NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
featedit_util.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objects/seqtable/Seq_table.hpp>
#include <objects/seqtable/SeqTable_column.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objmgr/scope.hpp>
#include <gui/packages/pkg_sequence_edit/field_handler.hpp>
#include <gui/packages/pkg_sequence_edit/seqtable_util.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
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Classes

class  CFeatureSeqTableColumnBase
 
class  CFeatureSeqTableColumnBaseFactory
 
class  CPartialStartColumn
 
class  CPartialStopColumn
 
class  CCommentColumn
 
class  CExceptionColumn
 
class  CGbQualColumn
 
class  CRptUnitRangeColumn
 
class  CRptUnitSeqColumn
 
class  CSatelliteColumn
 
class  CSatelliteTypeNameColumn
 
class  CProductColumn
 
class  CCodonStartColumn
 
class  CGeneticCodeColumn
 
class  CDescriptionColumn
 
class  CGeneRefColumn
 
class  CProtRefColumn
 
class  CNcrnaClassColumn
 
class  CDbXrefColumn
 
class  CEvidenceColumn
 
class  CRegionColumn
 
class  CLocationColumn
 
class  CCodonsRecColumn
 
class  CAntiCodonColumn
 
class  CTagPeptideColumn
 
class  CCitationColumn
 
class  CInferenceColumn
 

Typedefs

typedef vector< CRef< CFeatureSeqTableColumnBase > > TFeatureSeqTableColumnList
 

Functions

int FindHighestFeatureId (const objects::CSeq_entry_Handle &entry)
 
CRef< objects::CSeq_table > BuildFeatureSeqTableFromSeqEntry (objects::CSeq_entry_Handle entry, const SAnnotSelector &sel)
 
void AddColumnsToFeatureTable (const vector< string > &fields, CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry)
 
CRef< CCmdCompositeApplyFeatureSeqTableToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry)
 
CRef< objects::CSeq_loc > CreateFeatLocation (const objects::CBioseq_Handle &bsh, int from, int to, bool ispartial5, bool ispartial3)
 
CRef< objects::CSeq_feat > AddRibosomalRNA (const objects::CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)
 
CRef< CCmdCompositeAddNamedrRna (objects::CSeq_entry_Handle entry, string rna_name, bool ispartial5, bool ispartial3)
 
CRef< objects::CSeq_feat > AddMiscRNA (const objects::CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)
 
CRef< CCmdCompositeCreateControlRegion (objects::CSeq_entry_Handle entry)
 
CRef< CCmdCompositeCreateMicrosatellite (objects::CSeq_entry_Handle entry)
 
void SetRnaProductName (objects::CRNA_ref &rna, const string &product, string &remainder, objects::edit::EExistingText existing_text)
 

Variables

const string kStartColLabel = "Start"
 
const string kStopColLabel = "Stop"
 
const string kFeatureID = "FeatureID"
 
const string kPartialStart = "5' Partial"
 
const string kPartialStop = "3' Partial"
 
const string kProblems = "Problems"
 
static const string kSatelliteTypes [] = {"satellite", "microsatellite", "minisatellite" }
 
static const int kNumSatelliteTypes = sizeof (kSatelliteTypes) / sizeof (string)
 

Typedef Documentation

◆ TFeatureSeqTableColumnList

Definition at line 93 of file featedit_util.hpp.

Function Documentation

◆ AddColumnsToFeatureTable()

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

◆ AddMiscRNA()

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

◆ AddNamedrRna()

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

◆ AddRibosomalRNA()

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

◆ ApplyFeatureSeqTableToSeqEntry()

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

◆ BuildFeatureSeqTableFromSeqEntry()

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

◆ CreateControlRegion()

CRef<CCmdComposite> CreateControlRegion ( objects::CSeq_entry_Handle  entry)

◆ CreateFeatLocation()

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

◆ CreateMicrosatellite()

CRef<CCmdComposite> CreateMicrosatellite ( objects::CSeq_entry_Handle  entry)

◆ FindHighestFeatureId()

int FindHighestFeatureId ( const objects::CSeq_entry_Handle &  entry)

◆ SetRnaProductName()

void SetRnaProductName ( objects::CRNA_ref &  rna,
const string product,
string remainder,
objects::edit::EExistingText  existing_text 
)

Variable Documentation

◆ kFeatureID

const string kFeatureID = "FeatureID"

◆ kNumSatelliteTypes

const int kNumSatelliteTypes = sizeof (kSatelliteTypes) / sizeof (string)
static

◆ kPartialStart

const string kPartialStart = "5' Partial"

◆ kPartialStop

const string kPartialStop = "3' Partial"

◆ kProblems

const string kProblems = "Problems"

◆ kSatelliteTypes

const string kSatelliteTypes[] = {"satellite", "microsatellite", "minisatellite" }
static

◆ kStartColLabel

const string kStartColLabel = "Start"

◆ kStopColLabel

const string kStopColLabel = "Stop"
Modified on Fri May 24 14:55:42 2024 by modify_doxy.py rev. 669887