ARB
Classes | Enumerations | 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 <arb_global_defs.h>
Include dependency graph for adali.cxx:

Go to the source code of this file.

Classes

struct  gene_part_pos
 

Enumerations

enum  CopyMoveDelMode { COPY, MOVE, DELETE }
 

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 *gb_main, const char *name, long len, long aligned, long security, const char *type, const char *why_created)
 
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, CopyMoveDelMode mode)
 
static GB_ERROR copy_move_del_alignment (GBDATA *gbMain, const char *source, const char *dest, CopyMoveDelMode mode)
 
GB_ERROR GBT_copy_alignment (GBDATA *gbMain, const char *source, const char *dest)
 
GB_ERROR GBT_rename_alignment (GBDATA *gbMain, const char *source, const char *dest)
 
GB_ERROR GBT_delete_alignment (GBDATA *gbMain, const char *source)
 
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)
 
static charget_default_alignment (GBDATA *gb_main, bool use_startup_ali)
 
charGBT_get_default_alignment (GBDATA *gb_main)
 
charGBT_get_startup_alignment (GBDATA *gb_main)
 
GB_ERROR GBT_set_default_alignment (GBDATA *gb_main, const char *alignment_name)
 
GB_ERROR GBT_set_startup_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
 

Enumeration Type Documentation

Enumerator
COPY 
MOVE 
DELETE 

Definition at line 452 of file adali.cxx.

Function Documentation

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

Definition at line 20 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 34 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 GB_clear_error(), GBS_global_string_copy(), GBT_get_alignment(), and NULp.

Referenced by copy_move_del_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 gb_main,
const char name,
long  len,
long  aligned,
long  security,
const char type,
const char why_created 
)
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,
CopyMoveDelMode  mode 
)
static
static GB_ERROR copy_move_del_alignment ( GBDATA gbMain,
const char source,
const char dest,
CopyMoveDelMode  mode 
)
static
GB_ERROR GBT_copy_alignment ( GBDATA gbMain,
const char source,
const char dest 
)

Definition at line 584 of file adali.cxx.

References COPY, and copy_move_del_alignment().

Referenced by copy_rename_handler().

GB_ERROR GBT_rename_alignment ( GBDATA gbMain,
const char source,
const char dest 
)

Definition at line 587 of file adali.cxx.

References copy_move_del_alignment(), and MOVE.

Referenced by copy_rename_handler(), and MG_equal_alignments().

GB_ERROR GBT_delete_alignment ( GBDATA gbMain,
const char source 
)

Definition at line 590 of file adali.cxx.

References copy_move_del_alignment(), DELETE, and NULp.

Referenced by delete_ali_cb(), and split_alignment().

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 
)
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 
)
static char* get_default_alignment ( GBDATA gb_main,
bool  use_startup_ali 
)
static

behavior

See also
GBT_get_default_alignment.
Parameters
use_startup_aliif 'true' -> always return the value seen when first called with 'true' + make calls with 'false' always return an error. The intention is to be able to force that an applications sticks with the alignment found at startup and ignores if alignment is changed in arb_ntree.

Definition at line 713 of file adali.cxx.

References ARB_strBeginsWith(), ARB_strdup(), gb_assert, GB_DEFAULT_ALIGNMENT, GB_export_error(), GB_export_errorf(), GB_have_error(), GBT_read_string(), NO_ALI_SELECTED, and NULp.

Referenced by GBT_get_default_alignment(), and GBT_get_startup_alignment().

char* GBT_get_default_alignment ( GBDATA gb_main)
Returns
default alignment returns
  • the alignment that was selected in ARB alignment admin, when GBT_get_startup_alignment was called first OR
  • the alignment currently selected in ARB alignment admin OR
  • NULp if NO (valid) alignment selected. An error is exported in that case!

Definition at line 747 of file adali.cxx.

References get_default_alignment().

Referenced by AP_calc_pos_var_pars(), AP_create_consensus_var(), ARB_main(), AWTC_pars_names(), AWTC_recreate_name(), calculateEndPosition(), CON_calc_max_freq_cb(), create_splitAlignment_awars(), DI_create_matrix_variables(), 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(), GBT_set_startup_alignment(), gde_filter_weights(), getArbFilter(), BI_helix::init(), BI_ecoli_ref::init(), 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(), resolve_IUPAC_target_string(), SEC_db_interface::SEC_db_interface(), show_count(), split_ali_cb(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), StaticData::track_ali(), track_ali_change_cb(), and translateSAItoColors().

char* GBT_get_startup_alignment ( GBDATA gb_main)

same interface as GBT_get_default_alignment. When this was called once w/o error, calls to GBT_get_default_alignment always return the alignment which was default then.

Definition at line 757 of file adali.cxx.

References get_default_alignment().

Referenced by GBT_set_startup_alignment(), ED4_root::init_alignment(), and propertyName().

GB_ERROR GBT_set_default_alignment ( GBDATA gb_main,
const char alignment_name 
)

Definition at line 765 of file adali.cxx.

References GB_DEFAULT_ALIGNMENT, and GBT_write_string().

Referenced by ARB_main(), and GBT_set_startup_alignment().

GB_ERROR GBT_set_startup_alignment ( GBDATA gb_main,
const char alignment_name 
)
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 858 of file adali.cxx.

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

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

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 897 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 917 of file adali.cxx.