#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 SVN repository for this file.

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< string >	GetMoleculeTypeOptions (CSourceRequirements::EWizardType wizard_type)

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

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

CRef< CCmdComposite >	ApplyMolInfoValuesTableToSeqEntry (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< CCmdComposite >	ApplyCommentValuesTableToSeqEntry (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< CCmdComposite >	ApplyChimeraValuesTableToSeqEntry (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< CCmdComposite >	ApplyDBLinkValuesTableToSeqEntry (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
	)

Definition at line 596 of file molinfoedit_util.cpp.

References cmd, NStr::Equal(), FindSeqTableColumnByName(), NStr::IsBlank(), kChimeraCommentStart, kSequenceIdColLabel, label, row, and NStr::StartsWith().

Referenced by CChimeraCommentDescriptorTableCommandConverter::GetCommandFromValuesTable().

◆ ApplyCommentValuesTableToSeqEntry()

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

Definition at line 465 of file molinfoedit_util.cpp.

References cmd, NStr::Equal(), FindSeqTableColumnByName(), kSequenceIdColLabel, label, and row.

Referenced by CCommentDescriptorTableCommandConverter::GetCommandFromValuesTable().

◆ ApplyDBLinkValuesTableToSeqEntry()

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

Definition at line 697 of file molinfoedit_util.cpp.

References cmd, columns, NStr::EqualNocase(), FindSeqTableColumnByName(), i, NStr::IsBlank(), kSequenceIdColLabel, row, and NStr::Split().

Referenced by CDBLinkTableCommandConverter::GetCommandFromValuesTable().

◆ ApplyMolInfoValuesTableToSeqEntry()

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

Definition at line 333 of file molinfoedit_util.cpp.

References cmd, FindSeqTableColumnByName(), kMoleculeType, kSequenceIdColLabel, row, s_GetBiomolValuesFromName(), s_TopologyFromName(), and CSubPrep_panel::SetWizardFieldInSeqEntry().

Referenced by CBulkMolinfoEditDlg::GetCommand().

◆ BuildChimeraValuesTableFromSeqEntry()

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