ARB
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#include "GDE_proto.h"
#include <aw_msg.hxx>
#include <AW_rename.hxx>
#include <AP_filter.hxx>
#include <aw_awar_defs.hxx>
#include <arb_progress.h>
#include <arb_global_defs.h>
#include <algorithm>
Go to the source code of this file.
Macros | |
#define | GET_FIELD_CONTENT(fieldname, buffer, bufsize) |
Typedefs | |
typedef unsigned int | UINT |
Functions | |
int | Arbdb_get_curelem (NA_Alignment &dataset) |
static void | set_constant_fields (NA_Sequence *this_elem) |
static void | AppendNA_and_free (NA_Sequence *this_elem, uchar *&sequfilt) |
static __ATTR__USERESULT int | InsertDatainGDE (NA_Alignment &dataset, GBDATA **the_species, unsigned char **the_names, unsigned char **the_sequences, unsigned long numberspecies, unsigned long maxalignlen, const AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo) |
int | ReadArbdb2 (NA_Alignment &dataset, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo) |
int | ReadArbdb (NA_Alignment &dataset, bool marked, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon, TypeInfo typeinfo) |
int | getelem (NA_Sequence *a, int b) |
void | putelem (NA_Sequence *a, int b, NA_Base c) |
#define GET_FIELD_CONTENT | ( | fieldname, | |
buffer, | |||
bufsize | |||
) |
Referenced by InsertDatainGDE().
Definition at line 16 of file GDE_arbdb_io.cxx.
int Arbdb_get_curelem | ( | NA_Alignment & | dataset | ) |
Definition at line 18 of file GDE_arbdb_io.cxx.
References ARB_alloc(), ARB_realloc(), NA_Alignment::element, NA_Alignment::maxnumelements, and NA_Alignment::numelements.
Referenced by InsertDatainGDE(), ReadGen(), and ReadNA_Flat().
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Definition at line 31 of file GDE_arbdb_io.cxx.
References ARB_strdup(), NA_Sequence::attr, NA_Sequence::col_lut, NA_Sequence::comments, NA_Sequence::comments_len, NA_Sequence::comments_maxlen, Default_PROColor_LKUP, DEFAULT_X_ATTR, NULp, NA_Sequence::rmatrix, and NA_Sequence::tmatrix.
Referenced by InsertDatainGDE().
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Definition at line 40 of file GDE_arbdb_io.cxx.
References AppendNA().
Referenced by InsertDatainGDE().
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Definition at line 45 of file GDE_arbdb_io.cxx.
References NA_Alignment::alignment_name, AppendNA_and_free(), ARB_alloc(), ARB_calloc(), Arbdb_get_curelem(), NA_Sequence::authority, aw_message(), AWAR_GDE_EXPORT_FILTER, AWTC_name_quality(), BASIC_TYPEINFO, COMPRESS_ALL, COMPRESS_NONINFO_COLUMNS, COMPRESS_VERTICAL_GAPS, db_access, DETAILED_TYPEINFO, DNA, NA_Alignment::element, NA_Sequence::elementtype, error(), fputs(), GB_AT_AA, GB_AT_DNA, GB_AT_RNA, GB_AT_UNKNOWN, gde_database_access::gb_main, NA_Alignment::gb_main, NA_Sequence::gb_species, GBS_global_string(), GBT_get_alignment_type(), GBT_write_string(), gde_assert, GET_FIELD_CONTENT, AP_filter::get_filtered_length(), AP_filter::get_length(), AP_filter::get_simplify_table(), NA_Sequence::id, arb_progress::inc_and_check_user_abort(), InitNASeq(), AP_filter::is_invalid(), GAP::is_std_gap(), max, NA_Alignment::maxlen, NULp, NA_Alignment::numelements, NA_Sequence::offset, PROTEIN, RNA, seq, NA_Sequence::seq_name, NA_Sequence::seqlen, set_constant_fields(), NA_Sequence::short_name, SIZE_AUTHORITY, SIZE_ID, SIZE_SEQ_NAME, SIZE_SHORT_NAME, strcpy_truncate(), ta, TEXT, AP_filter::to_string(), UNKNOWN_TYPEINFO, and AP_filter::use_position().
Referenced by ReadArbdb(), and ReadArbdb2().
int ReadArbdb2 | ( | NA_Alignment & | dataset, |
AP_filter * | filter, | ||
GapCompression | compress, | ||
bool | cutoff_stop_codon, | ||
TypeInfo | typeinfo | ||
) |
Definition at line 325 of file GDE_arbdb_io.cxx.
References aw_message(), db_access, error(), gde_assert, gde_database_access::get_sequences, InsertDatainGDE(), and NULp.
Referenced by GDE_startaction_cb().
int ReadArbdb | ( | NA_Alignment & | dataset, |
bool | marked, | ||
AP_filter * | filter, | ||
GapCompression | compress, | ||
bool | cutoff_stop_codon, | ||
TypeInfo | typeinfo | ||
) |
Definition at line 354 of file GDE_arbdb_io.cxx.
References NA_Alignment::alignment_name, ARB_alloc(), ARB_calloc(), aw_message(), db_access, gde_database_access::gb_main, NA_Alignment::gb_main, GB_read_char_pntr(), gb_species_data, GBS_global_string(), GBT_find_sequence(), GBT_first_marked_species_rel_species_data(), GBT_first_species_rel_species_data(), GBT_get_alignment_len(), GBT_get_species_data(), GBT_next_marked_species(), GBT_next_species(), gde_assert, InsertDatainGDE(), NULp, and strcpy_truncate().
Referenced by GDE_startaction_cb().
int getelem | ( | NA_Sequence * | a, |
int | b | ||
) |
Definition at line 419 of file GDE_arbdb_io.cxx.
References DNA, NA_Sequence::elementtype, MASK, offset, NA_Sequence::offset, PROTEIN, RNA, NA_Sequence::seqlen, NA_Sequence::sequence, and TEXT.
Referenced by WriteGDE(), WriteGen(), and WriteNA_Flat().
void putelem | ( | NA_Sequence * | a, |
int | b, | ||
NA_Base | c | ||
) |
Definition at line 436 of file GDE_arbdb_io.cxx.
References DNA, NA_Sequence::elementtype, MASK, NA_Sequence::offset, PROTEIN, RNA, NA_Sequence::seqlen, NA_Sequence::seqmaxlen, NA_Sequence::sequence, TEXT, and Warning().
Referenced by AppendNA().