(AW_window *aww, GBDATA *gb_main) { AW_root *root = aww->get_root(); GB_ERROR error = NULp; char *sequence = NULp; long int length = 0; if ((get_estimated_memory(root)/1024.0) > GB_get_usable_memory()) { if (aw_question(NULp, "ARB may crash due to memory problems.", "Continue, Abort") == 1) { return; } } { GB_transaction ta(gb_main); char *selected_species = root->awar(AWAR_SPECIES_NAME)->read_string(); GBDATA *gb_species = GBT_find_species(gb_main, selected_species); if (!gb_species) { error = "you have to select a species!"; } else { char *alignment = GBT_get_default_alignment(gb_main); if (!alignment) { error = GB_await_error(); } else { GBDATA *gb_seq = GBT_find_sequence(gb_species, alignment); if (!gb_seq) { error = GBS_global_string("Selected species has no sequence data in alignment '%s'", alignment); } else { sequence = GB_read_string(gb_seq); length = GB_read_count(gb_seq); } free(alignment); } } } if (!error) { arb_progress progress("Searching PCR primer pairs"); PrimerDesign *PD = new PrimerDesign(sequence, length, Range(root->awar(AWAR_PRIMER_DESIGN_LEFT_POS)->read_int(), root->awar(AWAR_PRIMER_DESIGN_LEFT_LENGTH)->read_int()), Range(root->awar(AWAR_PRIMER_DESIGN_RIGHT_POS)->read_int(), root->awar(AWAR_PRIMER_DESIGN_RIGHT_LENGTH)->read_int()), Range(root->awar(AWAR_PRIMER_DESIGN_LENGTH_MIN)->read_int(), root->awar(AWAR_PRIMER_DESIGN_LENGTH_MAX)->read_int()), Range(root->awar(AWAR_PRIMER_DESIGN_DIST_MIN)->read_int(), root->awar(AWAR_PRIMER_DESIGN_DIST_MAX)->read_int()), Range(root->awar(AWAR_PRIMER_DESIGN_GCRATIO_MIN)->read_int(), root->awar(AWAR_PRIMER_DESIGN_GCRATIO_MAX)->read_int()), Range(root->awar(AWAR_PRIMER_DESIGN_TEMPERATURE_MIN)->read_int(), root->awar(AWAR_PRIMER_DESIGN_TEMPERATURE_MAX)->read_int()), root->awar(AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST)->read_int(), (bool)root->awar(AWAR_PRIMER_DESIGN_EXPAND_IUPAC)->read_int(), root->awar(AWAR_PRIMER_DESIGN_MAX_PAIRS)->read_int(), (float)root->awar(AWAR_PRIMER_DESIGN_GC_FACTOR)->read_int()/100, (float)root->awar(AWAR_PRIMER_DESIGN_TEMP_FACTOR)->read_int()/100 ); try { PD->run(); } catch (string& s) { error = GBS_static_string(s.c_str()); } catch (...) { error = "Unknown error (maybe out of memory ? )"; } if (!error) error = PD->get_error(); if (!error) { if (!resultList) create_primer_design_result_window(aww); prd_assert(resultList); // create result-list: resultList->clear(); int max_primer_length = PD->get_max_primer_length(); int max_position_length = int(std::log10(double (PD->get_max_primer_pos())))+1; int max_length_length = int(std::log10(double(PD->get_max_primer_length())))+1; if (max_position_length < 3) max_position_length = 3; if (max_length_length < 3) max_length_length = 3; resultList->insert(GBS_global_string(" Rating | %-*s %-*s %-*s G/C Tmp | %-*s %-*s %-*s G/C Tmp", max_primer_length, "Left primer", max_position_length, "Pos", max_length_length, "Len", max_primer_length, "Right primer", max_position_length, "Pos", max_length_length, "Len"), ""); int r; for (r = 0; ; ++r) { const char *primers = NULp; const char *result = PD->get_result(r, primers, max_primer_length, max_position_length, max_length_length); if (!result) break; resultList->insert(result, primers); } resultList->insert_default(r ? "**** End of list" : "**** There are no results", ""); resultList->update(); pdrw->show(); } } if (sequence) free(sequence); if (error) aw_message(error); } static void primer_design_event_check_temp_factor(AW_window *aww) { AW_root *root = aww->get_root(); int temp = root->awar(AWAR_PRIMER_DESIGN_TEMP_FACTOR)->read_int(); if (temp > 100) temp = 100; if (temp < 0) temp = 0; root->awar(AWAR_PRIMER_DESIGN_TEMP_FACTOR)->write_int(temp); root->awar(AWAR_PRIMER_DESIGN_GC_FACTOR)->write_int(100-temp); } static void primer_design_event_check_gc_factor(AW_window *aww) { AW_root *root = aww->get_root(); int gc = root->awar(AWAR_PRIMER_DESIGN_GC_FACTOR)->read_int(); if (gc > 100) gc = 100; if (gc < 0) gc = 0; root->awar(AWAR_PRIMER_DESIGN_GC_FACTOR)->write_int(gc); root->awar(AWAR_PRIMER_DESIGN_TEMP_FACTOR)->write_int(100-gc); } static void primer_design_event_init(AW_window *aww, GBDATA *gb_main, bool from_gene) { GB_transaction ta(gb_main); AW_root *root = aww->get_root(); GB_ERROR error = NULp; char *selected_species = NULp; char *selected_gene = NULp; GBDATA *gb_species = NULp; GBDATA *gb_gene = NULp; GEN_position *genPos = NULp; GBDATA *gb_seq = NULp; bool is_genom_db = GEN_is_genome_db(gb_main, -1); if (is_genom_db && from_gene) { selected_species = root->awar(AWAR_ORGANISM_NAME)->read_string(); selected_gene = root->awar(AWAR_GENE_NAME)->read_string(); root->awar(AWAR_SPECIES_NAME)->write_string(selected_species); } else { selected_species = root->awar(AWAR_SPECIES_NAME)->read_string(); } gb_species = GBT_find_species(gb_main, selected_species); if (!gb_species) { error = "You have to select a species!"; } else { char *alignment = GBT_get_default_alignment(gb_main); if (!alignment) { error = GB_await_error(); } else { gb_seq = GBT_find_sequence(gb_species, alignment); if (!gb_seq) { error = GB_export_errorf("Species '%s' has no data in alignment '%s'", selected_species, alignment); } free(alignment); } } if (!error && from_gene) { prd_assert(is_genom_db); // otherwise button should not exist gb_gene = GEN_find_gene(gb_species, selected_gene); if (!gb_gene) { error = GB_export_errorf("Species '%s' has no gene named '%s'", selected_species, selected_gene); } else { genPos = GEN_read_position(gb_gene); if (!genPos) { error = GB_await_error(); } else if (!genPos->joinable) { error = GBS_global_string("Gene '%s' is not joinable", selected_gene); } } } if (!error && gb_seq) { SequenceIterator *i = NULp; PRD_Sequence_Pos length = 0; PRD_Sequence_Pos add_offset = 0; // offset to add to positions (used for genes) char *sequence = NULp; if (gb_gene) { size_t gene_length; sequence = GBT_read_gene_sequence_and_length(gb_gene, false, 0, &gene_length); if (!sequence) { error = GB_await_error(); } else { length = gene_length; add_offset = genPos->start_pos[0]; // @@@ does this work with split genes? warn about uncertainties? } } else { sequence = GB_read_string(gb_seq); length = strlen(sequence); } if (!error) { long int dist_min; long int dist_max; // find reasonable parameters // left pos (first base from start) long int left_len = root->awar(AWAR_PRIMER_DESIGN_LEFT_LENGTH)->read_int(); if (left_len == 0 || left_len<0) left_len = 100; i = new SequenceIterator(sequence, 0, SequenceIterator::IGNORE, left_len, SequenceIterator::FORWARD); i->nextBase(); // find first base from start PRD_Sequence_Pos left_min = i->pos; // store pos. of first base while (i->nextBase() != SequenceIterator::EOS) ; // step to 'left_len'th base from start PRD_Sequence_Pos left_max = i->pos; // store pos. of 'left_len'th base root->awar(AWAR_PRIMER_DESIGN_LEFT_POS)->write_int(left_min+add_offset); root->awar(AWAR_PRIMER_DESIGN_LEFT_LENGTH)->write_int(left_len); long int right_len = root->awar(AWAR_PRIMER_DESIGN_RIGHT_LENGTH)->read_int(); if (right_len == 0 || right_len<0) right_len = 100; // right pos ('right_len'th base from end) i->restart(length, 0, right_len, SequenceIterator::BACKWARD); i->nextBase(); // find last base PRD_Sequence_Pos right_max = i->pos; // store pos. of last base while (i->nextBase() != SequenceIterator::EOS) ; // step to 'right_len'th base from end PRD_Sequence_Pos right_min = i->pos; // store pos of 'right_len'th base from end root->awar(AWAR_PRIMER_DESIGN_RIGHT_POS)->write_int(right_min+add_offset); root->awar(AWAR_PRIMER_DESIGN_RIGHT_LENGTH)->write_int(right_len); // primer distance if (right_min >= left_max) { // non-overlapping ranges i->restart(left_max, right_min, SequenceIterator::IGNORE, SequenceIterator::FORWARD); long int bases_between = 0; // count bases from right_min to left_max while (i->nextBase() != SequenceIterator::EOS) ++bases_between; dist_min = bases_between; // take bases between as min distance } else { // overlapping ranges dist_min = right_min - left_min + 1; } dist_max = right_max - left_min; root->awar(AWAR_PRIMER_DESIGN_DIST_MIN)->write_int(dist_min); root->awar(AWAR_PRIMER_DESIGN_DIST_MAX)->write_int(dist_max); #if defined(DUMP_PRIMER) printf ("primer_design_event_init : left_min %7li\n", left_min); printf ("primer_design_event_init : left_max %7li\n", left_max); printf ("primer_design_event_init : right_min %7li\n", right_min); printf ("primer_design_event_init : right_max %7li\n", right_max); printf ("primer_design_event_init : dist_min %7li\n", dist_min); printf ("primer_design_event_init : dist_max %7li\n\n", dist_max); #endif } delete i; free(sequence); } if (error) { aw_message(error); } GEN_free_position(genPos); free(selected_gene); free(selected_species); } static AWT_config_mapping_def primer_design_config_mapping[] = { { AWAR_PRIMER_DESIGN_LEFT_POS, "lpos" }, { AWAR_PRIMER_DESIGN_LEFT_LENGTH, "llen" }, { AWAR_PRIMER_DESIGN_RIGHT_POS, "rpos" }, { AWAR_PRIMER_DESIGN_RIGHT_LENGTH, "rlen" }, { AWAR_PRIMER_DESIGN_LENGTH_MIN, "lenmin" }, { AWAR_PRIMER_DESIGN_LENGTH_MAX, "lenmax" }, { AWAR_PRIMER_DESIGN_DIST_MIN, "distmin" }, { AWAR_PRIMER_DESIGN_DIST_MAX, "distmax" }, { AWAR_PRIMER_DESIGN_GCRATIO_MIN, "gcmin" }, { AWAR_PRIMER_DESIGN_GCRATIO_MAX, "gcmax" }, { AWAR_PRIMER_DESIGN_TEMPERATURE_MIN, "tempmin" }, { AWAR_PRIMER_DESIGN_TEMPERATURE_MAX, "tempmax" }, { AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, "minmatchdist" }, { AWAR_PRIMER_DESIGN_EXPAND_IUPAC, "iupac" }, { AWAR_PRIMER_DESIGN_MAX_PAIRS, "maxpairs" }, { AWAR_PRIMER_DESIGN_GC_FACTOR, "gcfactor" }, { AWAR_PRIMER_DESIGN_TEMP_FACTOR, "temp_factor" }, { NULp, NULp } }; AW_window *create_primer_design_window(AW_root *root, GBDATA *gb_main) { bool is_genome_db; { GB_transaction ta(gb_main); char *selected_species = root->awar(AWAR_SPECIES_NAME)->read_string(); GBDATA *gb_species = GBT_find_species(gb_main, selected_species); if (!gb_species) { aw_message("You have to select a species!"); } is_genome_db = GEN_is_genome_db(gb_main, -1); } AW_window_simple *aws = new AW_window_simple; aws->init(root, "PRIMER_DESIGN", "PRIMER DESIGN"); aws->load_xfig("prd_main.fig"); aws->at("close"); aws->callback(AW_POPDOWN); aws->create_button("CLOSE", "CLOSE", "C"); aws->at("help"); aws->callback(makeHelpCallback("primer_new.hlp")); aws->create_button("HELP", "HELP", "H"); aws->at("init1"); aws->callback(makeWindowCallback(primer_design_event_init, gb_main, false)); aws->create_button("INIT_FROM_SPECIES", "Species", "I"); if (is_genome_db) { aws->at("init2"); aws->callback(makeWindowCallback(primer_design_event_init, gb_main, true)); aws->create_button("INIT_FROM_GENE", "Gene", "I"); } aws->at("design"); aws->callback(makeWindowCallback(primer_design_event_go, gb_main)); aws->create_button("GO", "GO", "G"); aws->highlight(); aws->at("minleft"); aws->create_input_field(AWAR_PRIMER_DESIGN_LEFT_POS, 7); aws->at("maxleft"); aws->create_input_field(AWAR_PRIMER_DESIGN_LEFT_LENGTH, 9); aws->at("minright"); aws->create_input_field(AWAR_PRIMER_DESIGN_RIGHT_POS, 7); aws->at("maxright"); aws->create_input_field(AWAR_PRIMER_DESIGN_RIGHT_LENGTH, 9); aws->at("minlen"); aws->create_input_field(AWAR_PRIMER_DESIGN_LENGTH_MIN, 7); aws->at("maxlen"); aws->create_input_field(AWAR_PRIMER_DESIGN_LENGTH_MAX, 7); aws->at("mindist"); aws->create_input_field(AWAR_PRIMER_DESIGN_DIST_MIN, 7); aws->at("maxdist"); aws->create_input_field(AWAR_PRIMER_DESIGN_DIST_MAX, 7); aws->at("mingc"); aws->create_input_field(AWAR_PRIMER_DESIGN_GCRATIO_MIN, 7); aws->at("maxgc"); aws->create_input_field(AWAR_PRIMER_DESIGN_GCRATIO_MAX, 7); aws->at("mintemp"); aws->create_input_field(AWAR_PRIMER_DESIGN_TEMPERATURE_MIN, 7); aws->at("maxtemp"); aws->create_input_field(AWAR_PRIMER_DESIGN_TEMPERATURE_MAX, 7); aws->at("allowed_match"); aws->create_input_field(AWAR_PRIMER_DESIGN_ALLOWED_MATCH_MIN_DIST, 7); aws->at("max_pairs"); aws->create_input_field(AWAR_PRIMER_DESIGN_MAX_PAIRS, 7); aws->at("expand_IUPAC"); aws->create_toggle(AWAR_PRIMER_DESIGN_EXPAND_IUPAC); aws->at("GC_factor"); aws->callback(primer_design_event_check_gc_factor); // @@@ used as INPUTFIELD_CB (see #559) aws->create_input_field(AWAR_PRIMER_DESIGN_GC_FACTOR, 7); aws->at("temp_factor"); aws->callback(primer_design_event_check_temp_factor); // @@@ used as INPUTFIELD_CB (see #559) aws->create_input_field(AWAR_PRIMER_DESIGN_TEMP_FACTOR, 7); aws->at("config"); AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "pcr_primer_design", primer_design_config_mapping); aws->at("aprox_mem"); aws->button_length(11); aws->create_button(NULp, AWAR_PRIMER_DESIGN_APROX_MEM, NULp, "+"); return aws; }