NCBI C++ ToolKit
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Search Toolkit Book for CImportFeatTable
#include <gui/packages/pkg_sequence_edit/import_feat_table.hpp>
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typedef CMatchFeatureTableDlg::TFeatSeqIDMap | TFeatSeqIDMap |
typedef CMatchFeatureTableDlg::TUniqueFeatTblIDs | TUniqueFeatTblIDs |
Public Member Functions | |
CImportFeatTable (objects::CSeq_entry_Handle seh) | |
~CImportFeatTable () | |
CIRef< IEditCommand > | ImportFeaturesFromFile (const wxString &workDir=wxEmptyString, const string &format_id=kEmptyStr) |
CIRef< IEditCommand > | ImportFeaturesFromClipboard (const wxString &workDir) |
CIRef< IEditCommand > | AddSeqAnnotToSeqEntry (const objects::CSeq_annot &orig_annot, TFeatSeqIDMap &ftbl_seqid_map, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk) |
CIRef< IEditCommand > | TestImport (const objects::CSeq_annot &orig_annot, TFeatSeqIDMap &ftbl_seqid_map, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk) |
Static Public Member Functions | |
static void | ShowTableInfo () |
Private Attributes | |
objects::CSeq_entry_Handle | m_Seh |
map< string, int > | m_OffsetForId |
string | m_Error |
bool | m_is_gff |
Definition at line 49 of file import_feat_table.hpp.
Definition at line 52 of file import_feat_table.hpp.
Definition at line 53 of file import_feat_table.hpp.
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Definition at line 55 of file import_feat_table.hpp.
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Definition at line 57 of file import_feat_table.hpp.
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CIRef< IEditCommand > CImportFeatTable::AddSeqAnnotToSeqEntry | ( | const objects::CSeq_annot & | orig_annot, |
TFeatSeqIDMap & | ftbl_seqid_map, | ||
unsigned int & | startingLocusTagNumber, | ||
unsigned int & | startingFeatureId, | ||
const string & | locus_tag, | ||
bool | euk | ||
) |
Definition at line 644 of file import_feat_table.cpp.
References _ASSERT, CCmdComposite::AddCommand(), CSeq_id::AsFastaString(), CSerialObject::Assign(), cmd, map_checker< Container >::end(), map_checker< Container >::find(), CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CSeqFeatData::GetSubtype(), NStr::IsBlank(), CSeqFeatData_Base::IsCdregion(), CSeq_annot::IsFtable(), CSeq_feat_Base::IsSetData(), m_Error, m_is_gff, m_Seh, result, s_RemapFeatureSeqIds(), CSeqFeatData::SubtypeValueToName(), x_DoImportCDS(), x_FindLocalBioseq_Handle(), and xPostProcessAnnot().
Referenced by TestImport(), and x_CreateCommand().
CIRef< IEditCommand > CImportFeatTable::ImportFeaturesFromClipboard | ( | const wxString & | workDir | ) |
Definition at line 154 of file import_feat_table.cpp.
References cmd, NStr::IsBlank(), m_Error, NULL, CGenericReportDlg::SetText(), ToWxString(), wxT, x_DoImportFeaturesFromClipboard(), and x_GatherAdditionalChanges().
Referenced by CEditingBtnsPanel::ImportFeatureTableClipboard(), and CSequenceEditingEventHandler::ImportFeatureTableClipboard().
CIRef< IEditCommand > CImportFeatTable::ImportFeaturesFromFile | ( | const wxString & | workDir = wxEmptyString , |
const string & | format_id = kEmptyStr |
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Definition at line 137 of file import_feat_table.cpp.
References cmd, NStr::IsBlank(), m_Error, NULL, CGenericReportDlg::SetText(), ToWxString(), wxT, x_DoImportFeaturesFromFile(), and x_GatherAdditionalChanges().
Referenced by CEditingBtnsPanel::ImportFeatureTable(), CSequenceEditingEventHandler::ImportFeatureTable(), CSubPrep_panel::ImportFeatureTableFile(), CSequenceEditingEventHandler::ImportGFF3(), and CSubAnnotationPanel::OnImportFeatTableClick().
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Definition at line 120 of file import_feat_table.cpp.
References kfeaturetableinstructions, NULL, and wxT.
Referenced by CSubPrep_panel::ImportFeatureTableFile().
CIRef< IEditCommand > CImportFeatTable::TestImport | ( | const objects::CSeq_annot & | orig_annot, |
TFeatSeqIDMap & | ftbl_seqid_map, | ||
unsigned int & | startingLocusTagNumber, | ||
unsigned int & | startingFeatureId, | ||
const string & | locus_tag, | ||
bool | euk | ||
) |
Definition at line 171 of file import_feat_table.cpp.
References AddSeqAnnotToSeqEntry(), cmd, and x_GatherAdditionalChanges().
Referenced by DoImportFTable().
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Definition at line 370 of file import_feat_table.cpp.
References CSeq_inst_Base::eMol_aa, CSeqFeatData::eSubtype_cdregion, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_id::GetSeqIdString(), CSeq_annot::IsFtable(), kEmptyStr, m_Seh, and msg().
Referenced by x_DoImportFeaturesFromClipboard(), and x_DoImportFeaturesFromFile().
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Definition at line 419 of file import_feat_table.cpp.
References CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_annot::IsFtable(), kEmptyStr, msg(), CSeq_id::ParseFastaIds(), and s_IsPseudo().
Referenced by x_DoImportFeaturesFromClipboard(), and x_DoImportFeaturesFromFile().
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returns true if the feature table contains at least one pair of duplicate protein/transcript ids
Definition at line 344 of file import_feat_table.cpp.
References CSeqFeatData::eSubtype_mRNA, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), and CSeq_annot::IsFtable().
Referenced by x_DoImportFeaturesFromClipboard(), and x_DoImportFeaturesFromFile().
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Definition at line 496 of file import_feat_table.cpp.
References AddSeqAnnotToSeqEntry(), cmd, CStopWatch::Elapsed(), set< Key, Compare >::empty(), CSerialObject::Equals(), ERR_POST, Error(), CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CLocusTagEukDlg::GetEuk(), CSeq_annot_Base::C_Data::GetFtable(), CMatchFeatureTableDlg::GetFtableIDToSeqIDMap(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CGene_ref_Base::GetLocus_tag(), CLocusTagEukDlg::GetLocusTag(), CSeq_feat::GetNamedQual(), CSeq_id_Handle::GetSeqId(), Info(), set< Key, Compare >::insert(), CSeq_annot::IsFtable(), CSeqFeatData_Base::IsGene(), CSeq_feat_Base::IsSetData(), CGene_ref_Base::IsSetLocus_tag(), ITERATE, LOG_POST, m_Error, m_is_gff, m_Seh, NULL, offset, result, NStr::SplitInTwo(), CStopWatch::Start(), NStr::StringToNonNegativeInt(), sw, and x_GetFixedId().
Referenced by x_DoImportFeaturesFromClipboard(), and x_DoImportFeaturesFromFile().
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Definition at line 758 of file import_feat_table.cpp.
References _ASSERT, AddProteinFeatureToProtein(), CSerialObject::Assign(), CSeq_id::BestRank(), NStr::eCase, CSeq_id::eContent, eExtreme_Biological, eExtreme_Positional, CCdregion_Base::eFrame_one, CSeq_inst_Base::eMol_aa, map_checker< Container >::end(), NStr::EndsWith(), CSeq_inst_Base::eRepr_raw, NStr::Find(), map_checker< Container >::find(), FindBestChoice(), CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), GetGeneticCodeForBioseq(), CSeq_loc::GetId(), CSeq_id::GetLabel(), CSeq_feat_Base::GetLocation(), CException::GetMsg(), CSeq_feat::GetNamedQual(), GetNewLocalProtId(), CSeq_feat_Base::GetProduct(), CSeq_feat::GetProtXref(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_loc::GetStop(), CSeq_loc_Base::GetWhole(), CSeqFeatData_Base::IsCdregion(), CSeq_id_Base::IsGenbank(), CSeq_id_Base::IsGeneral(), CSeq_id_Base::IsLocal(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), IsPseudo(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::IsSetProduct(), CSeq_loc_Base::IsWhole(), m_Error, m_OffsetForId, m_Seh, CSeq_id::Match(), NPOS, offset, CCleanup::ParseCodeBreaks(), CSeq_id::ParseFastaIds(), prot, CSeq_feat::RemoveQualifier(), s_GetIdBase(), CCdregion_Base::SetCode(), CSeq_feat_Base::SetData(), CCdregion_Base::SetFrame(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), SetMolinfoForProtein(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), NStr::StartsWith(), and CSeqTranslator::Translate().
Referenced by AddSeqAnnotToSeqEntry().
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Definition at line 283 of file import_feat_table.cpp.
References data, CTmpFile::eIfExists_ReturnCurrent, CTmpFile::eNoRemove, f, CRef< C, Locker >::GetPointer(), GUI_AsyncExecUnit(), msg(), CDirEntry::Remove(), CReportLoaderErrors::SetWorkDir(), ToWxString(), wxT, x_CheckCollidingIds(), x_CheckConsistentProteinIds(), x_ContainsDuplicateIds(), and x_CreateCommand().
Referenced by ImportFeaturesFromClipboard().
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Definition at line 212 of file import_feat_table.cpp.
References _, COpenObjectsDlg::GetObjectLoader(), CRef< C, Locker >::GetPointer(), GUI_AsyncExecUnit(), m_is_gff, msg(), NULL, IExecuteUnit::PostExecute(), IExecuteUnit::PreExecute(), CWizardDlg::SetHelpUrl(), COpenObjectsDlg::SetManagers(), CDialog::SetRegistryPath(), ToWxString(), wxT, x_CheckCollidingIds(), x_CheckConsistentProteinIds(), x_ContainsDuplicateIds(), and x_CreateCommand().
Referenced by ImportFeaturesFromFile().
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Definition at line 955 of file import_feat_table.cpp.
References CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), and m_Seh.
Referenced by AddSeqAnnotToSeqEntry().
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Definition at line 183 of file import_feat_table.cpp.
References CCmdComposite::AddCommand(), CCmdFeatIdXrefsFromQualifiers::Create(), and m_Seh.
Referenced by ImportFeaturesFromClipboard(), ImportFeaturesFromFile(), and TestImport().
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Definition at line 917 of file import_feat_table.cpp.
References CTSE_Handle::GetBioseqHandle(), CSeq_id_Handle::GetHandle(), GetId(), NStr::NumericToString(), CObject_id_Base::SetId(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), and NStr::StringToNonNegativeInt().
Referenced by x_CreateCommand().
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Definition at line 715 of file import_feat_table.cpp.
References cleanup().
Referenced by AddSeqAnnotToSeqEntry().
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Definition at line 109 of file import_feat_table.hpp.
Referenced by AddSeqAnnotToSeqEntry(), ImportFeaturesFromClipboard(), ImportFeaturesFromFile(), x_CreateCommand(), and x_DoImportCDS().
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Definition at line 110 of file import_feat_table.hpp.
Referenced by AddSeqAnnotToSeqEntry(), x_CreateCommand(), and x_DoImportFeaturesFromFile().
Definition at line 106 of file import_feat_table.hpp.
Referenced by x_DoImportCDS().
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Definition at line 104 of file import_feat_table.hpp.
Referenced by AddSeqAnnotToSeqEntry(), x_CheckCollidingIds(), x_CreateCommand(), x_DoImportCDS(), x_FindLocalBioseq_Handle(), and x_GatherAdditionalChanges().