NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objmgr/scope.hpp>
#include <objtools/readers/source_mod_parser.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>
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Functions | |
USING_SCOPE (objects) | |
bool | SetMolinfoCompleteness (CMolInfo &mi, bool partial5, bool partial3) |
void | SetMolinfoForProtein (CRef< objects::CSeq_entry > protein, bool partial5, bool partial3) |
CRef< objects::CSeq_feat > | AddEmptyProteinFeatureToProtein (CRef< objects::CSeq_entry > protein, bool partial5, bool partial3) |
CRef< objects::CSeq_feat > | AddProteinFeatureToProtein (CRef< objects::CSeq_entry > protein, bool partial5, bool partial3) |
CRef< objects::CSeq_entry > | CreateTranslatedProteinSequence (CRef< objects::CSeq_feat > cds, objects::CBioseq_Handle nuc_h, bool create_general_only, int *offset) |
CRef<objects::CSeq_feat> AddEmptyProteinFeatureToProtein | ( | CRef< objects::CSeq_entry > | protein, |
bool | partial5, | ||
bool | partial3 | ||
) |
Definition at line 180 of file cmd_add_seqentry.cpp.
References eExtreme_Biological, ftable, NON_CONST_ITERATE, and NULL.
Referenced by AddProteinFeatureToProtein(), TranslateCDSCommand(), CFeatureTableReader::x_AddProteinFeatureToProtein(), and CEditObjectSeq_feat::x_HandleCdsProduct().
CRef<objects::CSeq_feat> AddProteinFeatureToProtein | ( | CRef< objects::CSeq_entry > | protein, |
bool | partial5, | ||
bool | partial3 | ||
) |
Definition at line 222 of file cmd_add_seqentry.cpp.
References AddEmptyProteinFeatureToProtein().
Referenced by CBulkCDSAddPanel::AddOneCmd(), CAlignCDSAddPanel::AddOneCommand(), AddProteinToSeqEntry(), CMacroFunction_ApplyCDS::TheFunction(), CConvertFeatureBase::x_ConvertToCDS(), and CImportFeatTable::x_DoImportCDS().
CRef<objects::CSeq_entry> CreateTranslatedProteinSequence | ( | CRef< objects::CSeq_feat > | cds, |
objects::CBioseq_Handle | nuc_h, | ||
bool | create_general_only, | ||
int * | offset | ||
) |
Definition at line 239 of file cmd_add_seqentry.cpp.
References eExtreme_Biological, GetNewProtId(), offset, and SetMolinfoForProtein().
Referenced by CBulkCDSAddPanel::AddOneCmd(), CAlignCDSAddPanel::AddOneCommand(), CMacroFunction_ApplyCDS::TheFunction(), CConvertFeatureBase::x_ConvertToCDS(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), and CSequenceUpdater::x_RetranslateOldCDSProduct().
Definition at line 140 of file cmd_add_seqentry.cpp.
References CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::GetCompleteness(), CMolInfo_Base::IsSetCompleteness(), and CMolInfo_Base::SetCompleteness().
Referenced by SetMolinfoForProtein().
Definition at line 161 of file cmd_add_seqentry.cpp.
References NON_CONST_ITERATE, NULL, and SetMolinfoCompleteness().
Referenced by AddProteinToSeqEntry(), CreateTranslatedProteinSequence(), TranslateCDSCommand(), CImportFeatTable::x_DoImportCDS(), CEditObjectSeq_feat::x_HandleCdsProduct(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), and CFeatureTableReader::xAddProteinToSeqEntry().
USING_SCOPE | ( | objects | ) |