NCBI C++ ToolKit
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#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< CCmdComposite > | ApplyFeatureSeqTableToSeqEntry (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< CCmdComposite > | AddNamedrRna (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< CCmdComposite > | CreateControlRegion (objects::CSeq_entry_Handle entry) |
CRef< CCmdComposite > | CreateMicrosatellite (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 vector< CRef<CFeatureSeqTableColumnBase> > TFeatureSeqTableColumnList |
Definition at line 93 of file featedit_util.hpp.
void AddColumnsToFeatureTable | ( | const vector< string > & | fields, |
CRef< objects::CSeq_table > | table, | ||
objects::CSeq_entry_Handle | entry | ||
) |
CRef<CCmdComposite> AddNamedrRna | ( | objects::CSeq_entry_Handle | entry, |
string | rna_name, | ||
bool | ispartial5, | ||
bool | ispartial3 | ||
) |
Referenced by CSequenceEditingEventHandler::AddNamedrRNA(), CEditingBtnsPanel::AddNamedrRNA12S(), CEditingBtnsPanel::AddNamedrRNA26S(), CEditingBtnsPanel::AddNamedrRNA28S(), CEditingBtnsPanel::AddNamedrRNALarge(), CEditingBtnsPanel::AddNamedrRNASmall(), BOOST_AUTO_TEST_CASE(), CEditingBtnsPanel::OnAddrRNA16S(), CEditingBtnsPanel::OnAddrRNA18S(), and CEditingBtnsPanel::OnAddrRNA23S().
CRef<CCmdComposite> ApplyFeatureSeqTableToSeqEntry | ( | CRef< objects::CSeq_table > | table, |
objects::CSeq_entry_Handle | entry | ||
) |
CRef<objects::CSeq_table> BuildFeatureSeqTableFromSeqEntry | ( | objects::CSeq_entry_Handle | entry, |
const SAnnotSelector & | sel | ||
) |
CRef<CCmdComposite> CreateControlRegion | ( | objects::CSeq_entry_Handle | entry | ) |
CRef<objects::CSeq_loc> CreateFeatLocation | ( | const objects::CBioseq_Handle & | bsh, |
int | from, | ||
int | to, | ||
bool | ispartial5, | ||
bool | ispartial3 | ||
) |
CRef<CCmdComposite> CreateMicrosatellite | ( | objects::CSeq_entry_Handle | entry | ) |
Referenced by GetMiscTableFromSeqEntry().
void SetRnaProductName | ( | objects::CRNA_ref & | rna, |
const string & | product, | ||
string & | remainder, | ||
objects::edit::EExistingText | existing_text | ||
) |
Definition at line 51 of file featedit_util.hpp.
Referenced by AddFeatureSeqTableRowToSeqEntry(), AddFeatureToSeqTable(), BuildFeatureSeqTableFromSeqEntry(), and GetFeaturesFromSeqEntry().
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static |
Definition at line 57 of file featedit_util.hpp.
Referenced by AddFeatureToSeqTable(), CSatelliteColumn::x_AddSatellitePrefix(), CSatelliteColumn::x_AddSatelliteType(), CSatelliteColumn::x_GetSatelliteName(), and CSatelliteColumn::x_GetSatelliteType().
Definition at line 52 of file featedit_util.hpp.
Referenced by AddFeatureToSeqTable(), CFeatureSeqTableColumnBaseFactory::Create(), CFeatureTableCommandConverter::GetChoices(), CCdsFromGeneMrnaExon::GetCommand(), CConvertCdsToMiscFeat::GetCommand(), CConvertFeatDlg::GetCommand(), CExtendPartialFeatDlg::GetCommand(), CFuseFeaturesDlg::GetCommand(), CGeneFeatFromOtherFeatDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CResolveIntersectingFeats::GetCommand(), CtRNAFromGene::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), CBulkGene::GetCommandFromValuesTable(), CBulkMiscFeat::GetCommandFromValuesTable(), CBulkRna::GetCommandFromValuesTable(), CPartialStartColumn::GetLabel(), CBulkCDS::GetValuesTableFromSeqEntry(), CBulkGene::GetValuesTableFromSeqEntry(), CBulkMiscFeat::GetValuesTableFromSeqEntry(), CBulkRna::GetValuesTableFromSeqEntry(), CCdsToMatPeptide::Init(), and CSelectFeatures::OnAccept().
Definition at line 53 of file featedit_util.hpp.
Referenced by AddFeatureToSeqTable(), CFeatureSeqTableColumnBaseFactory::Create(), CFeatureTableCommandConverter::GetChoices(), CBulkCDS::GetCommandFromValuesTable(), CBulkGene::GetCommandFromValuesTable(), CBulkMiscFeat::GetCommandFromValuesTable(), CBulkRna::GetCommandFromValuesTable(), CPartialStopColumn::GetLabel(), CBulkCDS::GetValuesTableFromSeqEntry(), CBulkGene::GetValuesTableFromSeqEntry(), CBulkMiscFeat::GetValuesTableFromSeqEntry(), and CBulkRna::GetValuesTableFromSeqEntry().
Definition at line 54 of file featedit_util.hpp.
Referenced by AddProblemsColumnToFeatureSeqTable(), ApplySrcTableToSeqEntry(), CSourceRequirements::CheckSourceQuals(), CFeatureTableCommandConverter::MakeProblemsColumn(), RemoveProblemsColumn(), CSeqTableGridPanel::SetColumnSizesAndChoices(), CSeqTableGridPanel::x_MakeProblemsColumnReadOnly(), and CSeqIdFixDlg::x_RefreshProblems().
Definition at line 56 of file featedit_util.hpp.
Referenced by AddFeatureToSeqTable(), CMacroFunction_SatelliteFields::s_GetSatelliteName(), CMacroFunction_SatelliteFields::s_GetSatelliteType(), CMacroFunction_SatelliteFields::s_MakeSatellite(), CMacroFunction_AddorSetContElement::TheFunction(), CSatelliteColumn::x_AddSatellitePrefix(), CSatelliteColumn::x_AddSatelliteType(), CSatelliteColumn::x_GetSatelliteName(), and CSatelliteColumn::x_GetSatelliteType().
Definition at line 49 of file featedit_util.hpp.
Referenced by AddFeatureSeqTableRowToSeqEntry(), AddFeatureToSeqTable(), and GetFeaturesFromSeqEntry().
Definition at line 50 of file featedit_util.hpp.
Referenced by AddFeatureSeqTableRowToSeqEntry(), AddFeatureToSeqTable(), and GetFeaturesFromSeqEntry().