ARB
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Go to the source code of this file.
Classes | |
class | startsWithBlanks |
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#define | NOPERIOD 0 |
#define | PERIOD 1 |
Functions | |
void | genbank_key_word (const char *line, int index, char *key) |
static int | genbank_check_blanks (const char *line, int numb) |
static void | genbank_continue_line (char *&Str, int numb, Reader &reader) |
static void | genbank_one_entry_in (char *&datastring, Reader &reader) |
static void | genbank_one_comment_entry (char *&datastring, int start_index, Reader &reader) |
static void | genbank_source (GenBank &gbk, Reader &reader) |
static void | genbank_skip_unidentified (Reader &reader, int blank_num) |
static void | genbank_reference (GenBank &gbk, Reader &reader) |
static void | genbank_comments (GenBank &gbk, Reader &reader) |
bool | valid_acc_char (char ch) |
static void | genbank_verify_accession (GenBank &gbk) |
static void | genbank_verify_keywords (GenBank &gbk) |
static void | genbank_origin (Seq &seq, Reader &reader) |
static void | genbank_print_lines (Writer &write, const char *key, const char *content, const WrapMode &wrapMode) |
static void | genbank_out_one_entry (Writer &write, const char *key, const char *content, const WrapMode &wrapMode, int period) |
static void | genbank_out_one_reference (Writer &write, const GenbankRef &gbk_ref, int gbk_ref_num) |
static void | genbank_print_comment_if_content (Writer &write, const char *key, const char *content) |
static void | genbank_out_origin (const Seq &seq, Writer &write) |
void | genbank_print_completeness (Writer &write, char compX, char X) |
void | genbank_out_header (const GenBank &gbk, const Seq &seq, Writer &write) |
void | genbank_out_base_count (const Seq &seq, Writer &write) |
void | genbank_out (const GenBank &gbk, const Seq &seq, Writer &write) |
#define NOPERIOD 0 |
Definition at line 6 of file genbank.cxx.
Referenced by genbank_out_header(), and genbank_out_one_reference().
#define PERIOD 1 |
Definition at line 7 of file genbank.cxx.
Referenced by genbank_out_header().
Definition at line 9 of file genbank.cxx.
References ca_assert, GBINDENT, and parse_key_word().
Referenced by genbank_reference(), genbank_source(), GenbankReader::get_key_word(), gtom(), and GenbankParser::parse_section().
Definition at line 17 of file genbank.cxx.
Referenced by genbank_comments(), genbank_continue_line(), and startsWithBlanks::operator()().
Definition at line 33 of file genbank.cxx.
References genbank_check_blanks(), Reader::line(), LINESIZE, skip_eolnl_and_append_spaced(), and Skip_white_space().
Referenced by genbank_one_comment_entry(), genbank_one_entry_in(), and genbank_source().
Definition at line 55 of file genbank.cxx.
References GBINDENT, genbank_continue_line(), Reader::line(), and Skip_white_space().
Referenced by genbank_reference(), and genbank_source().
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Definition at line 60 of file genbank.cxx.
References genbank_continue_line(), Reader::line(), and Skip_white_space().
Referenced by genbank_comments().
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Definition at line 66 of file genbank.cxx.
References GBINDENT, genbank_continue_line(), genbank_key_word(), genbank_one_entry_in(), Reader::line(), NULp, Skip_white_space(), str_equal(), and TOKENSIZE.
Definition at line 89 of file genbank.cxx.
References Reader::skipOverLinesThat().
Referenced by genbank_reference().
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Definition at line 96 of file genbank.cxx.
References ASSERT_RESULT, GenbankRef::author, GBINDENT, genbank_key_word(), genbank_one_entry_in(), genbank_skip_unidentified(), has_content(), GenbankRef::journal, Reader::line(), GenbankRef::standard, str_equal(), terminate_with(), GenbankRef::title, TOKENSIZE, and warningf().
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Definition at line 138 of file genbank.cxx.
References Append(), ARB_strdup(), ca_assert, comment_subkey(), GBINDENT, genbank_check_blanks(), genbank_one_comment_entry(), Reader::line(), line, RDP_comments::others, parse_RDP_comment(), Reader::set_line(), Skip_white_space(), str0len(), and TOKENSIZE.
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Definition at line 180 of file genbank.cxx.
Referenced by genbank_verify_accession().
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Definition at line 182 of file genbank.cxx.
References Append(), ARB_strdup(), copy(), NULp, skip_eolnl_and_append(), str_equal(), strf(), throw_errorf(), and valid_acc_char().
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Definition at line 220 of file genbank.cxx.
References Warnings::shown(), str0len(), terminate_with(), and warning().
Definition at line 245 of file genbank.cxx.
References Seq::add(), ca_assert, has_content(), Seq::is_empty(), is_sequence_terminator(), and Reader::line().
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Definition at line 306 of file genbank.cxx.
References ca_assert, GBINDENT, GBMAXLINE, and WrapMode::print().
Referenced by genbank_out_one_entry().
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Definition at line 315 of file genbank.cxx.
References genbank_print_lines(), and has_content().
Referenced by genbank_out_header(), and genbank_out_one_reference().
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Definition at line 327 of file genbank.cxx.
References GenbankRef::author, genbank_out_one_entry(), has_content(), GenbankRef::journal, NOPERIOD, GenbankRef::ref, GenbankRef::standard, GenbankRef::title, and TOKENSIZE.
Referenced by genbank_out_header().
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Definition at line 347 of file genbank.cxx.
References GBINDENT, GBMAXLINE, has_content(), LINESIZE, WrapMode::print(), RDP_CONTINUED_INDENT, and RDP_SUBKEY_INDENT.
Referenced by genbank_out_header().
Definition at line 357 of file genbank.cxx.
References GENBANK, and Seq::out().
Referenced by genbank_out().
Definition at line 362 of file genbank.cxx.
References ca_assert, and Writer::outf().
Referenced by genbank_out_header().
Definition at line 368 of file genbank.cxx.
References OrgInfo::commname, SeqInfo::comp3, SeqInfo::comp5, OrgInfo::cultcoll, OrgInfo::exists(), SeqInfo::exists(), RDP_comments::exists(), OrgInfo::formname, GBINDENT, SeqInfo::gbkentry, genbank_out_one_entry(), genbank_out_one_reference(), genbank_print_comment_if_content(), genbank_print_completeness(), Seq::get_len(), OrgInfo::hostorg, length, SeqInfo::methods, OrgInfo::nickname, NOPERIOD, RDP_comments::orginf, RDP_comments::others, Writer::out(), Writer::outf(), PERIOD, SeqInfo::RDPid, Writer::repeated(), RDP_comments::seqinf, OrgInfo::source, and str0len().
Referenced by genbank_out(), and genbank_to_gcg().
Definition at line 440 of file genbank.cxx.
References BaseCounts::a, BaseCounts::c, Seq::count(), BaseCounts::g, BaseCounts::other, Writer::out(), Writer::outf(), and BaseCounts::t.
Referenced by genbank_out(), and genbank_to_gcg().
Definition at line 450 of file genbank.cxx.
References genbank_out_base_count(), genbank_out_header(), genbank_out_origin(), and Writer::out().
Referenced by write_to_genbank().