buff_size | MAl_Readonly | [protected] |
buffID_to_dbID | MAl_Readonly | [protected] |
buffID_to_ID | MAl_Readonly | [protected] |
commit_feat_to_db(size_t buffID, const string &feat_data_name) | MAl | [private] |
commit_seq_to_db(size_t buffID) | MAl | [private] |
create_seq(size_t length) | MAl | |
DNPs | MAl_Readonly | [protected] |
doc | MAl_Readonly | [protected] |
flush_buffer(size_t buffID) | MAl | [private, virtual] |
get_base(size_t ID, size_t index) | MAl_Readonly | |
get_base_global(size_t ID, size_t index) | MAl_Readonly | |
get_beginGood(size_t ID) | MAl_Readonly | |
get_beginGood_global(size_t ID) | MAl_Readonly | |
get_buffID(size_t ID) | MAl_Readonly | [protected] |
get_DNP_ID(size_t ID, size_t index) | MAl_Readonly | |
get_DNP_ID_global(size_t ID, size_t index) | MAl_Readonly | |
get_DNP_type(size_t ID, size_t index) | MAl_Readonly | |
get_DNP_type_global(size_t ID, size_t index) | MAl_Readonly | |
get_endGood(size_t ID) | MAl_Readonly | |
get_endGood_global(size_t ID) | MAl_Readonly | |
get_header(size_t ID) | MAl_Readonly | |
get_len(size_t ID) | MAl_Readonly | |
get_name(size_t ID) | MAl_Readonly | |
get_num_seq() | MAl_Readonly | |
get_qual(size_t ID, size_t index) | MAl_Readonly | |
get_qual_global(size_t ID, size_t index) | MAl_Readonly | |
get_seq(size_t ID) | MAl_Readonly | |
get_seq_begin(size_t ID) | MAl_Readonly | |
get_seq_begin_global(size_t ID) | MAl_Readonly | |
get_seq_end(size_t ID) | MAl_Readonly | |
get_seq_end_global(size_t ID) | MAl_Readonly | |
get_seq_row(size_t ID) | MAl_Readonly | |
get_strand(size_t ID) | MAl_Readonly | |
headers | MAl_Readonly | [protected] |
ID_to_buffID | MAl_Readonly | [protected] |
ID_to_dbID | MAl_Readonly | [protected] |
insert_gap(size_t ID, size_t index) | MAl | |
insert_gap_global(size_t ID, size_t index) | MAl | |
is_DNP(size_t ID, size_t index) | MAl_Readonly | |
is_DNP_global(size_t ID, size_t index) | MAl_Readonly | |
last_gap_vec | MAl | [private] |
MAl(size_t bufsize, std::set< db_recno_t > &recnolist, TrapperDoc *pdoc) | MAl | |
MAl_Readonly(size_t bufsize, std::set< db_recno_t > &recnolist, TrapperDoc *pdoc) | MAl_Readonly | |
mate_lengths | MAl_Readonly | [protected] |
mates | MAl_Readonly | [protected] |
names | MAl_Readonly | [protected] |
next_buffID() | MAl_Readonly | [protected] |
num_seq | MAl_Readonly | [protected] |
print_info(size_t ID) | MAl_Readonly | [inline] |
put_in_db | MAl_Readonly | [protected] |
quals | MAl_Readonly | [protected] |
read_feat_from_db(db_recno_t recno, size_t buffID, const string &data_type_name) | MAl_Readonly | [protected] |
read_from_db(size_t buffID, size_t ID) | MAl_Readonly | [protected] |
read_seq_from_db(db_recno_t recno, size_t buffID) | MAl_Readonly | [protected] |
remove_gap(size_t ID, size_t index) | MAl | |
remove_gap_global(size_t ID, size_t index) | MAl | |
select_read(size_t ID, bool status) | MAl_Readonly | |
selectedReads | MAl_Readonly | [protected] |
seq_begin_global | MAl_Readonly | [protected] |
seq_beginGood | MAl_Readonly | [protected] |
seq_end_global | MAl_Readonly | [protected] |
seq_endGood | MAl_Readonly | [protected] |
seq_rows | MAl_Readonly | [protected] |
seqs | MAl_Readonly | [protected] |
set_base(size_t ID, size_t index, base_t base) | MAl | |
set_base_global(size_t ID, size_t index, base_t base) | MAl | |
set_beginGood(size_t ID, size_t index) | MAl | |
set_beginGood_global(size_t ID, size_t index) | MAl | |
set_DNP(size_t ID, size_t index, bool status) | MAl | |
set_DNP_global(size_t ID, size_t index, bool status) | MAl | |
set_DNP_ID(size_t ID, size_t index, int dnpID) | MAl | |
set_DNP_ID_global(size_t ID, size_t index, int dnpID) | MAl | |
set_DNP_type(size_t ID, size_t index, int type) | MAl | |
set_DNP_type_global(size_t ID, size_t index, int type) | MAl | |
set_endGood(size_t ID, size_t index) | MAl | |
set_endGood_global(size_t ID, size_t index) | MAl | |
set_qual(size_t ID, size_t index, qual_t qual) | MAl | |
set_qual_global(size_t ID, size_t index, qual_t qual) | MAl | |
set_seq_begin_global(size_t ID, size_t index) | MAl | |
set_seq_end(size_t ID, size_t index) | MAl | |
set_seq_end_global(size_t ID, size_t index) | MAl | |
set_seq_row(size_t ID, size_t row) | MAl | |
strands | MAl_Readonly | [protected] |
~MAl() | MAl | |
~MAl_Readonly() | MAl_Readonly | [virtual] |