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MAl Member List

This is the complete list of members for MAl, including all inherited members.

buff_sizeMAl_Readonly [protected]
buffID_to_dbIDMAl_Readonly [protected]
buffID_to_IDMAl_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
DNPsMAl_Readonly [protected]
docMAl_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
headersMAl_Readonly [protected]
ID_to_buffIDMAl_Readonly [protected]
ID_to_dbIDMAl_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_vecMAl [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_lengthsMAl_Readonly [protected]
matesMAl_Readonly [protected]
namesMAl_Readonly [protected]
next_buffID()MAl_Readonly [protected]
num_seqMAl_Readonly [protected]
print_info(size_t ID)MAl_Readonly [inline]
put_in_dbMAl_Readonly [protected]
qualsMAl_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
selectedReadsMAl_Readonly [protected]
seq_begin_globalMAl_Readonly [protected]
seq_beginGoodMAl_Readonly [protected]
seq_end_globalMAl_Readonly [protected]
seq_endGoodMAl_Readonly [protected]
seq_rowsMAl_Readonly [protected]
seqsMAl_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
strandsMAl_Readonly [protected]
~MAl()MAl
~MAl_Readonly()MAl_Readonly [virtual]


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