NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
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::EStructVouchPartTStructVoucherPart
 
typedef CStaticArrayMap< string, CSrcStructuredVoucherPartColumn::EStructVouchPartTStrcVouchMap
 

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)
 
CSourceRequirementsGetSrcRequirements (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_tableGetSeqTableFromSeqEntry (CSeq_entry_Handle seh)
 
CRef< CSeq_tableGetSeqTableForSrcQualFromSeqEntry (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< CCmdCompositeApplySrcTableToSeqEntry (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

◆ TStrcVouchMap

Definition at line 1750 of file srcedit_util.cpp.

◆ 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 
)

◆ CompareExampleTableRows()

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

◆ 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 
)

◆ GetSeqTableFromSeqEntry()

CRef<CSeq_table> GetSeqTableFromSeqEntry ( CSeq_entry_Handle  seh)

◆ GetSrcRequirements()

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

◆ IsExampleTableRowAcceptable()

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

◆ IsFwdPrimerName()

bool IsFwdPrimerName ( string  name)

◆ IsFwdPrimerSeq()

bool IsFwdPrimerSeq ( string  name)

◆ IsRevPrimerName()

bool IsRevPrimerName ( string  name)

◆ IsRevPrimerSeq()

bool IsRevPrimerSeq ( string  name)

◆ 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

◆ RelaxedMatch()

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

◆ 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
Modified on Wed May 29 18:37:46 2024 by modify_doxy.py rev. 669887