NCBI C++ ToolKit
Functions
seqtable_util.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objects/seqtable/Seq_table.hpp>
#include <objects/seqtable/SeqTable_column.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objtools/edit/seqid_guesser.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
+ Include dependency graph for seqtable_util.hpp:
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Go to the source code of this file.

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Functions

 USING_SCOPE (ncbi::objects)
 
void RemoveRowsFromColumn (CRef< CSeqTable_column > col, const vector< size_t > &rows)
 
void RemoveRowsFromTable (CRef< CSeq_table > table, const vector< size_t > &rows)
 
void RemoveTableRowsThatDoNotMatchStringConstraint (CRef< CSeq_table > table, const string &field, CRef< edit::CStringConstraint > string_constraint)
 
void ApplyToTable (CRef< CSeq_table > table, const string &field, const string &val, edit::EExistingText existing_text=edit::eExistingText_replace_old)
 
void RemoveFromTable (CRef< CSeq_table > table, const string &field)
 
void ConvertTableColumns (CRef< CSeq_table > table, const string &field1, const string &field2, edit::EExistingText existing_text)
 
void SwapTableColumns (CRef< CSeq_table > table, const string &field1, const string &field2)
 
void CopyTableColumns (CRef< CSeq_table > table, const string &field1, const string &field2, edit::EExistingText existing_text)
 
CRef< CSeqTable_column > FindSeqTableColumnByName (CRef< objects::CSeq_table > values_table, string column_name)
 
bool RemoveSeqTableColumnByName (CRef< objects::CSeq_table > table, string column_name)
 
void AddValueToColumn (CRef< CSeqTable_column > column, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)
 
void AddValueToTable (CRef< CSeq_table > table, string subtype_name, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)
 
void AddValueToTable (CRef< CSeq_table > table, string subtype_name, int value, size_t row)
 
void SetColumnValue (CRef< CSeqTable_column > col, string val)
 
CRef< CSeqTable_column > AddStringColumnToTable (CRef< CSeq_table > table, string label)
 
CRef< CSeqTable_column > AddIntColumnToTable (CRef< CSeq_table > table, string label)
 
bool QualifierNamesAreEquivalent (string name1, string name2)
 
bool MatchColumnName (string name1, string name2)
 
bool IsOrgColumnName (string name)
 
bool IsSubSourceNoteName (const string &name)
 
bool IsOrgModNoteName (const string &name)
 
int CountColumnValueConflicts (CRef< CSeqTable_column > column1, CRef< CSeqTable_column > column2)
 
void FillShortColumns (CRef< objects::CSeq_table > values_table)
 

Function Documentation

◆ AddIntColumnToTable()

CRef<CSeqTable_column> AddIntColumnToTable ( CRef< CSeq_table >  table,
string  label 
)

Referenced by GetFeaturesFromSeqEntry().

◆ AddStringColumnToTable()

CRef<CSeqTable_column> AddStringColumnToTable ( CRef< CSeq_table >  table,
string  label 
)

Referenced by AddColumnsToFeatureTable(), AddMiscColumnsToTable(), BuildFeatureSeqTableFromSeqEntry(), GetFeaturesFromSeqEntry(), GetMiscTableFromSeqEntry(), CBulkCDS::GetValuesTableFromSeqEntry(), CBulkGene::GetValuesTableFromSeqEntry(), CBulkMiscFeat::GetValuesTableFromSeqEntry(), and CBulkRna::GetValuesTableFromSeqEntry().

◆ AddValueToColumn()

void AddValueToColumn ( CRef< CSeqTable_column >  column,
string  value,
size_t  row,
edit::EExistingText  existing_text = edit::eExistingText_replace_old 
)

Referenced by AddColumnsToFeatureTable(), AddMiscColumnsToTable(), AddToFeatureIdColumn(), GetMiscTableFromSeqEntry(), CBulkCDS::GetValuesTableFromSeqEntry(), CBulkGene::GetValuesTableFromSeqEntry(), CBulkMiscFeat::GetValuesTableFromSeqEntry(), and CBulkRna::GetValuesTableFromSeqEntry().

◆ AddValueToTable() [1/2]

void AddValueToTable ( CRef< CSeq_table >  table,
string  subtype_name,
int  value,
size_t  row 
)

◆ AddValueToTable() [2/2]

void AddValueToTable ( CRef< CSeq_table >  table,
string  subtype_name,
string  value,
size_t  row,
edit::EExistingText  existing_text = edit::eExistingText_replace_old 
)

Referenced by AddFeatureToSeqTable(), BuildDBLinkValuesTableFromSeqEntry(), CSequenceEditingEventHandler::ExportStructuredCommentsTable(), GetSeqTableFromSeqEntry(), CDBLinkTableCommandConverter::GetValuesTableFromSeqEntry(), and CStructuredCommentCommandConverter::GetValuesTableFromSeqEntry().

◆ ApplyToTable()

void ApplyToTable ( CRef< CSeq_table >  table,
const string &  field,
const string &  val,
edit::EExistingText  existing_text = edit::eExistingText_replace_old 
)

Definition at line 183 of file seqtable_util.cpp.

References AddValueToColumn(), column, FindSeqTableColumnByName(), row, table, and val.

◆ ConvertTableColumns()

void ConvertTableColumns ( CRef< CSeq_table >  table,
const string &  field1,
const string &  field2,
edit::EExistingText  existing_text 
)

Definition at line 208 of file seqtable_util.cpp.

References AddValueToColumn(), FindSeqTableColumnByName(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetString(), NStr::IsBlank(), orig, row, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetHeader(), ncbi::grid::netcache::search::fields::size, and table.

◆ CopyTableColumns()

void CopyTableColumns ( CRef< CSeq_table >  table,
const string &  field1,
const string &  field2,
edit::EExistingText  existing_text 
)

Definition at line 261 of file seqtable_util.cpp.

References AddValueToColumn(), FindSeqTableColumnByName(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetString(), NStr::IsBlank(), orig, row, CSeqTable_column_Base::SetHeader(), ncbi::grid::netcache::search::fields::size, and table.

◆ CountColumnValueConflicts()

int CountColumnValueConflicts ( CRef< CSeqTable_column >  column1,
CRef< CSeqTable_column >  column2 
)

Definition at line 504 of file seqtable_util.cpp.

References NStr::Equal(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetInt(), CSeqTable_multi_data_Base::GetString(), NStr::IsBlank(), CSeqTable_multi_data_Base::IsInt(), CSeqTable_column_Base::IsSetData(), and CSeqTable_multi_data_Base::IsString().

◆ FillShortColumns()

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

Definition at line 544 of file seqtable_util.cpp.

References NON_CONST_ITERATE.

Referenced by AddColumnsToFeatureTable(), AddMiscColumnsToTable(), BuildFeatureSeqTableFromSeqEntry(), CSequenceEditingEventHandler::ExportStructuredCommentsTable(), GetMiscTableFromSeqEntry(), CDBLinkTableCommandConverter::GetValuesTableFromSeqEntry(), CCommentDescriptorTableCommandConverter::GetValuesTableFromSeqEntry(), CChimeraCommentDescriptorTableCommandConverter::GetValuesTableFromSeqEntry(), CMolInfoTableCommandConverter::GetValuesTableFromSeqEntry(), CGenomeTableCommandConverter::GetValuesTableFromSeqEntry(), CPrimerTableCommandConverter::GetValuesTableFromSeqEntry(), CFeatureTableCommandConverter::GetValuesTableFromSeqEntry(), and CTblEditDlg::OnUpdateProblems().

◆ FindSeqTableColumnByName()

CRef<CSeqTable_column> FindSeqTableColumnByName ( CRef< objects::CSeq_table >  values_table,
string  column_name 
)

Definition at line 282 of file seqtable_util.cpp.

References ctll::empty(), ITERATE, and MatchColumnName().

Referenced by CSourceRequirements::AddColumnsToSeqTable(), AddFeatureSeqTableRowToSeqEntry(), AddIdsFromSeqEntryToTable(), AddIntColumnToTable(), AddStringColumnToTable(), ApplyChimeraValuesTableToSeqEntry(), ApplyCommentValuesTableToSeqEntry(), ApplyDBLinkValuesTableToSeqEntry(), ApplyMolInfoValuesTableToSeqEntry(), ApplyReplacementIds(), ApplySrcTableToSeqEntry(), SrcEditDialog::ApplySrcTableToSeqEntry(), ApplyToTable(), CCommentDescriptorTableCommandConverter::CheckForMixedValues(), CChimeraCommentDescriptorTableCommandConverter::CheckForMixedValues(), CTableCommandConverter::CheckForMixedValues(), CGenomeTableCommandConverter::CheckForMixedValues(), CPrimerTableCommandConverter::CheckForMixedValues(), CSourceRequirements::CheckSourceQuals(), SrcEditDialog::CombineTables(), CombineTables(), ConvertTableColumns(), CopyTableColumns(), SrcEditDialog::CountTableColumnConflicts(), CountTableColumnConflicts(), CSeqIdFixDlg::CreateControls(), CSubmissionPrepMainPanel::CreateVirusMoleculeOptions(), CPrimerTableCommandConverter::GetCommandFromValuesTable(), CStructuredCommentCommandConverter::GetCommandFromValuesTable(), GetReplacementSeqIds(), CSeqTableGrid::GetRowLabelValue(), GetSeqIdProblems(), GetSrcRequirements(), CPrimerTableCommandConverter::GetValuesTableFromSeqEntry(), CFeatureTableCommandConverter::GetValuesTableFromSeqEntry(), CSourceRequirements::PreferentiallyAddRequirement(), RemoveFromTable(), RemoveTableRowsThatDoNotMatchStringConstraint(), CSubPrep_panel::SetWizardType(), SwapTableColumns(), CSubPrepFieldEditor::UpdateValues(), CSourceRequirements::x_AddOneOfProblems(), CSourceRequirements::x_AddUniquenessProblems(), CSubPrep_panel::x_CheckSourceQuals(), CSubPrep_panel::x_GetSequenceLengths(), CSubPrep_panel::x_NeedUniqueMicrosatelliteNames(), CSeqIdFixDlg::x_RefreshProblems(), and CSubPrepFieldEditor::x_SetOneValue().

◆ IsOrgColumnName()

bool IsOrgColumnName ( string  name)

Definition at line 461 of file seqtable_util.cpp.

References NStr::EqualNocase().

Referenced by CSourceRequirements::AddRequirement(), CFieldChoicePanel::AutoMatchSrc(), and MatchColumnName().

◆ IsOrgModNoteName()

bool IsOrgModNoteName ( const string &  name)

Definition at line 487 of file seqtable_util.cpp.

References NStr::EqualNocase().

Referenced by CFieldChoicePanel::AutoMatchSrc().

◆ IsSubSourceNoteName()

bool IsSubSourceNoteName ( const string &  name)

Definition at line 474 of file seqtable_util.cpp.

References NStr::EqualNocase().

Referenced by CFieldChoicePanel::AutoMatchSrc().

◆ MatchColumnName()

bool MatchColumnName ( string  name1,
string  name2 
)

Definition at line 441 of file seqtable_util.cpp.

References NStr::Find(), IsOrgColumnName(), and QualifierNamesAreEquivalent().

Referenced by CSourceRequirements::AddRequirement(), FindSeqTableColumnByName(), GetColumnRuleForFeatureSeqTable(), RemoveSeqTableColumnByName(), and CSubPrepFieldEditor::UpdateValues().

◆ QualifierNamesAreEquivalent()

bool QualifierNamesAreEquivalent ( string  name1,
string  name2 
)

Definition at line 415 of file seqtable_util.cpp.

References NStr::EqualNocase(), NStr::ReplaceInPlace(), and NStr::StartsWith().

Referenced by CFieldChoicePanel::AutoMatchCGP(), CFieldChoicePanel::AutoMatchDBLink(), CFieldChoicePanel::AutoMatchFeat(), CFieldChoicePanel::AutoMatchMisc(), CFieldChoicePanel::AutoMatchMolInfo(), CFieldChoicePanel::AutoMatchPub(), CFieldChoicePanel::AutoMatchRNA(), BOOST_AUTO_TEST_CASE(), CConvertGeneToImp::Convert(), CFieldHandlerFactory::Create(), CFeatureSeqTableColumnBaseFactory::Create(), CSatelliteColumn::CSatelliteColumn(), CMolInfoFieldType::GetBiomolFromLabel(), CMolInfoFieldType::GetCompletenessFromLabel(), CSourceFieldNamePanel::GetMacroFieldName(), CMolInfoFieldType::GetMolFromLabel(), CMolInfoFieldType::GetReprFromLabel(), CPubFieldType::GetStatusFromString(), CMolInfoFieldType::GetStrandFromLabel(), CMolInfoFieldType::GetTechFromLabel(), CMolInfoFieldType::GetTopologyFromLabel(), MatchColumnName(), CMiscSeqTableColumn::s_IsSequenceIDField(), CGeneFieldPanel::SetFieldName(), CMiscFieldPanel::SetFieldName(), CProteinFieldPanel::SetFieldName(), CCDSGeneProtFieldNamePanel::SetFieldName(), CFieldHandlerNamePanel::SetFieldName(), CSourceFieldNamePanel::SetFieldName(), CMacroEditorContext::x_GetAsnPathToBsrcText(), CGeneRefColumn::x_GetFieldTypeFromString(), and CProtRefColumn::x_GetFieldTypeFromString().

◆ RemoveFromTable()

void RemoveFromTable ( CRef< CSeq_table >  table,
const string &  field 
)

Definition at line 197 of file seqtable_util.cpp.

References AddValueToColumn(), column, FindSeqTableColumnByName(), row, and table.

◆ RemoveRowsFromColumn()

void RemoveRowsFromColumn ( CRef< CSeqTable_column >  col,
const vector< size_t > &  rows 
)

Definition at line 41 of file seqtable_util.cpp.

References CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::IsBit(), CSeqTable_multi_data_Base::IsBytes(), CSeqTable_multi_data_Base::IsId(), CSeqTable_multi_data_Base::IsInt(), CSeqTable_multi_data_Base::IsReal(), CSeqTable_multi_data_Base::IsString(), and CSeqTable_column_Base::SetData().

Referenced by RemoveRowsFromTable().

◆ RemoveRowsFromTable()

void RemoveRowsFromTable ( CRef< CSeq_table >  table,
const vector< size_t > &  rows 
)

Definition at line 125 of file seqtable_util.cpp.

References NON_CONST_ITERATE, RemoveRowsFromColumn(), and table.

Referenced by RemoveTableRowsThatDoNotMatchStringConstraint().

◆ RemoveSeqTableColumnByName()

bool RemoveSeqTableColumnByName ( CRef< objects::CSeq_table >  table,
string  column_name 
)

Definition at line 295 of file seqtable_util.cpp.

References MatchColumnName(), and table.

◆ RemoveTableRowsThatDoNotMatchStringConstraint()

void RemoveTableRowsThatDoNotMatchStringConstraint ( CRef< CSeq_table >  table,
const string &  field,
CRef< edit::CStringConstraint >  string_constraint 
)

Definition at line 136 of file seqtable_util.cpp.

References column, FindSeqTableColumnByName(), NStr::NumericToString(), RemoveRowsFromTable(), row, and table.

◆ SetColumnValue()

void SetColumnValue ( CRef< CSeqTable_column >  col,
string  val 
)

Referenced by CSubPrep_panel::SetWizardType().

◆ SwapTableColumns()

void SwapTableColumns ( CRef< CSeq_table >  table,
const string &  field1,
const string &  field2 
)

Definition at line 230 of file seqtable_util.cpp.

References FindSeqTableColumnByName(), CSeqTable_column_Base::GetData(), CSeqTable_multi_data_Base::GetString(), row, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetHeader(), ncbi::grid::netcache::search::fields::size, and table.

◆ USING_SCOPE()

USING_SCOPE ( ncbi::objects  )
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