ARB
Classes | Functions | Variables
adali.cxx File Reference
#include <arbdbt.h>
#include <adGene.h>
#include "gb_local.h"
#include <arb_strarray.h>
#include <arb_str.h>
Include dependency graph for adali.cxx:

Go to the source code of this file.

Classes

struct  gene_part_pos
 

Functions

static void check_for_species_without_data (const char *species_name, long value, void *counterPtr)
 
GBDATAGBT_get_presets (GBDATA *gb_main)
 
int GBT_count_alignments (GBDATA *gb_main)
 
static GB_ERROR GBT_check_alignment (GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash)
 
GB_ERROR GBT_check_data (GBDATA *Main, const char *alignment_name)
 
void GBT_get_alignment_names (ConstStrArray &names, GBDATA *gbd)
 
static chargbt_nonexisting_alignment (GBDATA *gbMain)
 
GB_ERROR GBT_check_alignment_name (const char *alignment_name)
 
static GB_ERROR create_ali_strEntry (GBDATA *gb_ali, const char *field, const char *strval, long write_protection)
 
static GB_ERROR create_ali_intEntry (GBDATA *gb_ali, const char *field, int intval, long write_protection)
 
GBDATAGBT_create_alignment (GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type)
 
static GB_ERROR gbt_rename_alignment_of_item (GBDATA *gb_item_container, const char *item_name, const char *item_entry_name, const char *source, const char *dest, int copy, int dele)
 
GB_ERROR GBT_rename_alignment (GBDATA *gbMain, const char *source, const char *dest, int copy, int dele)
 
NOT4PERL GBDATAGBT_add_data (GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)
 
NOT4PERL GBDATAGBT_create_sequence_data (GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write)
 
GBDATAGBT_gen_accession_number (GBDATA *gb_species, const char *ali_name)
 
int GBT_is_partial (GBDATA *gb_species, int default_value, bool define_if_undef)
 
GBDATAGBT_find_sequence (GBDATA *gb_species, const char *aliname)
 
charGBT_get_default_alignment (GBDATA *gb_main)
 
GB_ERROR GBT_set_default_alignment (GBDATA *gb_main, const char *alignment_name)
 
GBDATAGBT_get_alignment (GBDATA *gb_main, const char *aliname)
 
long GBT_get_alignment_len (GBDATA *gb_main, const char *aliname)
 
GB_ERROR GBT_set_alignment_len (GBDATA *gb_main, const char *aliname, long new_len)
 
charGBT_get_alignment_type_string (GBDATA *gb_main, const char *aliname)
 
GB_alignment_type GBT_get_alignment_type (GBDATA *gb_main, const char *aliname)
 
bool GBT_is_alignment_protein (GBDATA *gb_main, const char *alignment_name)
 
static const chargb_cache_genome (GBDATA *gb_genome)
 
static void init_gpp (int parts)
 
static void getPartPositions (const GEN_position *pos, int part, size_t *startPos, size_t *stopPos)
 
NOT4PERL charGBT_read_gene_sequence_and_length (GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length)
 
charGBT_read_gene_sequence (GBDATA *gb_gene, bool use_revComplement, char partSeparator)
 

Variables

static gene_part_posgpp = NULp
 

Function Documentation

static void check_for_species_without_data ( const char species_name,
long  value,
void *  counterPtr 
)
static

Definition at line 19 of file adali.cxx.

References GB_warningf().

Referenced by GBT_check_data().

GBDATA* GBT_get_presets ( GBDATA gb_main)
int GBT_count_alignments ( GBDATA gb_main)

Definition at line 33 of file adali.cxx.

References GB_entry(), GB_nextEntry(), and GBT_get_presets().

Referenced by NT_format_all_alignments().

static GB_ERROR GBT_check_alignment ( GBDATA gb_main,
GBDATA preset_alignment,
GB_HASH species_name_hash 
)
static
GB_ERROR GBT_check_data ( GBDATA Main,
const char alignment_name 
)
void GBT_get_alignment_names ( ConstStrArray names,
GBDATA gbd 
)
static char* gbt_nonexisting_alignment ( GBDATA gbMain)
static

Definition at line 330 of file adali.cxx.

References GBS_global_string_copy(), GBT_get_alignment(), and NULp.

Referenced by GBT_rename_alignment().

GB_ERROR GBT_check_alignment_name ( const char alignment_name)
static GB_ERROR create_ali_strEntry ( GBDATA gb_ali,
const char field,
const char strval,
long  write_protection 
)
static
static GB_ERROR create_ali_intEntry ( GBDATA gb_ali,
const char field,
int  intval,
long  write_protection 
)
static
GBDATA* GBT_create_alignment ( GBDATA gbd,
const char name,
long  len,
long  aligned,
long  security,
const char type 
)
static GB_ERROR gbt_rename_alignment_of_item ( GBDATA gb_item_container,
const char item_name,
const char item_entry_name,
const char source,
const char dest,
int  copy,
int  dele 
)
static
GB_ERROR GBT_rename_alignment ( GBDATA gbMain,
const char source,
const char dest,
int  copy,
int  dele 
)
NOT4PERL GBDATA* GBT_add_data ( GBDATA species,
const char ali_name,
const char key,
GB_TYPES  type 
)
NOT4PERL GBDATA* GBT_create_sequence_data ( GBDATA species,
const char ali_name,
const char key,
GB_TYPES  type,
int  security_write 
)

Definition at line 605 of file adali.cxx.

References error(), GB_export_error(), GB_write_security_write(), GBT_add_data(), and NULp.

Referenced by ArbImporter::read_data().

GBDATA* GBT_gen_accession_number ( GBDATA gb_species,
const char ali_name 
)
int GBT_is_partial ( GBDATA gb_species,
int  default_value,
bool  define_if_undef 
)
GBDATA* GBT_find_sequence ( GBDATA gb_species,
const char aliname 
)
char* GBT_get_default_alignment ( GBDATA gb_main)

Definition at line 675 of file adali.cxx.

References gb_assert, GB_DEFAULT_ALIGNMENT, GB_have_error(), and GBT_read_string().

Referenced by AP_calc_pos_var_pars(), AP_create_consensus_var(), ARB_main(), AWTC_pars_names(), AWTC_recreate_name(), build_reverse_complement(), calculateEndPosition(), CON_calc_max_freq_cb(), create_new_species(), createDataFromConsensus(), DI_create_matrix_variables(), ED4_get_marked_from_menu(), ED4_getSaiColorString(), ED4_propertyName(), edit_SAI_description(), export_seq_data(), export_sequence_data::export_sequence_data(), FastAligner_start(), Structure3D::FindTypeOfRNA(), FINAL_TYPE< SEQTYPE >::finish(), gbl_ali_name(), gbl_read_seq_sai_or_species(), gbl_sequence(), gbl_sequence_type(), gde_filter_weights(), getArbFilter(), BI_helix::init(), BI_ecoli_ref::init(), ED4_root::init_alignment(), main(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_gene_species_using_current_alignment(), mark_nontree_cb(), mark_tree_cb(), modify_target_string(), NA_Alignment::NA_Alignment(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_createConcatenationAwars(), NT_import_sequences(), NT_mark_all_cb(), ALI_ARBDB::open(), pars_create_all_awars(), pd_export_pt_server(), pd_get_the_names(), PH_create_filter_variables(), predef_prg(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), pt_init_main_struct(), PT_prepare_data(), PV_WriteTranslatedSequenceToDB(), resolve_IUPAC_target_string(), Aligner::run(), SEC_db_interface::SEC_db_interface(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), StaticData::track_ali(), track_ali_change_cb(), TranslateGeneToAminoAcidSequence(), and translateSAItoColors().

GB_ERROR GBT_set_default_alignment ( GBDATA gb_main,
const char alignment_name 
)

Definition at line 680 of file adali.cxx.

References GB_DEFAULT_ALIGNMENT, and GBT_write_string().

Referenced by ARB_main().

GBDATA* GBT_get_alignment ( GBDATA gb_main,
const char aliname 
)
long GBT_get_alignment_len ( GBDATA gb_main,
const char aliname 
)
GB_ERROR GBT_set_alignment_len ( GBDATA gb_main,
const char aliname,
long  new_len 
)
char* GBT_get_alignment_type_string ( GBDATA gb_main,
const char aliname 
)
Returns
type-string of alignment 'aliname' or NULp if alignment not found (error exported in that case)

Definition at line 727 of file adali.cxx.

References gb_assert, GBT_get_alignment(), GBT_read_string(), NULp, and result.

Referenced by ED4_propertyName(), gbl_sequence_type(), GBT_get_alignment_type(), MG_copy_and_check_alignments(), MG_equal_alignments(), NT_createConcatenationAwars(), and NT_import_sequences().

GB_alignment_type GBT_get_alignment_type ( GBDATA gb_main,
const char aliname 
)
bool GBT_is_alignment_protein ( GBDATA gb_main,
const char alignment_name 
)
static const char* gb_cache_genome ( GBDATA gb_genome)
static

Definition at line 764 of file adali.cxx.

References GB_read_string(), and NULp.

Referenced by GBT_read_gene_sequence_and_length().

static void init_gpp ( int  parts)
static
static void getPartPositions ( const GEN_position pos,
int  part,
size_t *  startPos,
size_t *  stopPos 
)
static
NOT4PERL char* GBT_read_gene_sequence_and_length ( GBDATA gb_gene,
bool  use_revComplement,
char  partSeparator,
size_t *  gene_length 
)
char* GBT_read_gene_sequence ( GBDATA gb_gene,
bool  use_revComplement,
char  partSeparator 
)

Variable Documentation

gene_part_pos* gpp = NULp
static

Definition at line 784 of file adali.cxx.