| buff_size | MAl_Readonly | [protected] |
| buffID_to_dbID | MAl_Readonly | [protected] |
| buffID_to_ID | MAl_Readonly | [protected] |
| comp_base(const char &base) | MAl_Readonly | [protected] |
| DNPs | MAl_Readonly | [protected] |
| doc | MAl_Readonly | [protected] |
| flush_buffer(size_t buffID) | MAl_Readonly | [protected, 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_expression(size_t ID, size_t expression_index) | MAl_Readonly | |
| get_header(size_t ID) | MAl_Readonly | |
| get_len(size_t ID) | MAl_Readonly | |
| get_max_expression(size_t ID) | MAl_Readonly | |
| get_name(size_t ID) | MAl_Readonly | |
| get_num_expression_points(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] |
| is_DNP(size_t ID, size_t index) | MAl_Readonly | |
| is_DNP_global(size_t ID, size_t index) | MAl_Readonly | |
| MAl_Readonly(size_t bufsize, std::set< db_recno_t > &recnolist, TrapperDoc *pdoc) | MAl_Readonly | |
| MAlWrapper class | MAl_Readonly | [friend] |
| 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] |
| 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] |
| strands | MAl_Readonly | [protected] |
| tags | MAl_Readonly | [protected] |
| time_course | MAl_Readonly | [protected] |
| ~MAl_Readonly() | MAl_Readonly | [virtual] |
