NCBI C++ ToolKit
Functions | Variables
molinfoedit_util.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_field.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_util.hpp>
#include <gui/packages/pkg_sequence_edit/srcedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/seqtable_util.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_panel.hpp>
#include <gui/packages/pkg_sequence_edit/molinfoedit_util.hpp>
#include <gui/widgets/object_list/object_list_widget.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/cmd_change_bioseq_inst.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
+ Include dependency graph for molinfoedit_util.cpp:

Go to the source code of this file.

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Functions

objects::CSeq_inst::ETopology s_TopologyFromName (string name)
 
string s_GetBiomolName (objects::CSeq_inst::EMol mol, objects::CMolInfo::TBiomol biomol)
 
static void s_GetBiomolValuesFromName (string name, objects::CSeq_inst::EMol &mol, objects::CMolInfo::EBiomol &biomol)
 
vector< stringGetMoleculeTypeOptions (CSourceRequirements::EWizardType wizard_type)
 
vector< stringGetSrcGenomeOptions (CSourceRequirements::EWizardType wizard_type, CSourceRequirements::EWizardSrcType src_type)
 
CRef< objects::CSeq_table > BuildMolInfoValuesTableFromSeqEntry (objects::CSeq_entry_Handle seh, CSourceRequirements::EWizardType wizard_type)
 
CRef< CCmdCompositeApplyMolInfoValuesTableToSeqEntry (CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh, bool add_confirmed)
 
CRef< objects::CSeq_table > BuildCommentDescriptorValuesTableFromSeqEntry (objects::CSeq_entry_Handle seh, const string &label)
 
CRef< CCmdCompositeApplyCommentValuesTableToSeqEntry (CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh, const string &label)
 
static bool s_WantChimeraForSource (const objects::CBioSource &src, CSourceRequirements::EWizardSrcType src_type)
 
CRef< objects::CSeq_table > BuildChimeraValuesTableFromSeqEntry (objects::CSeq_entry_Handle seh, const string &label, CSourceRequirements::EWizardSrcType src_type)
 
CRef< CCmdCompositeApplyChimeraValuesTableToSeqEntry (CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh, const string &label)
 
CRef< objects::CSeq_table > BuildDBLinkValuesTableFromSeqEntry (objects::CSeq_entry_Handle seh)
 
CRef< CCmdCompositeApplyDBLinkValuesTableToSeqEntry (CRef< objects::CSeq_table >values_table, objects::CSeq_entry_Handle seh)
 

Variables

const string kChimeraCommentStart = "Sequences were screened for chimeras by the submitter using "
 

Function Documentation

◆ ApplyChimeraValuesTableToSeqEntry()

CRef<CCmdComposite> ApplyChimeraValuesTableToSeqEntry ( CRef< objects::CSeq_table >  values_table,
objects::CSeq_entry_Handle  seh,
const string label 
)

◆ ApplyCommentValuesTableToSeqEntry()

CRef<CCmdComposite> ApplyCommentValuesTableToSeqEntry ( CRef< objects::CSeq_table >  values_table,
objects::CSeq_entry_Handle  seh,
const string label 
)

◆ ApplyDBLinkValuesTableToSeqEntry()

CRef<CCmdComposite> ApplyDBLinkValuesTableToSeqEntry ( CRef< objects::CSeq_table >  values_table,
objects::CSeq_entry_Handle  seh 
)

◆ ApplyMolInfoValuesTableToSeqEntry()

CRef<CCmdComposite> ApplyMolInfoValuesTableToSeqEntry ( CRef< objects::CSeq_table >  values_table,
objects::CSeq_entry_Handle  seh,
bool  add_confirmed 
)

◆ BuildChimeraValuesTableFromSeqEntry()

CRef<objects::CSeq_table> BuildChimeraValuesTableFromSeqEntry ( objects::CSeq_entry_Handle  seh,
const string label,
CSourceRequirements::EWizardSrcType  src_type 
)

◆ BuildCommentDescriptorValuesTableFromSeqEntry()

CRef<objects::CSeq_table> BuildCommentDescriptorValuesTableFromSeqEntry ( objects::CSeq_entry_Handle  seh,
const string label 
)

◆ BuildDBLinkValuesTableFromSeqEntry()

CRef<objects::CSeq_table> BuildDBLinkValuesTableFromSeqEntry ( objects::CSeq_entry_Handle  seh)

◆ BuildMolInfoValuesTableFromSeqEntry()

CRef<objects::CSeq_table> BuildMolInfoValuesTableFromSeqEntry ( objects::CSeq_entry_Handle  seh,
CSourceRequirements::EWizardType  wizard_type 
)

◆ GetMoleculeTypeOptions()

vector<string> GetMoleculeTypeOptions ( CSourceRequirements::EWizardType  wizard_type)

◆ GetSrcGenomeOptions()

vector<string> GetSrcGenomeOptions ( CSourceRequirements::EWizardType  wizard_type,
CSourceRequirements::EWizardSrcType  src_type 
)

◆ s_GetBiomolName()

string s_GetBiomolName ( objects::CSeq_inst::EMol  mol,
objects::CMolInfo::TBiomol  biomol 
)

Definition at line 85 of file molinfoedit_util.cpp.

References kDefaultMoleculeType.

Referenced by BuildMolInfoValuesTableFromSeqEntry().

◆ s_GetBiomolValuesFromName()

static void s_GetBiomolValuesFromName ( string  name,
objects::CSeq_inst::EMol &  mol,
objects::CMolInfo::EBiomol &  biomol 
)
static

Definition at line 139 of file molinfoedit_util.cpp.

References NStr::EqualNocase(), and kDefaultMoleculeType.

Referenced by ApplyMolInfoValuesTableToSeqEntry().

◆ s_TopologyFromName()

objects::CSeq_inst::ETopology s_TopologyFromName ( string  name)

Definition at line 69 of file molinfoedit_util.cpp.

References NStr::EqualNocase().

Referenced by ApplyMolInfoValuesTableToSeqEntry().

◆ s_WantChimeraForSource()

static bool s_WantChimeraForSource ( const objects::CBioSource &  src,
CSourceRequirements::EWizardSrcType  src_type 
)
static

Variable Documentation

◆ kChimeraCommentStart

const string kChimeraCommentStart = "Sequences were screened for chimeras by the submitter using "
Modified on Tue Feb 27 05:53:47 2024 by modify_doxy.py rev. 669887