NCBI C++ ToolKit
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#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>
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Variables | |
static const string | kIgnoreColumns [] = {kStartColLabel, kStopColLabel, kFeatureID, kProblems } |
static const int | kNumIgnoreColumns = sizeof (kIgnoreColumns) / sizeof (string) |
const string | kSatellite = "satellite" |
void AddColumnsToFeatureTable | ( | const vector< string > & | fields, |
CRef< CSeq_table > | table, | ||
CSeq_entry_Handle | entry | ||
) |
Definition at line 2029 of file featedit_util.cpp.
References AddStringColumnToTable(), AddValueToColumn(), CFeatureSeqTableColumnBaseFactory::Create(), NStr::eNocase, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, f, FillShortColumns(), CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), GetFeatureFromTableId(), CSeq_loc::GetId(), CSeq_feat_Handle::GetLocation(), GetOverlappingGene(), GetOverlappingmRNA(), CSeq_feat_Handle::GetProduct(), CSeq_entry_Handle::GetScope(), CSeq_feat_Handle::GetSeq_feat(), CSeqFeatData::GetSubtype(), i, CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CSeqFeatData_Base::IsProt(), CSeq_feat_Handle::IsSetProduct(), ITERATE, prot, row, NStr::StartsWith(), table, and val.
CRef<CSeq_feat> AddMiscRNA | ( | const CBioseq_Handle & | bsh, |
string | name, | ||
int | from, | ||
int | to, | ||
bool | ispartial5, | ||
bool | ispartial3 | ||
) |
Definition at line 2278 of file featedit_util.cpp.
References CreateFeatLocation(), CRNA_ref_Base::eType_miscRNA, rna, CRNA_ref_Base::SetExt(), and CRNA_ref_Base::SetType().
CRef<CCmdComposite> AddNamedrRna | ( | CSeq_entry_Handle | entry, |
string | rna_name, | ||
bool | ispartial5, | ||
bool | ispartial3 | ||
) |
Definition at line 2312 of file featedit_util.cpp.
References AddRibosomalRNA(), cmd, CSeq_inst_Base::eMol_na, ctll::empty(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetSeq_entry_Handle(), NStr::IsBlank(), and NULL.
CRef<CSeq_feat> AddRibosomalRNA | ( | const CBioseq_Handle & | bsh, |
string | name, | ||
int | from, | ||
int | to, | ||
bool | ispartial5, | ||
bool | ispartial3 | ||
) |
Definition at line 2295 of file featedit_util.cpp.
References CreateFeatLocation(), CRNA_ref_Base::eType_rRNA, rna, CRNA_ref_Base::SetExt(), and CRNA_ref_Base::SetType().
Referenced by AddNamedrRna().
void AddToFeatureIdColumn | ( | CSeq_feat_Handle | feat, |
CRef< CSeqTable_column > | column, | ||
size_t | row, | ||
int & | top_id | ||
) |
Definition at line 1960 of file featedit_util.cpp.
References AddValueToColumn(), column, CObject_id_Base::GetId(), CSeq_feat_Handle::GetId(), CFeat_id_Base::GetLocal(), CObject_id_Base::IsId(), CFeat_id_Base::IsLocal(), CSeq_feat_Handle::IsSetId(), NStr::NumericToString(), row, and CSeq_feat_EditHandle::SetFeatId().
Referenced by BuildFeatureSeqTableFromSeqEntry().
CRef<CCmdComposite> ApplyFeatureSeqTableToSeqEntry | ( | CRef< CSeq_table > | table, |
CSeq_entry_Handle | entry | ||
) |
Definition at line 2100 of file featedit_util.cpp.
References CSerialObject::Assign(), cmd, CFeatureSeqTableColumnBaseFactory::Create(), eExistingText_replace_old, NStr::eNocase, NStr::Equal(), CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CRNA_ref_Base::eType_mRNA, f, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), GetFeatureFromTableId(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Handle::GetLocation(), GetOverlappingGene(), GetOverlappingmRNA(), CSeq_feat_Handle::GetProduct(), CSeq_entry_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_feat_Handle::GetSeq_feat(), CScope::GetSeq_featHandle(), CSeqFeatData::GetSubtype(), NStr::IsBlank(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CSeq_feat_Handle::IsSetProduct(), NULL, prot, row, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), ncbi::grid::netcache::search::fields::size, NStr::StartsWith(), and table.
CRef<CSeq_table> BuildFeatureSeqTableFromSeqEntry | ( | CSeq_entry_Handle | entry, |
const SAnnotSelector & | sel | ||
) |
Definition at line 1994 of file featedit_util.cpp.
References AddStringColumnToTable(), AddToFeatureIdColumn(), CSeqTable_column_info_Base::eField_id_location_id, FillShortColumns(), FindHighestFeatureId(), CSeq_entry_Handle::GetBioseqHandle(), CSeq_loc::GetId(), CMappedFeat::GetLocation(), CMappedFeat::GetSeq_feat_Handle(), CBioseq_Handle::GetSeqId(), kFeatureID, kSequenceIdColLabel, row, CSeqTable_column_Base::SetHeader(), and table.
CRef<CCmdComposite> CreateControlRegion | ( | CSeq_entry_Handle | entry | ) |
Definition at line 2331 of file featedit_util.cpp.
References cmd, CreateFeatLocation(), CSeq_inst_Base::eMol_na, ctll::empty(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetSeq_entry_Handle(), NULL, CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetPartial().
CRef<CSeq_loc> CreateFeatLocation | ( | const CBioseq_Handle & | bsh, |
int | from, | ||
int | to, | ||
bool | ispartial5, | ||
bool | ispartial3 | ||
) |
Definition at line 2261 of file featedit_util.cpp.
References eExtreme_Biological, eNa_strand_plus, CBioseq_Handle::GetCompleteBioseq(), CBioseq_Base::GetId(), CSeq_loc::SetInt(), CSeq_loc::SetPartialStart(), and CSeq_loc::SetPartialStop().
Referenced by AddMiscRNA(), AddRibosomalRNA(), CreateControlRegion(), and CreateMicrosatellite().
CRef<CCmdComposite> CreateMicrosatellite | ( | CSeq_entry_Handle | entry | ) |
Definition at line 2359 of file featedit_util.cpp.
References cmd, CreateFeatLocation(), CSeq_inst_Base::eMol_na, ctll::empty(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetSeq_entry_Handle(), NULL, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_feat_Base::SetQual().
int FindHighestFeatureId | ( | const CSeq_entry_Handle & | entry | ) |
Definition at line 1945 of file featedit_util.cpp.
References GetId(), CObject_id_Base::GetId(), and CFeat_id_Base::GetLocal().
Referenced by BuildFeatureSeqTableFromSeqEntry().
Definition at line 1036 of file featedit_util.cpp.
References NStr::Equal().
Referenced by GetReplacementSeqIds(), GetSeqIdProblems(), CSatelliteTypeNameColumn::IsValid(), and CSubPrep_panel::x_NeedUniqueMicrosatelliteNames().
CSeq_feat_Handle GetFeatureFromTableId | ( | const string & | id_string, |
CSeq_entry_Handle | entry | ||
) |
Definition at line 1976 of file featedit_util.cpp.
References CSeqFeatData_Base::e_not_set, Error(), CTSE_Handle::GetFeatureWithId(), CException::GetMsg(), CSeq_entry_Handle::GetTopLevelEntry(), CSeq_entry_Handle::GetTSE_Handle(), LOG_POST, NStr::StringToInt(), and CException::what().
Referenced by AddColumnsToFeatureTable(), and ApplyFeatureSeqTableToSeqEntry().
string GetIntervalString | ( | const CSeq_interval & | seq_int | ) |
Definition at line 245 of file featedit_util.cpp.
References CSeq_interval_Base::CanGetStrand(), eExtreme_Biological, eExtreme_Positional, eNa_strand_minus, CSeq_interval::GetStart(), CSeq_interval::GetStop(), CSeq_interval_Base::GetStrand(), CSeq_interval::IsPartialStart(), CSeq_interval::IsPartialStop(), kEmptyStr, string, and NStr::UIntToString().
Referenced by CAntiCodonColumn::GetFromFeat().
Definition at line 734 of file featedit_util.cpp.
References isalpha(), isdigit(), and ITERATE.
Referenced by CRptUnitSeqColumn::IsValid().
void SetRnaProductName | ( | CRNA_ref & | rna, |
const string & | product, | ||
string & | remainder, | ||
EExistingText | existing_text | ||
) |
Definition at line 1136 of file featedit_util.cpp.
References AddValueToString(), NStr::IsBlank(), and rna.
Referenced by CProductColumn::AddToFeature(), and CProductColumn::ClearInFeature().
Definition at line 1074 of file featedit_util.cpp.
References NStr::Equal().
Referenced by CSubPrep_panel::x_UpdateFeatureStatus().
USING_SCOPE | ( | edit | ) |
USING_SCOPE | ( | ncbi::objects | ) |
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static |
Definition at line 72 of file featedit_util.cpp.
Referenced by CFeatureSeqTableColumnBaseFactory::Create().
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static |
Definition at line 73 of file featedit_util.cpp.
Referenced by CFeatureSeqTableColumnBaseFactory::Create().
Definition at line 763 of file featedit_util.cpp.
Referenced by CSatelliteTypeNameColumn::AddToFeature(), CSatelliteColumn::x_AddSatelliteName(), CSatelliteColumn::x_AddSatellitePrefix(), CSatelliteColumn::x_AddSatelliteType(), CSatelliteColumn::x_ClearSatelliteSubFields(), and CSatelliteTypeNameColumn::x_IsQualAMatch().