srcedit_util.cpp File Reference

#include <ncbi_pch.hpp>
#include <util/static_map.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objects/submit/Contact_info.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/general/Name_std.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/PCRReactionSet.hpp>
#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/PCRPrimerSeq.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/misc/sequence_macros.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/srcedit_util.hpp>
#include <gui/widgets/object_list/object_list_widget.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/widgets/wx/csv_exporter.hpp>
#include <gui/widgets/edit/biosource_autocomplete.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objects/general/Dbtag.hpp>
#include <objtools/edit/source_edit.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_util.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>

Include dependency graph for srcedit_util.cpp:

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Classes
struct	exampletable

Typedefs
typedef struct exampletable	ExampleTableData
typedef SStaticPair< const char *, CSrcStructuredVoucherPartColumn::EStructVouchPart >	TStructVoucherPart
typedef CStaticArrayMap< string, CSrcStructuredVoucherPartColumn::EStructVouchPart >	TStrcVouchMap

Functions
	USING_SCOPE (objects)
	USING_SCOPE (edit)
static bool	s_IsAllNumbers (string val)
static string	s_MakeUniquenessVal (vector< CRef< CSeqTable_column > > cols, size_t row)
static bool	IsExampleTableRowAcceptable (const ExampleTableData *e1, string field_name, CSourceRequirements::EWizardType wizard_type, CSourceRequirements::EWizardSrcType src_type)
static int	CompareExampleTableRows (const ExampleTableData *e1, const ExampleTableData *e2)
CSourceRequirements *	GetSrcRequirements (CSourceRequirements::EWizardType wizard_type, CSourceRequirements::EWizardSrcType source_type, CRef< CSeq_table > values_table)
string	GetPrimerSetNameValues (const CPCRPrimerSet &primer_set)
string	GetPrimerSetSeqValues (const CPCRPrimerSet &primer_set)
void	RemoveLastCharacter (string &str)
string	JoinValues (const string &name, const vector< string > &values)
void	SplitValues (const string &name, const string &newValue, vector< string > &values)
CRef< CSeq_table >	GetSeqTableFromSeqEntry (CSeq_entry_Handle seh)
CRef< CSeq_table >	GetSeqTableForSrcQualFromSeqEntry (CSeq_entry_Handle seh, vector< string > qual_names)
	DEFINE_STATIC_ARRAY_MAP (TStrcVouchMap, sm_VouchMap, s_StrVouchPartName)
bool	IsFwdPrimerName (string name)
bool	IsRevPrimerName (string name)
bool	IsFwdPrimerSeq (string name)
bool	IsRevPrimerSeq (string name)
CRef< CCmdComposite >	ApplySrcTableToSeqEntry (CRef< CSeq_table >values_table, CSeq_entry_Handle seh)
bool	RelaxedMatch (CRef< CSeq_id > id1, CRef< CSeq_id > id2)
static bool	OneRowOk (CRef< CSeq_id > id, CRef< CSeqTable_column > id_col, CSeq_entry_Handle seh)

Variables
static const ExampleTableData	s_ExampleTable []
static const int	k_NumExampleTableRows = sizeof (s_ExampleTable) / sizeof (ExampleTableData)
static const string	nomial_keywords []
static const TStructVoucherPart	s_StrVouchPartName []

Typedef Documentation

ExampleTableData

typedef struct exampletable ExampleTableData

TStrcVouchMap

typedef CStaticArrayMap<string, CSrcStructuredVoucherPartColumn::EStructVouchPart> TStrcVouchMap

Definition at line 1750 of file srcedit_util.cpp.

TStructVoucherPart

typedef SStaticPair<const char*, CSrcStructuredVoucherPartColumn::EStructVouchPart> TStructVoucherPart

Definition at line 1742 of file srcedit_util.cpp.

Function Documentation

ApplySrcTableToSeqEntry()

CRef<CCmdComposite> ApplySrcTableToSeqEntry	(	CRef< CSeq_table >	values_table,
		CSeq_entry_Handle	seh
	)

Definition at line 2804 of file srcedit_util.cpp.

References CSerialObject::Assign(), CBioSourceAutoComplete::AutoFill(), cmd, columns, CSrcTableColumnBaseFactory::Create(), CSeqdesc_Base::e_Source, CBioseq_set_Base::eClass_nuc_prot, eExistingText_replace_old, NStr::EqualNocase(), FindSeqTableColumnByName(), CSeq_entry_Handle::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_table_Base::GetColumns(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetId(), CSeq_table_Base::GetNum_rows(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_Handle::GetParentEntry(), CBioseq_set_Handle::GetParentEntry(), CSeqdesc_CI::GetSeq_entry_Handle(), CBioseq_set_Handle::IsSetClass(), CSeq_table_Base::IsSetColumns(), ITERATE, kProblems, kSequenceIdColLabel, NULL, row, CBioSource_Base::SetOrg(), and CSeqdesc_Base::SetSource().

CompareExampleTableRows()

static int CompareExampleTableRows ( const ExampleTableData *  e1, const ExampleTableData *  e2  )

static

Definition at line 772 of file srcedit_util.cpp.

References exampletable::src_type, and exampletable::wizard_type.

Referenced by CSourceRequirements::SetExamples().

DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP	(	TStrcVouchMap	,
		sm_VouchMap	,
		s_StrVouchPartName
	)

GetPrimerSetNameValues()

string GetPrimerSetNameValues

(

const CPCRPrimerSet &

primer_set

)

Definition at line 947 of file srcedit_util.cpp.

References CPCRPrimerSet_Base::Get(), ITERATE, NStr::Join(), and names.

Referenced by GetSeqTableFromSeqEntry().

GetPrimerSetSeqValues()

string GetPrimerSetSeqValues

(

const CPCRPrimerSet &

primer_set

)

Definition at line 963 of file srcedit_util.cpp.

References CPCRPrimerSet_Base::Get(), NStr::IsBlank(), and ITERATE.

Referenced by GetSeqTableFromSeqEntry().

GetSeqTableForSrcQualFromSeqEntry()

CRef<CSeq_table> GetSeqTableForSrcQualFromSeqEntry	(	CSeq_entry_Handle	seh,
		vector< string >	qual_names
	)

Definition at line 1153 of file srcedit_util.cpp.

References CSrcTableColumnBaseFactory::Create(), CSeqdesc_Base::e_Source, CSeqTable_column_info_Base::eField_id_location_id, CSeq_inst_Base::eMol_na, CBioseq_Handle::GetSeqId(), CSeqdesc_Base::GetSource(), i, ITERATE, kSequenceIdColLabel, row, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetHeader(), and table.

GetSeqTableFromSeqEntry()

CRef<CSeq_table> GetSeqTableFromSeqEntry

(

CSeq_entry_Handle

seh

)

Definition at line 1008 of file srcedit_util.cpp.

References AddValueToTable(), CSeqdesc_Base::e_Source, CSeqTable_column_info_Base::eField_id_location_id, CBioSource_Base::eGenome_unknown, CSeq_inst_Base::eMol_na, NStr::EqualNocase(), FOR_EACH_DBXREF_ON_ORGREF, CPCRReactionSet_Base::Get(), CSeqTable_column_Base::GetData(), CBioSource_Base::GetGenome(), COrgName_Base::GetMod(), CBioSource_Base::GetOrg(), CBioSource::GetOrganelleByGenome(), CBioSource::GetOrgname(), CBioSource_Base::GetPcr_primers(), GetPrimerSetNameValues(), GetPrimerSetSeqValues(), CBioseq_Handle::GetSeqId(), CSeqdesc_Base::GetSource(), CSeqTable_multi_data_Base::GetString(), CBioSource_Base::GetSubtype(), CSubSource::GetSubtypeName(), COrgMod::GetSubtypeName(), CBioSource::GetTaxname(), set< Key, Compare >::insert(), NStr::IntToString(), NStr::IsBlank(), COrg_ref_Base::IsSetDb(), CBioSource_Base::IsSetGenome(), CBioSource_Base::IsSetOrg(), CBioSource::IsSetOrgMod(), CBioSource_Base::IsSetPcr_primers(), CBioSource_Base::IsSetSubtype(), CBioSource::IsSetTaxname(), ITERATE, NStr::Join(), JoinValues(), kDbXref, kOrgModNote, kSequenceIdColLabel, kSubSourceNote, CSubSource::NeedsNoText(), RemoveLastCharacter(), row, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetHeader(), table, tag, and val.

GetSrcRequirements()

CSourceRequirements* GetSrcRequirements	(	CSourceRequirements::EWizardType	wizard_type,
		CSourceRequirements::EWizardSrcType	source_type,
		CRef< CSeq_table >	values_table
	)

Definition at line 808 of file srcedit_util.cpp.

References CSourceRequirements::AddOneOfList(), CSourceRequirements::AddRequirement(), CSourceRequirements::AddUniquenessList(), CSourceRequirements::eWizardSrcType_animal, CSourceRequirements::eWizardSrcType_bacteria_or_archaea, CSourceRequirements::eWizardSrcType_cultured_fungus, CSourceRequirements::eWizardSrcType_plant, CSourceRequirements::eWizardSrcType_virus_foot_and_mouth, CSourceRequirements::eWizardSrcType_virus_influenza, CSourceRequirements::eWizardSrcType_virus_norovirus, CSourceRequirements::eWizardSrcType_virus_rotavirus, CSourceRequirements::eWizardSrcType_vouchered_fungus, CSourceRequirements::eWizardType_d_loop, CSourceRequirements::eWizardType_igs, CSourceRequirements::eWizardType_rrna_its_igs, CSourceRequirements::eWizardType_uncultured_samples, CSourceRequirements::eWizardType_viruses, FindSeqTableColumnByName(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetString(), kHost, CSourceRequirements::PreferentiallyAddRequirement(), row, CSourceRequirements::SetExamples(), and NStr::StartsWith().

IsExampleTableRowAcceptable()

static bool IsExampleTableRowAcceptable ( const ExampleTableData *  e1, string  field_name, CSourceRequirements::EWizardType  wizard_type, CSourceRequirements::EWizardSrcType  src_type  )

static

Definition at line 754 of file srcedit_util.cpp.

References NStr::EqualNocase(), exampletable::field_name, NULL, exampletable::src_type, and exampletable::wizard_type.

Referenced by CSourceRequirements::SetExamples().

IsFwdPrimerName()

bool IsFwdPrimerName

(

string

name

)

Definition at line 2384 of file srcedit_util.cpp.

References NStr::EqualNocase().

Referenced by CSrcTableColumnBaseFactory::Create(), CSrcTablePrimerColumn::GetPrimerColumnType(), and CPrimerTableCommandConverter::RemapColumnName().

IsFwdPrimerSeq()

bool IsFwdPrimerSeq

(

string

name

)

Definition at line 2398 of file srcedit_util.cpp.

References NStr::EqualNocase().

Referenced by CSrcTableColumnBaseFactory::Create(), CSrcTablePrimerColumn::GetPrimerColumnType(), and CPrimerTableCommandConverter::RemapColumnName().

IsRevPrimerName()

bool IsRevPrimerName

(

string

name

)

Definition at line 2391 of file srcedit_util.cpp.

References NStr::EqualNocase().

Referenced by CSrcTableColumnBaseFactory::Create(), CSrcTablePrimerColumn::GetPrimerColumnType(), and CPrimerTableCommandConverter::RemapColumnName().

IsRevPrimerSeq()

bool IsRevPrimerSeq

(

string

name

)

Definition at line 2405 of file srcedit_util.cpp.

References NStr::EqualNocase().

Referenced by CSrcTableColumnBaseFactory::Create(), CSrcTablePrimerColumn::GetPrimerColumnType(), and CPrimerTableCommandConverter::RemapColumnName().

JoinValues()

string JoinValues	(	const string &	name,
		const vector< string > &	values
	)

Definition at line 989 of file srcedit_util.cpp.

References NStr::Join().

Referenced by GetSeqTableFromSeqEntry().

OneRowOk()

static bool OneRowOk ( CRef< CSeq_id >  id, CRef< CSeqTable_column >  id_col, CSeq_entry_Handle  seh  )

static

Definition at line 2910 of file srcedit_util.cpp.

References b, CSeq_id::e_DIFF, CSeq_id::e_YES, CSeq_entry_Handle::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetId(), ITERATE, RelaxedMatch(), and row.

RelaxedMatch()

bool RelaxedMatch	(	CRef< CSeq_id >	id1,
		CRef< CSeq_id >	id2
	)

Definition at line 2885 of file srcedit_util.cpp.

References CSeq_id::eContent, NStr::EndsWith(), NStr::Equal(), NStr::Find(), CSeq_id::GetLabel(), and CSeq_id_Base::IsLocal().

Referenced by OneRowOk().

RemoveLastCharacter()

void RemoveLastCharacter

(

string &

str

)

Definition at line 981 of file srcedit_util.cpp.

References len, and str().

Referenced by GetSeqTableFromSeqEntry().

s_IsAllNumbers()

static bool s_IsAllNumbers ( string  val )

static

Definition at line 172 of file srcedit_util.cpp.

References NStr::IsBlank(), isdigit(), and val.

Referenced by COrgModQual::GetFormatErrors(), and CSubSrcQual::GetFormatErrors().

s_MakeUniquenessVal()

static string s_MakeUniquenessVal ( vector< CRef< CSeqTable_column > >  cols, size_t  row  )

static

Definition at line 362 of file srcedit_util.cpp.

References i, row, and NStr::ToUpper().

Referenced by CSourceRequirements::x_AddUniquenessProblems().

SplitValues()

void SplitValues	(	const string &	name,
		const string &	newValue,
		vector< string > &	values
	)

Definition at line 998 of file srcedit_util.cpp.

References NStr::Split().

USING_SCOPE() [1/2]

USING_SCOPE

(

edit

)

USING_SCOPE() [2/2]

USING_SCOPE

(

objects

)

Variable Documentation

k_NumExampleTableRows

const int k_NumExampleTableRows = sizeof (s_ExampleTable) / sizeof (ExampleTableData)

static

Definition at line 751 of file srcedit_util.cpp.

Referenced by CSourceRequirements::SetExamples().

nomial_keywords

const string nomial_keywords[]

static

Initial value:

= {
"f. sp. ",
"var",
"pv.",
"bv.",
"serovar",
"subsp."
}

Definition at line 1362 of file srcedit_util.cpp.

Referenced by CSrcTaxnameAfterBinomialColumn::x_GetTextAfterNomial().

s_ExampleTable

const ExampleTableData s_ExampleTable[]

static

Definition at line 653 of file srcedit_util.cpp.

Referenced by CSourceRequirements::SetExamples().

s_StrVouchPartName

const TStructVoucherPart s_StrVouchPartName[]

static

Initial value:

= {
    { "",        CSrcStructuredVoucherPartColumn::eUnknown },
    { "coll",    CSrcStructuredVoucherPartColumn::eColl },
    { "inst",    CSrcStructuredVoucherPartColumn::eInst },
    { "specid",  CSrcStructuredVoucherPartColumn::eSpecid },
}

Definition at line 1743 of file srcedit_util.cpp.