// =============================================================== // // // // File : NT_trackAliChanges.cxx // // Purpose : Track alignment and sequences changes // // // // Coded by Ralf Westram (coder@reallysoft.de) in June 2007 // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include "NT_local.h" #include #include #include #include #include #include #include #include #include #include #include #define AWAR_TRACK_BASE "track/" #define AWAR_TRACK_ALI AWAR_TRACK_BASE "ali" #define AWAR_TRACK_ID AWAR_TRACK_BASE "initials" // [historical] #define SEQ_HISTORY_FIELD "seq_history" using std::string; using std::list; static GB_ERROR writeHistory(GBDATA *gb_species, const char *stamp, const char *entry) { char *newContent = GBS_global_string_copy("%s %s", stamp, entry); GB_ERROR error = NULp; GBDATA *gb_history = GB_entry(gb_species, SEQ_HISTORY_FIELD); if (!gb_history) error = GBT_write_string(gb_species, SEQ_HISTORY_FIELD, newContent); else { size_t oldSize = GB_read_string_count(gb_history); size_t newSize = strlen(newContent); GBS_strstruct content(oldSize+newSize+3); content.ncat(newContent, newSize); content.put('\n'); content.ncat(GB_read_char_pntr(gb_history), oldSize); error = GB_write_string(gb_history, content.get_data()); } free(newContent); return error; } static void trackAlignmentChanges(AW_window *aww) { GB_transaction ta(GLOBAL.gb_main); AW_root *root = aww->get_root(); char *ali = root->awar(AWAR_TRACK_ALI)->read_string(); char *checksum_field = GBS_string_2_key(GBS_global_string("checksum_%s", ali)); GB_ERROR error = NULp; char *stamp; { const char *sessionID = root->awar(AWAR_TRACK_ID)->read_char_pntr(); char atime[256]; time_t t = time(NULp); struct tm *tms = localtime(&t); strftime(atime, 255, "%Y/%m/%d %k:%M", tms); stamp = GBS_global_string_copy("%s %s", atime, sessionID); } arb_progress progress(GBS_global_string("Tracking changes in '%s'", ali), GBT_get_species_count(GLOBAL.gb_main)); // add changekeys for generated fields: GB_warning_if(GBT_add_new_species_changekey(GLOBAL.gb_main, checksum_field, GB_STRING)); GB_warning_if(GBT_add_new_species_changekey(GLOBAL.gb_main, SEQ_HISTORY_FIELD, GB_STRING)); size_t newSpecies = 0; size_t ali_changed = 0; size_t seq_changed = 0; size_t unchanged = 0; for (GBDATA *gb_species = GBT_first_species(GLOBAL.gb_main); gb_species && !error; gb_species = GBT_next_species(gb_species)) { GBDATA *gb_seq = GBT_find_sequence(gb_species, ali); if (gb_seq) { // has data in wanted alignment const char *seq = GB_read_char_pntr(gb_seq); long char_cs = GBS_checksum(seq, 0, ".-"); long ali_cs = GBS_checksum(seq, 0, ""); char *char_entry = GBS_global_string_copy("%lx", char_cs); char *ali_entry = GBS_global_string_copy("%lx", ali_cs); const char *save_comment = NULp; GBDATA *gb_checksum = GB_entry(gb_species, checksum_field); if (!gb_checksum) { newSpecies++; gb_checksum = GB_create(gb_species, checksum_field, GB_STRING); if (!gb_checksum) error = GB_await_error(); else save_comment = "new"; } else { char *oldValue = GB_read_string(gb_checksum); if (!oldValue) error = GB_await_error(); else { char *comma = strchr(oldValue, ','); if (!comma) { error = GBS_global_string("Invalid value '%s' in field '%s'", oldValue, checksum_field); } else { comma[0] = 0; if (strcmp(char_entry, oldValue) == 0) { // seq checksum is equal if (strcmp(ali_entry, comma+1) == 0) { // ali checksum is equal unchanged++; } else { // only alignment checksum changed ali_changed++; save_comment = "alignment changed"; } } else { seq_changed++; save_comment = "sequence changed"; } } free(oldValue); } } if (save_comment) { error = GB_write_string(gb_checksum, GBS_global_string("%s,%s", char_entry, ali_entry)); if (!error) error = writeHistory(gb_species, stamp, GBS_global_string("%s %s", ali, save_comment)); } if (error) { error = GBS_global_string("%s (%s)", error, GBT_get_name_or_description(gb_species)); } free(ali_entry); free(char_entry); } progress.inc_and_check_user_abort(error); } if (error) aw_message(error); else { struct ReportLine { string tag; size_t amount; ReportLine(string tag_, size_t amount_) : tag(tag_), amount(amount_) { } }; list reports; if (newSpecies) reports.push_back(ReportLine("previously untracked", newSpecies)); if (unchanged) reports.push_back(ReportLine("unchanged", unchanged)); if (ali_changed) reports.push_back(ReportLine("only alignment changed", ali_changed)); if (seq_changed) reports.push_back(ReportLine("sequence changed", seq_changed)); if (!reports.empty()) { size_t tagMaxLen = 0; size_t amountMax = 0; for (list::const_iterator r = reports.begin(); r != reports.end(); ++r) { tagMaxLen = std::max(tagMaxLen, r->tag.length()); amountMax = std::max(amountMax, r->amount); } size_t amountMaxLen = std::to_string(amountMax).length(); GBS_strstruct msg; for (list::const_iterator r = reports.begin(); r != reports.end(); ++r) { msg.catPadded(GBS_global_string("%s:", r->tag.c_str()), tagMaxLen+2); msg.nprintf(amountMaxLen, "%*zu", int(amountMaxLen), r->amount); msg.cat(" species\n"); } msg.cut_tail(1); // remove final LF aw_message(msg.get_data()); } } free(stamp); free(checksum_field); free(ali); } void NT_create_trackAliChanges_Awars(AW_root *root, AW_default properties) { root->awar_string(AWAR_TRACK_ALI, "???", GLOBAL.gb_main); root->awar_string(AWAR_TRACK_ID, GB_getenvUSER(), properties); } AW_window *NT_create_trackAliChanges_window(AW_root *root) { AW_window_simple *aws = new AW_window_simple; aws->init(root, "TRACK_ALI_CHANGES", "Track alignment changes"); aws->load_xfig("trackali.fig"); aws->at("close"); aws->callback(AW_POPDOWN); aws->create_button("CLOSE", "CLOSE", "C"); aws->at("help"); aws->callback(makeHelpCallback("track_ali_changes.hlp")); aws->create_button("HELP", "HELP", "H"); aws->at("id"); aws->create_input_field(AWAR_TRACK_ID); aws->at("ali_sel"); awt_create_ALI_selection_list(GLOBAL.gb_main, aws, AWAR_TRACK_ALI, "*="); aws->at("go"); aws->callback(trackAlignmentChanges); aws->create_autosize_button("TRACK", "Track changes", "T"); return aws; }