NCBI C++ ToolKit
Functions | Variables
featedit_util.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seqfeat/Gene_ref.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/RNA_qual.hpp>
#include <objects/seqfeat/RNA_qual_set.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqset/seqset_macros.hpp>
#include <objects/seqloc/Na_strand.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_feat_handle.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objtools/edit/gene_utils.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/packages/pkg_sequence_edit/featedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/seqtable_util.hpp>
#include <gui/packages/pkg_sequence_edit/seq_table_grid.hpp>
+ Include dependency graph for featedit_util.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (ncbi::objects)
 
 USING_SCOPE (edit)
 
string GetIntervalString (const CSeq_interval &seq_int)
 
static bool IsAllRptUnitSeqChars (string seq)
 
vector< stringFindNonUniqueStrings (const vector< string > &values)
 
vector< stringSortUniqueStrings (const vector< string > &values)
 
void SetRnaProductName (CRNA_ref &rna, const string &product, string &remainder, EExistingText existing_text)
 
int FindHighestFeatureId (const CSeq_entry_Handle &entry)
 
void AddToFeatureIdColumn (CSeq_feat_Handle feat, CRef< CSeqTable_column > column, size_t row, int &top_id)
 
CSeq_feat_Handle GetFeatureFromTableId (const string &id_string, CSeq_entry_Handle entry)
 
CRef< CSeq_tableBuildFeatureSeqTableFromSeqEntry (CSeq_entry_Handle entry, const SAnnotSelector &sel)
 
void AddColumnsToFeatureTable (const vector< string > &fields, CRef< CSeq_table > table, CSeq_entry_Handle entry)
 
CRef< CCmdCompositeApplyFeatureSeqTableToSeqEntry (CRef< CSeq_table > table, CSeq_entry_Handle entry)
 
CRef< CSeq_locCreateFeatLocation (const CBioseq_Handle &bsh, int from, int to, bool ispartial5, bool ispartial3)
 
CRef< CSeq_featAddMiscRNA (const CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)
 
CRef< CSeq_featAddRibosomalRNA (const CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)
 
CRef< CCmdCompositeAddNamedrRna (CSeq_entry_Handle entry, string rna_name, bool ispartial5, bool ispartial3)
 
CRef< CCmdCompositeCreateControlRegion (CSeq_entry_Handle entry)
 
CRef< CCmdCompositeCreateMicrosatellite (CSeq_entry_Handle entry)
 

Variables

static const string kIgnoreColumns [] = {kStartColLabel, kStopColLabel, kFeatureID, kProblems }
 
static const int kNumIgnoreColumns = sizeof (kIgnoreColumns) / sizeof (string)
 
const string kSatellite = "satellite"
 

Function Documentation

◆ AddColumnsToFeatureTable()

void AddColumnsToFeatureTable ( const vector< string > &  fields,
CRef< CSeq_table table,
CSeq_entry_Handle  entry 
)

◆ AddMiscRNA()

CRef<CSeq_feat> AddMiscRNA ( const CBioseq_Handle bsh,
string  name,
int  from,
int  to,
bool  ispartial5,
bool  ispartial3 
)

◆ AddNamedrRna()

CRef<CCmdComposite> AddNamedrRna ( CSeq_entry_Handle  entry,
string  rna_name,
bool  ispartial5,
bool  ispartial3 
)

◆ AddRibosomalRNA()

CRef<CSeq_feat> AddRibosomalRNA ( const CBioseq_Handle bsh,
string  name,
int  from,
int  to,
bool  ispartial5,
bool  ispartial3 
)

◆ AddToFeatureIdColumn()

void AddToFeatureIdColumn ( CSeq_feat_Handle  feat,
CRef< CSeqTable_column column,
size_t  row,
int top_id 
)

◆ ApplyFeatureSeqTableToSeqEntry()

CRef<CCmdComposite> ApplyFeatureSeqTableToSeqEntry ( CRef< CSeq_table table,
CSeq_entry_Handle  entry 
)

◆ BuildFeatureSeqTableFromSeqEntry()

CRef<CSeq_table> BuildFeatureSeqTableFromSeqEntry ( CSeq_entry_Handle  entry,
const SAnnotSelector sel 
)

◆ CreateControlRegion()

CRef<CCmdComposite> CreateControlRegion ( CSeq_entry_Handle  entry)

◆ CreateFeatLocation()

CRef<CSeq_loc> CreateFeatLocation ( const CBioseq_Handle bsh,
int  from,
int  to,
bool  ispartial5,
bool  ispartial3 
)

◆ CreateMicrosatellite()

CRef<CCmdComposite> CreateMicrosatellite ( CSeq_entry_Handle  entry)

◆ FindHighestFeatureId()

int FindHighestFeatureId ( const CSeq_entry_Handle entry)

◆ FindNonUniqueStrings()

vector<string> FindNonUniqueStrings ( const vector< string > &  values)

◆ GetFeatureFromTableId()

CSeq_feat_Handle GetFeatureFromTableId ( const string id_string,
CSeq_entry_Handle  entry 
)

◆ GetIntervalString()

string GetIntervalString ( const CSeq_interval seq_int)

◆ IsAllRptUnitSeqChars()

static bool IsAllRptUnitSeqChars ( string  seq)
static

Definition at line 734 of file featedit_util.cpp.

References isalpha(), isdigit(), and ITERATE.

Referenced by CRptUnitSeqColumn::IsValid().

◆ SetRnaProductName()

void SetRnaProductName ( CRNA_ref rna,
const string product,
string remainder,
EExistingText  existing_text 
)

◆ SortUniqueStrings()

vector<string> SortUniqueStrings ( const vector< string > &  values)

Definition at line 1074 of file featedit_util.cpp.

References NStr::Equal().

Referenced by CSubPrep_panel::x_UpdateFeatureStatus().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( edit  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( ncbi::objects  )

Variable Documentation

◆ kIgnoreColumns

const string kIgnoreColumns[] = {kStartColLabel, kStopColLabel, kFeatureID, kProblems }
static

Definition at line 72 of file featedit_util.cpp.

Referenced by CFeatureSeqTableColumnBaseFactory::Create().

◆ kNumIgnoreColumns

const int kNumIgnoreColumns = sizeof (kIgnoreColumns) / sizeof (string)
static

Definition at line 73 of file featedit_util.cpp.

Referenced by CFeatureSeqTableColumnBaseFactory::Create().

◆ kSatellite

const string kSatellite = "satellite"
Modified on Tue Jun 18 13:41:13 2024 by modify_doxy.py rev. 669887