static int quoted_word(GtStr *word, GtIO *bed_file, GtError *err) { bool break_while = false; int had_err; gt_error_check(err); gt_str_reset(word); had_err = gt_io_expect(bed_file, QUOTE_CHAR, err); while (!had_err) { switch (gt_io_peek(bed_file)) { case QUOTE_CHAR: case GT_CARRIAGE_RETURN: case GT_END_OF_LINE: case GT_END_OF_FILE: break_while = true; break; default: gt_str_append_char(word, gt_io_next(bed_file)); } if (break_while) break; } if (!had_err) had_err = gt_io_expect(bed_file, QUOTE_CHAR, err); return had_err; }
static int tag_line(GtIO *obo_file, GtStr *tag, GtStr *value, GtError *err) { int had_err; gt_error_check(err); gt_assert(obo_file && tag && value); do { had_err = proc_any_char(obo_file, tag, false, err); } while (!had_err && any_char(obo_file, false)); if (!had_err) had_err = gt_io_expect(obo_file, OBO_SEPARATOR_CHAR, err); while (!had_err && gt_io_peek(obo_file) == OBO_BLANK_CHAR) gt_io_next(obo_file); if (!had_err) { do { had_err = proc_any_char(obo_file, value, true, err); } while (!had_err && any_char(obo_file, true)); } if (!had_err) { if (gt_io_peek(obo_file) == OBO_COMMENT_CHAR) had_err = comment_line(obo_file, err); else had_err = gt_io_expect(obo_file, GT_END_OF_LINE, err); } return had_err; }
static int gt_xrf_abbr_parse_tree_blank_line(GtIO *xrf_abbr_file, GtError *err) { int had_err; gt_error_check(err); gt_log_log("blank"); had_err = gt_io_expect(xrf_abbr_file, XRF_BLANK_CHAR, err); while (!had_err) { char cc = gt_io_peek(xrf_abbr_file); if (cc == XRF_COMMENT_CHAR) return gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err); else if (cc == GT_CARRIAGE_RETURN) { gt_io_next(xrf_abbr_file); if (gt_io_peek(xrf_abbr_file) == GT_END_OF_LINE) gt_io_next(xrf_abbr_file); break; } else if ((cc == GT_END_OF_LINE) || (cc == GT_END_OF_FILE)) { gt_io_next(xrf_abbr_file); break; } else had_err = gt_io_expect(xrf_abbr_file, XRF_BLANK_CHAR, err); } return had_err; }
static int parse_bed_file(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err) { int had_err = 0; gt_error_check(err); gt_assert(bed_file); while (!had_err && gt_io_has_char(bed_file)) { switch (gt_io_peek(bed_file)) { case BLANK_CHAR: had_err = bed_parser_blank_line(bed_file, err); break; case COMMENT_CHAR: had_err = bed_parser_comment_line(bed_file, err); break; case GT_CARRIAGE_RETURN: gt_io_next(bed_file); if (gt_io_peek(bed_file) == GT_END_OF_LINE) gt_io_next(bed_file); break; case GT_END_OF_LINE: gt_io_next(bed_file); break; default: had_err = bed_line(bed_parser, bed_file, err); } } if (!had_err) had_err = gt_io_expect(bed_file, GT_END_OF_FILE, err); return had_err; }
static int gt_xrf_abbr_parse_tree_comment_line(GtIO *xrf_abbr_file, GtError *err) { int had_err; gt_error_check(err); gt_log_log("comment"); had_err = gt_io_expect(xrf_abbr_file, XRF_COMMENT_CHAR, err); while (!had_err) { switch (gt_io_peek(xrf_abbr_file)) { case GT_CARRIAGE_RETURN: gt_io_next(xrf_abbr_file); if (gt_io_peek(xrf_abbr_file) == GT_END_OF_LINE) gt_io_next(xrf_abbr_file); return had_err; case GT_END_OF_LINE: gt_io_next(xrf_abbr_file); /*@fallthrough@*/ case GT_END_OF_FILE: return had_err; default: gt_io_next(xrf_abbr_file); } } return had_err; }
static int stanza_line(GtIO *obo_file, GtStr *type, GtError *err) { int had_err; gt_error_check(err); gt_assert(obo_file && type); had_err = gt_io_expect(obo_file, OBO_STANZA_OPEN_CHAR, err); if (!had_err) { do { had_err = proc_any_char(obo_file, type, false, err); } while (!had_err && any_char(obo_file, false)); } if (!had_err) had_err = gt_io_expect(obo_file, OBO_STANZA_CLOSE_CHAR, err); if (!had_err) had_err = gt_io_expect(obo_file, GT_END_OF_LINE, err); return had_err; }
static int bed_parser_comment_line(GtIO *bed_file, GtError *err) { int had_err; gt_error_check(err); had_err = gt_io_expect(bed_file, COMMENT_CHAR, err); if (!had_err) rest_line(bed_file); return had_err; }
static int track_rest(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err) { char cc; int had_err = 0; gt_error_check(err); bed_parser->offset = 0; /* reset offset for new track line */ if (bed_separator(bed_file)) /* skip to first attribute=value pair */ had_err = skip_blanks(bed_file, err); while (!had_err && (cc = gt_io_peek(bed_file)) != GT_END_OF_LINE && cc != GT_CARRIAGE_RETURN) { /* parse attribute */ word(bed_parser->word, bed_file); had_err = gt_io_expect(bed_file, PAIR_SEPARATOR, err); /* parse value */ if (!had_err) { if (gt_io_peek(bed_file) == QUOTE_CHAR) had_err = quoted_word(bed_parser->another_word, bed_file, err); else word(bed_parser->another_word, bed_file); } /* process offset if necessary */ if (!had_err && !strcmp(gt_str_get(bed_parser->word), OFFSET_KEYWORD)) { if (gt_parse_word(&bed_parser->offset, gt_str_get(bed_parser->another_word))) { gt_error_set(err, "file \"%s\": line "GT_WU": could not parse offset value " "'%s'", gt_io_get_filename(bed_file), gt_io_get_line_number(bed_file), gt_str_get(bed_parser->another_word)); had_err = -1; } } /* skip blanks up to next attribute or end-of-line */ if (!had_err && bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* the end of the line should now be reached */ if (!had_err) had_err = gt_io_expect(bed_file, GT_END_OF_LINE, err); return had_err; }
static int bed_parser_blank_line(GtIO *bed_file, GtError *err) { int had_err = 0; gt_error_check(err); had_err = gt_io_expect(bed_file, BLANK_CHAR, err); while (!had_err) { char cc = gt_io_peek(bed_file); if (cc == GT_CARRIAGE_RETURN) { gt_io_next(bed_file); if (gt_io_peek(bed_file) == GT_END_OF_LINE) gt_io_next(bed_file); break; } else if ((cc == GT_END_OF_LINE) || (cc == GT_END_OF_FILE)) { gt_io_next(bed_file); break; } else had_err = gt_io_expect(bed_file, BLANK_CHAR, err); } return had_err; }
static int blank_line(GtIO *obo_file, GtError *err) { int had_err; gt_error_check(err); had_err = gt_io_expect(obo_file, OBO_BLANK_CHAR, err); while (!had_err) { char cc = gt_io_peek(obo_file); if (cc == OBO_COMMENT_CHAR) return comment_line(obo_file, err); else if (cc == GT_CARRIAGE_RETURN) { gt_io_next(obo_file); if (gt_io_peek(obo_file) == GT_END_OF_LINE) gt_io_next(obo_file); break; } else if ((cc == GT_END_OF_LINE) || (cc == GT_END_OF_FILE)) { gt_io_next(obo_file); break; } else had_err = gt_io_expect(obo_file, OBO_BLANK_CHAR, err); } return had_err; }
static int gt_xrf_abbr_parse_tree_tag_line(GtIO *xrf_abbr_file, GtStr *tag, GtStr *value, GtError *err) { int had_err = 0; gt_error_check(err); gt_log_log("tag"); gt_assert(xrf_abbr_file && tag && value); do { had_err = gt_xrf_abbr_parse_tree_proc_any_char(xrf_abbr_file, tag, false, err); } while (!had_err && gt_xrf_abbr_parse_tree_any_char(xrf_abbr_file, false)); if (!had_err) had_err = gt_io_expect(xrf_abbr_file, XRF_SEPARATOR_CHAR, err); while (!had_err && gt_io_peek(xrf_abbr_file) == XRF_BLANK_CHAR) gt_io_next(xrf_abbr_file); if (!had_err) { do { had_err = gt_xrf_abbr_parse_tree_proc_any_char(xrf_abbr_file, value, true, err); } while (!had_err && gt_xrf_abbr_parse_tree_any_char(xrf_abbr_file, true)); } if (!had_err) { if (gt_io_peek(xrf_abbr_file) == XRF_COMMENT_CHAR) had_err = gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err); else had_err = gt_io_expect(xrf_abbr_file, GT_END_OF_LINE, err); } if (!had_err && !gt_xrf_abbr_parse_tree_valid_label(gt_str_get(tag))) { gt_warning("file \"%s\": line "GT_WU": unknown label \"%s\"", gt_io_get_filename(xrf_abbr_file), gt_io_get_line_number(xrf_abbr_file), gt_str_get(tag)); } gt_log_log("parsed line %s/%s", gt_str_get(tag), gt_str_get(value)); return had_err; }
static int comment_line(GtIO *obo_file, GtError *err) { int had_err; gt_error_check(err); had_err = gt_io_expect(obo_file, OBO_COMMENT_CHAR, err); while (!had_err) { switch (gt_io_peek(obo_file)) { case GT_CARRIAGE_RETURN: gt_io_next(obo_file); if (gt_io_peek(obo_file) == GT_END_OF_LINE) gt_io_next(obo_file); return had_err; case GT_END_OF_LINE: gt_io_next(obo_file); /*@fallthrough@*/ case GT_END_OF_FILE: return had_err; default: gt_io_next(obo_file); } } return had_err; }
static int parse_obo_file(GtOBOParseTree *obo_parse_tree, GtIO *obo_file, GtError *err) { int had_err = 0; gt_error_check(err); gt_assert(obo_parse_tree && obo_file); while (!had_err && ignored_char(obo_file)) { had_err = ignored_line(obo_file, err); } if (!had_err) had_err = header(obo_parse_tree, obo_file, err); while (!had_err && gt_io_has_char(obo_file)) { switch (gt_io_peek(obo_file)) { case OBO_BLANK_CHAR: had_err = blank_line(obo_file, err); break; case OBO_COMMENT_CHAR: had_err = comment_line(obo_file, err); break; case GT_CARRIAGE_RETURN: gt_io_next(obo_file); if (gt_io_peek(obo_file) == GT_END_OF_LINE) gt_io_next(obo_file); break; case GT_END_OF_LINE: gt_io_next(obo_file); break; default: had_err = stanza(obo_parse_tree, obo_file, err); } } if (!had_err) had_err = gt_io_expect(obo_file, GT_END_OF_FILE, err); if (!had_err) had_err = gt_obo_parse_tree_validate_stanzas(obo_parse_tree, err); return had_err; }
static int parse_xrf_abbr_file(GtXRFAbbrParseTree *xrf_abbr_parse_tree, GtIO *xrf_abbr_file, GtError *err) { int had_err = 0; gt_error_check(err); gt_assert(xrf_abbr_parse_tree && xrf_abbr_file); while (!had_err && gt_xrf_abbr_parse_tree_ignored_char(xrf_abbr_file)) { had_err = gt_xrf_abbr_parse_tree_ignored_line(xrf_abbr_file, err); } while (!had_err && gt_io_has_char(xrf_abbr_file)) { switch (gt_io_peek(xrf_abbr_file)) { case XRF_BLANK_CHAR: had_err = gt_xrf_abbr_parse_tree_blank_line(xrf_abbr_file, err); break; case XRF_COMMENT_CHAR: had_err = gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err); break; case GT_CARRIAGE_RETURN: gt_io_next(xrf_abbr_file); if (gt_io_peek(xrf_abbr_file) == GT_END_OF_LINE) gt_io_next(xrf_abbr_file); break; case GT_END_OF_LINE: gt_io_next(xrf_abbr_file); break; default: had_err = gt_xrf_abbr_parse_tree_entry(xrf_abbr_parse_tree, xrf_abbr_file, err); } } if (!had_err) had_err = gt_io_expect(xrf_abbr_file, GT_END_OF_FILE, err); if (!had_err) had_err = gt_xrf_abbr_parse_tree_validate_entries(xrf_abbr_parse_tree, err); return had_err; }
static int bed_rest(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err) { GtUword block_count = 0; GtGenomeNode *gn = NULL; GtRange range; GtStr *seqid; int had_err; gt_error_check(err); /* column 1.: chrom */ seqid = get_seqid(bed_parser); had_err = skip_blanks(bed_file, err); /* column 2.: chromStart */ if (!had_err) { word(bed_parser->word, bed_file); had_err = skip_blanks(bed_file, err); } /* column 3.: chromEnd */ if (!had_err) { word(bed_parser->another_word, bed_file); had_err = parse_bed_range(&range, bed_parser->word, bed_parser->another_word, bed_parser->offset, bed_file, false, err); } if (!had_err) { /* add region */ gt_region_node_builder_add_region(bed_parser->region_node_builder, gt_str_get(seqid), range); /* create feature */ gn = gt_feature_node_new(seqid, bed_parser->feature_type ? bed_parser->feature_type : BED_FEATURE_TYPE, range.start, range.end, GT_STRAND_BOTH); gt_queue_add(bed_parser->feature_nodes, gn); if (bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* optional column 4.: name */ if (!had_err) { word(bed_parser->word, bed_file); if (gt_str_length(bed_parser->word)) { gt_feature_node_add_attribute((GtFeatureNode*) gn, GT_GFF_NAME, gt_str_get(bed_parser->word)); } if (bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* optional column 5.: score */ if (!had_err) { word(bed_parser->word, bed_file); if (gt_str_length(bed_parser->word)) { bool score_is_defined; float score_value; had_err = gt_parse_score(&score_is_defined, &score_value, gt_str_get(bed_parser->word), gt_io_get_line_number(bed_file), gt_io_get_filename(bed_file), err); if (!had_err && score_is_defined) gt_feature_node_set_score((GtFeatureNode*) gn, score_value); } } if (!had_err && bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); /* optional column 6.: strand */ if (!had_err) { word(bed_parser->word, bed_file); if (gt_str_length(bed_parser->word)) { GtStrand strand; had_err = gt_parse_strand(&strand, gt_str_get(bed_parser->word), gt_io_get_line_number(bed_file), gt_io_get_filename(bed_file), err); if (!had_err) gt_feature_node_set_strand((GtFeatureNode*) gn, strand); } } if (!had_err && bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); /* optional column 7.: thickStart */ if (!had_err) { word(bed_parser->word, bed_file); if (bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* optional column 8.: thickEnd */ if (!had_err) { word(bed_parser->another_word, bed_file); if (gt_str_length(bed_parser->another_word)) { gt_assert(gt_str_length(bed_parser->word)); /* got a thickStart and a thickEnd -> construct corresponding feature */ had_err = parse_bed_range(&range, bed_parser->word, bed_parser->another_word, bed_parser->offset, bed_file, true, err); if (!had_err && range.start <= range.end) construct_thick_feature(bed_parser, (GtFeatureNode*) gn, range); } } if (!had_err && bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); /* optional column 9.: itemRgb */ if (!had_err) { word(bed_parser->word, bed_file); /* we do not use the RGB values */ if (bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* optional column 10.: blockCount */ if (!had_err) { word(bed_parser->word, bed_file); if (gt_str_length(bed_parser->word)) { if (gt_parse_uword(&block_count, gt_str_get(bed_parser->word))) { gt_error_set(err, "file \"%s\": line "GT_WU": could not parse blockCount", gt_io_get_filename(bed_file), gt_io_get_line_number(bed_file)); had_err = -1; } else { /* reset to parse/process blockSizes and blockStarts properly */ gt_str_reset(bed_parser->word); gt_str_reset(bed_parser->another_word); } } } if (!had_err && bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); /* optional column 11.: blockSizes */ if (!had_err) { word(bed_parser->word, bed_file); if (bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* optional column 12.: blockStarts */ if (!had_err) { word(bed_parser->another_word, bed_file); if (bed_separator(bed_file)) had_err = skip_blanks(bed_file, err); } /* process blocks if necessary */ if (!had_err && block_count) { had_err = process_blocks(bed_parser, (GtFeatureNode*) gn, block_count, bed_parser->word, bed_parser->another_word, bed_file, err); } /* the end of the line should now be reached */ if (!had_err) had_err = gt_io_expect(bed_file, GT_END_OF_LINE, err); return had_err; }