ARB
Classes | Macros | Enumerations | Functions
NT_concatenate.cxx File Reference
#include "NT_local.h"
#include <items.h>
#include <item_sel_list.h>
#include <awt_sel_boxes.hxx>
#include <AW_rename.hxx>
#include <aw_question.hxx>
#include <aw_awar.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <arb_progress.h>
#include <arb_strbuf.h>
#include <arb_strarray.h>
#include <awt_modules.hxx>
#include <arb_global_defs.h>
Include dependency graph for NT_concatenate.cxx:

Go to the source code of this file.

Classes

struct  SpeciesConcatenateList
 

Macros

#define AWAR_CON_SEQUENCE_TYPE   "tmp/concat/sequence_type"
 
#define AWAR_CON_NEW_ALIGNMENT_NAME   "tmp/concat/new_alignment_name"
 
#define AWAR_CON_ALIGNMENT_SEPARATOR   "tmp/concat/alignment_separator"
 
#define AWAR_CON_SELECTED_ALI   "tmp/concat/database_alignments"
 
#define AWAR_CON_MERGE_FIELD   "tmp/concat/merge_field"
 
#define AWAR_CON_STORE_SIM_SP_NO   "tmp/concat/store_sim_sp_no"
 
#define AWAR_CON_ALLOW_OVERWRITE_ALI   "tmp/concat/overwrite"
 
#define AWAR_CON_INSGAPS_FOR_MISS_ALIS   "tmp/concat/insgaps"
 
#define MOVE_DOWN   0
 
#define MOVE_UP   1
 

Enumerations

enum  MergeSpeciesType { MERGE_SPECIES_SIMPLE, MERGE_SPECIES_AND_CONCAT_ALI }
 

Functions

void NT_createConcatenationAwars (AW_root *aw_root, AW_default aw_def, GBDATA *gb_main)
 
charget_alitype_eval (AW_root *aw_root)
 
static void alitype_changed_cb (AW_root *aw_root, AW_DB_selection *db_sel)
 
static AW_DB_selectioncreateSelectionList (GBDATA *gb_main, AW_window *aws, const char *awarName)
 
static GB_ERROR create_concatInfo_SAI (GBDATA *gb_main, const char *new_ali_name, const char *ali_separator, const StrArray &ali_names)
 
static void concatenateAlignments (AW_window *aws, AW_selection *selected_alis)
 
static void addSpeciesToConcatenateList (SpeciesConcatenateList **sclp, GB_CSTR species_name)
 
static void freeSpeciesConcatenateList (SpeciesConcatenateList *scl)
 
static GB_ERROR checkAndMergeFields (GBDATA *gb_new_species, GB_ERROR error, SpeciesConcatenateList *scl)
 
static GBDATAconcatenateFieldsCreateNewSpecies (AW_window *, GBDATA *gb_species, SpeciesConcatenateList *scl)
 
static void mergeSimilarSpecies (AW_window *aws, MergeSpeciesType mergeType, AW_selection *selected_alis)
 
static AW_windowcreateMergeSimilarSpeciesWindow (AW_root *aw_root, MergeSpeciesType mergeType, AW_selection *selected_alis)
 
AW_windowNT_createMergeSimilarSpeciesWindow (AW_root *aw_root)
 
static AW_windowNT_createMergeSimilarSpeciesAndConcatenateWindow (AW_root *aw_root, AW_selection *selected_alis)
 
static void useSelectedAlignment (AW_window *aww)
 
AW_windowNT_createConcatenationWindow (AW_root *aw_root)
 

Macro Definition Documentation

#define AWAR_CON_SEQUENCE_TYPE   "tmp/concat/sequence_type"
#define AWAR_CON_NEW_ALIGNMENT_NAME   "tmp/concat/new_alignment_name"
#define AWAR_CON_ALIGNMENT_SEPARATOR   "tmp/concat/alignment_separator"
#define AWAR_CON_SELECTED_ALI   "tmp/concat/database_alignments"
#define AWAR_CON_MERGE_FIELD   "tmp/concat/merge_field"
#define AWAR_CON_STORE_SIM_SP_NO   "tmp/concat/store_sim_sp_no"
#define AWAR_CON_ALLOW_OVERWRITE_ALI   "tmp/concat/overwrite"
#define AWAR_CON_INSGAPS_FOR_MISS_ALIS   "tmp/concat/insgaps"
#define MOVE_DOWN   0

Definition at line 41 of file NT_concatenate.cxx.

#define MOVE_UP   1

Definition at line 42 of file NT_concatenate.cxx.

Enumeration Type Documentation

Enumerator
MERGE_SPECIES_SIMPLE 
MERGE_SPECIES_AND_CONCAT_ALI 

Definition at line 575 of file NT_concatenate.cxx.

Function Documentation

void NT_createConcatenationAwars ( AW_root aw_root,
AW_default  aw_def,
GBDATA gb_main 
)
char* get_alitype_eval ( AW_root aw_root)
inline
static void alitype_changed_cb ( AW_root aw_root,
AW_DB_selection db_sel 
)
static
static AW_DB_selection* createSelectionList ( GBDATA gb_main,
AW_window aws,
const char awarName 
)
static
static GB_ERROR create_concatInfo_SAI ( GBDATA gb_main,
const char new_ali_name,
const char ali_separator,
const StrArray &  ali_names 
)
static
static void concatenateAlignments ( AW_window aws,
AW_selection selected_alis 
)
static
static void addSpeciesToConcatenateList ( SpeciesConcatenateList **  sclp,
GB_CSTR  species_name 
)
static
static void freeSpeciesConcatenateList ( SpeciesConcatenateList scl)
static
static GB_ERROR checkAndMergeFields ( GBDATA gb_new_species,
GB_ERROR  error,
SpeciesConcatenateList scl 
)
static
static GBDATA* concatenateFieldsCreateNewSpecies ( AW_window ,
GBDATA gb_species,
SpeciesConcatenateList scl 
)
static
static void mergeSimilarSpecies ( AW_window aws,
MergeSpeciesType  mergeType,
AW_selection selected_alis 
)
static
static AW_window* createMergeSimilarSpeciesWindow ( AW_root aw_root,
MergeSpeciesType  mergeType,
AW_selection selected_alis 
)
static
AW_window* NT_createMergeSimilarSpeciesWindow ( AW_root aw_root)
static AW_window* NT_createMergeSimilarSpeciesAndConcatenateWindow ( AW_root aw_root,
AW_selection selected_alis 
)
static
static void useSelectedAlignment ( AW_window aww)
static
AW_window* NT_createConcatenationWindow ( AW_root aw_root)