Go to the source code of this file.
Go to the SVN repository for this file.
TWizardNameList GetWizardNameList () CSourceRequirements::EWizardType GetWizardTypeFromName (string wizard_name) static bool OneRowOk (CRef< objects::CSeq_id > id, CRef< objects::CSeqTable_column > id_col, objects::CSeq_entry_Handle seh) void FixTableAfterImport (CRef< objects::CSeq_table > input_table) string FindBadRows (CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst, objects::CSeq_entry_Handle seh) CRef< objects::CSeqTable_column > FindSeqIDColumn (const objects::CSeq_table &table) int FindRowForSeqId (CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id) int CountColumnRowConflicts (CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col) int CountTableColumnConflicts (CRef< objects::CSeq_table > dst, const objects::CSeq_table &src) void DeleteTableRow (CRef< objects::CSeq_table > table, int row) static void CombineColumns (CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col) int CombineTables (CRef< objects::CSeq_table > dst, const objects::CSeq_table &src) bool SaveTableFile (wxWindow *parent, wxString &save_file_dir, wxString &save_file_name, CRef< objects::CSeq_table > values_table) bool AreAllColumnValuesTheSame (CRef< objects::CSeqTable_column > col, string default_val) bool AreAnyColumnValuesMissing (CRef< objects::CSeqTable_column > col) bool DoesColumnHaveValue (CRef< objects::CSeqTable_column > col, string val) bool AreAnyColumnValuesPresent (CRef< objects::CSeqTable_column > col, string default_val) static void s_ExtendIntervalToEnd (objects::CSeq_interval &ival, objects::CBioseq_Handle bsh) bool AddProteinToSeqEntry (const objects::CSeq_entry *protein, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool create_general_only) static void s_ReportMixError () void ParseTitlesToNewSeqEntries (CRef< objects::CSeq_entry > entry) bool AddSeqEntryToSeqEntry (const objects::CSeq_entry *entry, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool &has_nuc, bool &has_prot, bool create_general_only) string CheckFeatureAnnotation (objects::CSeq_entry_Handle entry, bool &is_ok) vector< string > GetTrueFalseList () bool IsSynonymForTrue (const string &val) bool IsSynonymForFalse (const string &val) bool IsTrueFalseList (const vector< string > &choices) int AddFeatureToSeqTable (const objects::CSeq_feat &f, CRef< objects::CSeq_table > table) static bool s_OkToAddFeature (const objects::CSeq_feat &f1, const objects::CSeq_feat &f2, const TFeatureSeqTableColumnList &reqs) CRef< objects::CSeq_table > GetFeaturesFromSeqEntry (objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs) void AddFeatureSeqTableRowToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, unsigned int row, TFeatureSeqTableColumnList &vecColEditFactories, CRef< CCmdComposite > cmd) CRef< CCmdComposite > AddFeatureSeqTableToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts) void MergeStringVectors (vector< string > &problems, vector< string > add) static void AddProblemsToColumn (CRef< objects::CSeqTable_column > val_col, CRef< CFeatureSeqTableColumnBase > rule_col, vector< string > &problems) void RemoveProblemsColumn (CRef< objects::CSeq_table > values_table) CRef< CFeatureSeqTableColumnBase > GetColumnRuleForFeatureSeqTable (CRef< objects::CSeqTable_column > col, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts) void AddProblemsColumnToFeatureSeqTable (CRef< objects::CSeq_table > table, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts) bool HasLocalIntFeatureId (const objects::CSeq_feat &feat) CRef< CCmdComposite > RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry (objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs) wxString GetAsnSqnExtensions () bool IsWizardObject (const objects::CUser_object &user) CRef< objects::CUser_object > MakeWizardObject () void SetWizardFieldInSeqEntryNoUndo (objects::CSeq_entry_Handle entry, string field_name, string value) bool IsBankItSubmissionObject (const objects::CUser_object &user) CRef< objects::CUser_object > MakeBankItSubmissionObject () string GetFieldFromWizardObject (const objects::CUser_object &user, string field_name) string GetDescAlternateEmailAddress (const objects::CSeqdesc &desc) string GetAlternateEmailAddress (objects::CSeq_entry_Handle entry) void SetUserAlternateEmailAddress (objects::CUser_object &u, string alt_email) void SetAlternateEmailAddress (objects::CSeq_entry_Handle entry, string alt_email) bool IsValidEmail (string email) static void AddIdsFromSeqEntryToTable (const objects::CSeq_entry &entry, CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeqTable_column > pos_col, CRef< objects::CSeqTable_column > np_col, CRef< objects::CSeqTable_column > title_col, int &pos, size_t &row) static CRef< objects::CSeqTable_column > s_MakeIdTableIdCol () static CRef< objects::CSeqTable_column > s_MakePosCol () static CRef< objects::CSeqTable_column > s_MakeNpCol () static CRef< objects::CSeqTable_column > s_MakeTitleCol () void AddIdsFromSeqEntryToTable (const objects::CSeq_entry &entry, CRef< objects::CSeq_table > table) CRef< objects::CSeq_table > GetIdsFromSeqEntry (const objects::CSeq_entry &entry) static string GetIdValueFromColumn (CRef< objects::CSeqTable_column > id_col, int pos) CRef< objects::CSeqTable_column > GetSeqIdProblems (CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len) string SummarizeIdProblems (CRef< objects::CSeqTable_column > problems) CRef< objects::CSeqTable_column > GetReplacementSeqIds (CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len) static void TransformSeqAnnot (objects::CSeq_annot &annot, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id) static void TransformSeqAnnots (objects::CBioseq &bioseq, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id) void ApplyReplacementIds (objects::CSeq_entry &entry, CRef< objects::CSeq_table > table) bool AlreadyHasFeature (objects::CBioseq_Handle bh, string key, string comment) bool AlreadyHasFeature (objects::CBioseq_Handle bh, objects::CSeqFeatData::ESubtype subtype) ◆ AddFeatureSeqTableRowToSeqEntry()Definition at line 1182 of file subprep_util.cpp.
References cmd, e_not_set, eExistingText_replace_old, eNa_strand_minus, eNa_strand_plus, FindSeqTableColumnByName(), i, NStr::IsBlank(), ncbi::grid::netcache::search::fields::key, kFeatureID, kSequenceIdColLabel, kSkipColumns, kStartColLabel, kStopColLabel, NULL, NStr::NumericToString(), row, ncbi::grid::netcache::search::fields::size, NStr::StringToInt(), table, and wxT.
Referenced by AddFeatureSeqTableToSeqEntry().
◆ AddFeatureSeqTableToSeqEntry() ◆ AddFeatureToSeqTable() int AddFeatureToSeqTable ( const objects::CSeq_feat & f, CRef< objects::CSeq_table > table )Definition at line 1089 of file subprep_util.cpp.
References AddValueToTable(), eExtreme_Biological, NStr::EqualNocase(), f, i, ITERATE, kFeatureID, kNumSatelliteTypes, kPartialStart, kPartialStop, kSatelliteTypes, kStartColLabel, kStopColLabel, NStr::NumericToString(), row, NStr::StartsWith(), table, NStr::TruncateSpacesInPlace(), and val.
Referenced by GetFeaturesFromSeqEntry(), and CFeatureTableCommandConverter::GetValuesTableFromSeqEntry().
◆ AddIdsFromSeqEntryToTable() [1/2] void AddIdsFromSeqEntryToTable ( const objects::CSeq_entry & entry, CRef< objects::CSeq_table > table ) ◆ AddIdsFromSeqEntryToTable() [2/2] static void AddIdsFromSeqEntryToTable ( const objects::CSeq_entry & entry, CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeqTable_column > pos_col, CRef< objects::CSeqTable_column > np_col, CRef< objects::CSeqTable_column > title_col, int & pos, size_t & row ) static ◆ AddProblemsColumnToFeatureSeqTable() ◆ AddProblemsToColumn() ◆ AddProteinToSeqEntry() bool AddProteinToSeqEntry ( const objects::CSeq_entry * protein, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool create_general_only )Definition at line 719 of file subprep_util.cpp.
References AddProteinFeatureToProtein(), cmd, eContent, eExtreme_Biological, CProSplignOutputOptions::ePassThrough, CProSplign::FindAlignment(), GetNewProtId(), ITERATE, label, NULL, offset, s_ExtendIntervalToEnd(), SetMolinfoForProtein(), ToWxString(), and wxT.
Referenced by AddSeqEntryToSeqEntry().
◆ AddSeqEntryToSeqEntry() ◆ AlreadyHasFeature() [1/2] bool AlreadyHasFeature ( objects::CBioseq_Handle bh, objects::CSeqFeatData::ESubtype subtype ) ◆ AlreadyHasFeature() [2/2] bool AlreadyHasFeature ( objects::CBioseq_Handle bh, string key, string comment )Definition at line 2033 of file subprep_util.cpp.
References NStr::Equal(), NStr::EqualNocase(), f, NStr::IsBlank(), and ncbi::grid::netcache::search::fields::key.
Referenced by CBulkCDSAddPanel::AddOneCmd(), CBulkOtherAddPanel::AddOneCommand(), CBulkRNAAddPanel::AddOneCommand(), CIGSPanel::GetCommand(), CRNANamePanel::GetCommand(), CVirusNonCodingFeaturesPanel::GetCommand(), and CBulkFeatureAddDlgStd::x_CreateImportFeatures().
◆ ApplyReplacementIds() void ApplyReplacementIds ( objects::CSeq_entry & entry, CRef< objects::CSeq_table > table ) ◆ AreAllColumnValuesTheSame() bool AreAllColumnValuesTheSame ( CRef< objects::CSeqTable_column > col, string default_val )Definition at line 596 of file subprep_util.cpp.
References NStr::Equal(), NStr::IsBlank(), row, and val.
Referenced by CCommentDescriptorTableCommandConverter::CheckForMixedValues(), CChimeraCommentDescriptorTableCommandConverter::CheckForMixedValues(), CTableCommandConverter::CheckForMixedValues(), CGenomeTableCommandConverter::CheckForMixedValues(), CPrimerTableCommandConverter::CheckForMixedValues(), CSubPrep_panel::OkToBulkEditSeqTech(), CSubPrep_panel::SetWizardType(), CSubmissionPrepMainPanel::UpdateSeqTechCtrls(), and CSubPrepFieldEditor::UpdateValues().
◆ AreAnyColumnValuesMissing() bool AreAnyColumnValuesMissing ( CRef< objects::CSeqTable_column > col ) ◆ AreAnyColumnValuesPresent() bool AreAnyColumnValuesPresent ( CRef< objects::CSeqTable_column > col, string default_val ) ◆ CheckFeatureAnnotation() string CheckFeatureAnnotation ( objects::CSeq_entry_Handle entry, bool & is_ok ) ◆ CombineColumns() static void CombineColumns ( CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col ) static ◆ CombineTables() int CombineTables ( CRef< objects::CSeq_table > dst, const objects::CSeq_table & src ) ◆ CountColumnRowConflicts() int CountColumnRowConflicts ( CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col ) ◆ CountTableColumnConflicts() int CountTableColumnConflicts ( CRef< objects::CSeq_table > dst, const objects::CSeq_table & src ) ◆ DeleteTableRow() void DeleteTableRow ( CRef< objects::CSeq_table > table, int row ) ◆ DoesColumnHaveValue() bool DoesColumnHaveValue ( CRef< objects::CSeqTable_column > col, string val ) ◆ FindBadRows() string FindBadRows ( CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst, objects::CSeq_entry_Handle seh ) ◆ FindRowForSeqId() int FindRowForSeqId ( CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id ) ◆ FindSeqIDColumn() CRef<objects::CSeqTable_column> FindSeqIDColumn ( const objects::CSeq_table & table ) ◆ FixTableAfterImport() void FixTableAfterImport ( CRef< objects::CSeq_table > input_table )Definition at line 219 of file subprep_util.cpp.
References DeleteTableRow(), eContent, NStr::Equal(), NStr::EqualNocase(), FindSeqIDColumn(), NStr::IsBlank(), ITERATE, NON_CONST_ITERATE, NStr::NumericToString(), NStr::ReplaceInPlace(), ncbi::grid::netcache::search::fields::size, and val.
Referenced by CTblEditDlg::OnImportTableClick().
◆ GetAlternateEmailAddress() string GetAlternateEmailAddress ( objects::CSeq_entry_Handle entry ) ◆ GetAsnSqnExtensions() wxString GetAsnSqnExtensions ( ) ◆ GetColumnRuleForFeatureSeqTable() ◆ GetDescAlternateEmailAddress() string GetDescAlternateEmailAddress ( const objects::CSeqdesc & desc ) ◆ GetFeaturesFromSeqEntry() ◆ GetFieldFromWizardObject() string GetFieldFromWizardObject ( const objects::CUser_object & user, string field_name ) ◆ GetIdsFromSeqEntry() CRef<objects::CSeq_table> GetIdsFromSeqEntry ( const objects::CSeq_entry & entry ) ◆ GetIdValueFromColumn() ◆ GetReplacementSeqIds() CRef<objects::CSeqTable_column> GetReplacementSeqIds ( CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len )Definition at line 1873 of file subprep_util.cpp.
References eContent, NStr::EqualNocase(), FindNonUniqueStrings(), FindSeqTableColumnByName(), i, ITERATE, kSequenceIdColLabel, log, NULL, NStr::NumericToString(), offset, CRef< C, Locker >::Reset(), NStr::StartsWith(), str(), and NStr::StringToInt().
◆ GetSeqIdProblems() CRef<objects::CSeqTable_column> GetSeqIdProblems ( CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len )Definition at line 1769 of file subprep_util.cpp.
References eContent, NStr::EqualNocase(), FindNonUniqueStrings(), FindSeqTableColumnByName(), GetIdValueFromColumn(), i, NStr::IsBlank(), ITERATE, kIdDuplicate, kIdMissing, kIdTooLong, kNewId, kSequenceIdColLabel, NULL, CRef< C, Locker >::Reset(), str(), and val.
Referenced by CAddSequences::apply(), CSeqIdFixDlg::CreateControls(), CSeqIdFixDlg::GetReplacementTable(), CSubPrep_panel::OnAddSequenceBtnClick(), and CSeqIdFixDlg::x_RefreshProblems().
◆ GetTrueFalseList() vector<string> GetTrueFalseList ( ) ◆ GetWizardNameList() ◆ GetWizardTypeFromName() ◆ HasLocalIntFeatureId() bool HasLocalIntFeatureId ( const objects::CSeq_feat & feat ) ◆ IsBankItSubmissionObject() bool IsBankItSubmissionObject ( const objects::CUser_object & user ) ◆ IsSynonymForFalse() ◆ IsSynonymForTrue() ◆ IsTrueFalseList() ◆ IsValidEmail() ◆ IsWizardObject() bool IsWizardObject ( const objects::CUser_object & user ) ◆ MakeBankItSubmissionObject() CRef<objects::CUser_object> MakeBankItSubmissionObject ( ) ◆ MakeWizardObject() CRef<objects::CUser_object> MakeWizardObject ( ) ◆ MergeStringVectors() void MergeStringVectors ( vector< string > & problems, vector< string > add ) ◆ OneRowOk() static bool OneRowOk ( CRef< objects::CSeq_id > id, CRef< objects::CSeqTable_column > id_col, objects::CSeq_entry_Handle seh ) static ◆ ParseTitlesToNewSeqEntries() void ParseTitlesToNewSeqEntries ( CRef< objects::CSeq_entry > entry ) ◆ RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry() ◆ RemoveProblemsColumn() void RemoveProblemsColumn ( CRef< objects::CSeq_table > values_table ) ◆ s_ExtendIntervalToEnd() static void s_ExtendIntervalToEnd ( objects::CSeq_interval & ival, objects::CBioseq_Handle bsh ) static ◆ s_MakeIdTableIdCol() static CRef<objects::CSeqTable_column> s_MakeIdTableIdCol ( ) static ◆ s_MakeNpCol() static CRef<objects::CSeqTable_column> s_MakeNpCol ( ) static ◆ s_MakePosCol() static CRef<objects::CSeqTable_column> s_MakePosCol ( ) static ◆ s_MakeTitleCol() static CRef<objects::CSeqTable_column> s_MakeTitleCol ( ) static ◆ s_OkToAddFeature() ◆ s_ReportMixError() static void s_ReportMixError ( ) static ◆ SaveTableFile() bool SaveTableFile ( wxWindow * parent, wxString & save_file_dir, wxString & save_file_name, CRef< objects::CSeq_table > values_table )Definition at line 533 of file subprep_util.cpp.
References eContent, CCSVExporter::Field(), CFileExtensions::GetDialogFilter(), i, ITERATE, CFileExtensions::kAllFiles, CFileExtensions::kTable, label, CCSVExporter::NewRow(), out(), and wxT.
Referenced by CAssemblyTrackingPanel::OnExportIntervalsBtnClick(), and CTblEditDlg::OnExportTableClick().
◆ SetAlternateEmailAddress() void SetAlternateEmailAddress ( objects::CSeq_entry_Handle entry, string alt_email ) ◆ SetUserAlternateEmailAddress() void SetUserAlternateEmailAddress ( objects::CUser_object & u, string alt_email ) ◆ SetWizardFieldInSeqEntryNoUndo() void SetWizardFieldInSeqEntryNoUndo ( objects::CSeq_entry_Handle entry, string field_name, string value ) ◆ SummarizeIdProblems() string SummarizeIdProblems ( CRef< objects::CSeqTable_column > problems ) ◆ TransformSeqAnnot() static void TransformSeqAnnot ( objects::CSeq_annot & annot, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id ) static ◆ TransformSeqAnnots() static void TransformSeqAnnots ( objects::CBioseq & bioseq, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id ) static ◆ k_NumWizardNames ◆ kBankItAltEmailPrefix ◆ kBankitSubmissionLabel ◆ kIdDuplicate ◆ kIdMissing ◆ kIdTooLong ◆ kSMARTComment ◆ s_WizardNamesRetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4