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NCBI C++ ToolKit: include/gui/packages/pkg_sequence_edit/srcedit_util.hpp Source File

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vector<string>

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objects::CBioSource & biosrc )

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User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static string GetSubtypeName(const CSubSource &qual)

CGenomeQual()

Constructors.

virtual ~CGenomeQual()

Destructor.

virtual string GetValue(const objects::CBioSource &src)

virtual string GetFormatErrors(string value)

CGenomeQual(string name, bool required, bool report_missing=false, string example="")

objects::COrgMod::TSubtype m_Subtype

virtual ~COrgModQual()

Destructor.

COrgModQual()

Constructors.

virtual string GetValue(const objects::CBioSource &src)

virtual string GetFormatErrors(string value)

@OrgMod.hpp User-defined methods of the data storage class.

void AddColumnsToSeqTable(CRef< objects::CSeq_table > values_table)

void x_AddOneOfProblems(CRef< objects::CSeq_table >, vector< string > one_of_list, CRef< objects::CSeqTable_column > problems)

int x_AddUniquenessProblems(CRef< objects::CSeq_table > values_table, vector< string > uniqueness_list, vector< string > &row_problems)

void SetExamples(EWizardType wizard_type, EWizardSrcType src_type)

@ eWizardSrcType_cultured_fungus

@ eWizardSrcType_virus_norovirus

@ eWizardSrcType_virus_foot_and_mouth

@ eWizardSrcType_bacteria_or_archaea

@ eWizardSrcType_uncultured_fungus

@ eWizardSrcType_virus_influenza

@ eWizardSrcType_vouchered_fungus

@ eWizardSrcType_virus_rotavirus

CSourceRequirements()

Constructors.

virtual ~CSourceRequirements()

Destructor.

void AddUniquenessList(vector< string > list)

void AddOneOfList(vector< string > list)

TSrcQualList m_Requirements

vector< vector< string > > m_UniquenessLists

void AddRequirement(string name, bool required, string example="")

vector< vector< string > > m_OneOfLists

@ eWizardType_uncultured_samples

@ eWizardType_microsatellite

@ eWizardType_rrna_its_igs

void PreferentiallyAddRequirement(CRef< objects::CSeq_table > values_table, string choice1, string choice2, bool required)

CRef< objects::CSeqTable_column > CheckSourceQuals(CRef< objects::CSeq_table > values_table)

void SetReportMissing(bool report_missing)

virtual string GetFormatErrors(string value)

void SetExample(string example)

virtual ~CSrcQual()

Destructor.

void SetRequired(bool required)

virtual string GetExample()

virtual string GetValue(const objects::CBioSource &src)

void x_ParsePartsFromStructuredVoucher(const string &qualifier, string &inst, string &coll, string &id) const

virtual string GetLabel() const

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &src) const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

CSrcStructuredVoucherPartColumn(objects::COrgMod::TSubtype subtype, EStructVouchPart epart)

static const string & GetName_StrVoucherPart(EStructVouchPart stype_part)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

EStructVouchPart m_SubtypePart

static EStructVouchPart GetStrVoucherPart_FromName(const string &name)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual bool AllowMultipleValues()

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &src) const

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &src) const

CSrcTableAllPrimersColumn()

virtual bool AllowMultipleValues()

static CRef< CSrcTableColumnBase > Create(const objects::CSeqTable_column &column)

virtual string GetLabel() const

virtual void SetConstraint(const string &field_name, CConstRef< edit::CStringConstraint > string_constraint)

virtual vector< string > IsValid(const vector< string > &values)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &src) const

vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(CBioseq_Handle bsh)

string GetVal(const CObject &object)

vector< string > GetVals(const CObject &object)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const =0

vector< CConstRef< CObject > > GetObjects(CBioseq_Handle bsh)

void SetSourceType(ESourceType type)

void ClearVal(CObject &object)

virtual bool AllowMultipleValues()

virtual bool AddToBioSource(objects::CBioSource &in_out_bioSource, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual bool AllowMultipleValues()

CSrcTableDbxrefColumn(const string &db_name=kEmptyStr)

virtual bool AddToBioSource(objects::CBioSource &in_out_bioSource, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

CSrcTableFwdPrimerNameColumn()

virtual string GetLabel() const

virtual string GetLabel() const

CSrcTableFwdPrimerSeqColumn()

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual vector< string > IsValid(const vector< string > &values)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetLabel() const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

CSrcTableGenomeColumn(const string &organelle=kEmptyStr)

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetLabel() const

virtual bool AllowMultipleValues()

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

CSrcTableOrgModColumn(objects::COrgMod::TSubtype subtype)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

objects::COrgMod::TSubtype m_Subtype

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetLabel() const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetLabel() const

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual vector< string > IsValid(const vector< string > &values)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual vector< string > GetValsFromBioSource(const CBioSource &src) const

bool x_ApplyStringToReaction(const string &val, CPCRReaction &reaction, objects::edit::EExistingText existing_text)

bool x_DoesPrimerSetHaveSpace(const CPCRPrimerSet &set)

bool x_DoesReactionMatchConstraint(const CPCRReaction &reaction) const

bool x_ApplyStringToSrc(const string &val, CBioSource &src, objects::edit::EExistingText existing_text)

virtual void SetConstraint(const string &field_name, CConstRef< edit::CStringConstraint > string_constraint)

bool x_AddFieldToPrimerSet(const string &val, CPCRPrimerSet &set)

virtual bool AllowMultipleValues()

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

bool x_ApplyStringToPrimerSet(const string &val, CPCRPrimerSet &set, objects::edit::EExistingText existing_text)

bool x_DoesReactionHaveSpace(const CPCRReaction &reaction)

void x_RemoveEmptyValues(CBioSource &src)

static EPrimerColType GetPrimerColumnType(const string &field_name)

virtual void ClearInBioSource(objects::CBioSource &src)

virtual string GetFromBioSource(const objects::CBioSource &src) const

CSrcTablePrimerColumn(EPrimerColType col_type)

CRef< edit::CStringConstraint > m_StringConstraint

EPrimerColType m_ConstraintCol

vector< string > x_GetValues(EPrimerColType col, const CBioSource &src) const

virtual string GetLabel() const

CSrcTableRevPrimerNameColumn()

CSrcTableRevPrimerSeqColumn()

virtual string GetLabel() const

objects::CSubSource::TSubtype m_Subtype

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetLabel() const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual bool AllowMultipleValues()

CSrcTableSubSourceColumn(objects::CSubSource::TSubtype subtype)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual bool AddToBioSource(objects::CBioSource &in_out_bioSource, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual string GetLabel() const

string x_GetTextAfterNomial(const string &taxname) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetLabel() const

vector< string > m_BadIsolationSourceValues

objects::CSubSource::TSubtype m_Subtype

virtual string GetFormatErrors(string value)

virtual ~CSubSrcQual()

Destructor.

CSubSrcQual()

Constructors.

virtual string GetValue(const objects::CBioSource &src)

CTaxnameQual()

Constructors.

CTaxnameQual(string name, bool required, bool report_missing=false, string example="")

virtual string GetValue(const objects::CBioSource &src)

virtual string GetFormatErrors(string value)

virtual ~CTaxnameQual()

Destructor.

CUnculturedTaxnameQual(string name, bool required, bool report_missing=false, string example="")

CUnculturedTaxnameQual()

Constructors.

virtual ~CUnculturedTaxnameQual()

Destructor.

virtual string GetFormatErrors(string value)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char * column

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

fallback to Cassandra storage</td > n</tr > n</table > n</td > n< td > no and not provided</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> exclude_blobs</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> A comma separated list of blob identifiers which client already has If provided then n if the resolution of sequence identifier sequence identifier type matches one of the n blob identifiers in the list then the blob will not be sent The format of the blob n identifier depends on a processor For example

const GenericPointer< typename T::ValueType > T2 value

vector< CSrcQual * > TSrcQualList

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

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

bool IsFwdPrimerSeq(string name)

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

bool IsRevPrimerSeq(string name)

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

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

bool IsFwdPrimerName(string name)

bool IsRevPrimerName(string name)

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