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CImportFeatTable Class Reference

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#include <gui/packages/pkg_sequence_edit/import_feat_table.hpp>

+ Collaboration diagram for CImportFeatTable:

Public Types

typedef CMatchFeatureTableDlg::TFeatSeqIDMap TFeatSeqIDMap
 
typedef CMatchFeatureTableDlg::TUniqueFeatTblIDs TUniqueFeatTblIDs
 

Public Member Functions

 CImportFeatTable (objects::CSeq_entry_Handle seh)
 
 ~CImportFeatTable ()
 
CIRef< IEditCommandImportFeaturesFromFile (const wxString &workDir=wxEmptyString, const string &format_id=kEmptyStr)
 
CIRef< IEditCommandImportFeaturesFromClipboard (const wxString &workDir)
 
CIRef< IEditCommandAddSeqAnnotToSeqEntry (const objects::CSeq_annot &orig_annot, TFeatSeqIDMap &ftbl_seqid_map, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk)
 
CIRef< IEditCommandTestImport (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 Member Functions

CIRef< IEditCommandx_DoImportFeaturesFromFile (const wxString &workDir, const string &format_id=kEmptyStr)
 
CIRef< IEditCommandx_DoImportFeaturesFromClipboard (const wxString &workDir)
 
CIRef< IEditCommandx_CreateCommand (const IObjectLoader::TObjects &objects)
 
CIRef< IEditCommandx_DoImportCDS (CRef< objects::CSeq_feat > feat)
 
CIRef< IEditCommandx_GatherAdditionalChanges (CIRef< IEditCommand > &start_cmd)
 
objects::CBioseq_Handle x_FindLocalBioseq_Handle (const objects::CSeq_feat &feat, const objects::CTSE_Handle &tseh) const
 
objects::CSeq_id_Handle x_GetFixedId (const objects::CSeq_id &id, const objects::CTSE_Handle &tseh) const
 
bool x_ContainsDuplicateIds (const IObjectLoader::TObjects &objects)
 returns true if the feature table contains at least one pair of duplicate protein/transcript ids More...
 
string x_CheckCollidingIds (const IObjectLoader::TObjects &objects)
 
string x_CheckConsistentProteinIds (const IObjectLoader::TObjects &objects)
 
void xPostProcessAnnot (objects::CSeq_annot &annot, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk)
 
 CImportFeatTable (const CImportFeatTable &)
 
CImportFeatTableoperator= (const CImportFeatTable &)
 

Private Attributes

objects::CSeq_entry_Handle m_Seh
 
map< string, intm_OffsetForId
 
string m_Error
 
bool m_is_gff
 

Detailed Description

Definition at line 49 of file import_feat_table.hpp.

Member Typedef Documentation

◆ TFeatSeqIDMap

Definition at line 52 of file import_feat_table.hpp.

◆ TUniqueFeatTblIDs

Definition at line 53 of file import_feat_table.hpp.

Constructor & Destructor Documentation

◆ CImportFeatTable() [1/2]

CImportFeatTable::CImportFeatTable ( objects::CSeq_entry_Handle  seh)
inline

Definition at line 55 of file import_feat_table.hpp.

◆ ~CImportFeatTable()

CImportFeatTable::~CImportFeatTable ( )
inline

Definition at line 57 of file import_feat_table.hpp.

◆ CImportFeatTable() [2/2]

CImportFeatTable::CImportFeatTable ( const CImportFeatTable )
private

Member Function Documentation

◆ AddSeqAnnotToSeqEntry()

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 
)

◆ ImportFeaturesFromClipboard()

CIRef< IEditCommand > CImportFeatTable::ImportFeaturesFromClipboard ( const wxString &  workDir)

◆ ImportFeaturesFromFile()

CIRef< IEditCommand > CImportFeatTable::ImportFeaturesFromFile ( const wxString &  workDir = wxEmptyString,
const string format_id = kEmptyStr 
)

◆ operator=()

CImportFeatTable& CImportFeatTable::operator= ( const CImportFeatTable )
private

◆ ShowTableInfo()

void CImportFeatTable::ShowTableInfo ( )
static

Definition at line 120 of file import_feat_table.cpp.

References kfeaturetableinstructions, NULL, and wxT.

Referenced by CSubPrep_panel::ImportFeatureTableFile().

◆ TestImport()

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().

◆ x_CheckCollidingIds()

string CImportFeatTable::x_CheckCollidingIds ( const IObjectLoader::TObjects objects)
private

◆ x_CheckConsistentProteinIds()

string CImportFeatTable::x_CheckConsistentProteinIds ( const IObjectLoader::TObjects objects)
private

◆ x_ContainsDuplicateIds()

bool CImportFeatTable::x_ContainsDuplicateIds ( const IObjectLoader::TObjects objects)
private

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().

◆ x_CreateCommand()

CIRef< IEditCommand > CImportFeatTable::x_CreateCommand ( const IObjectLoader::TObjects objects)
private

◆ x_DoImportCDS()

CIRef< IEditCommand > CImportFeatTable::x_DoImportCDS ( CRef< objects::CSeq_feat >  feat)
private

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().

◆ x_DoImportFeaturesFromClipboard()

CIRef< IEditCommand > CImportFeatTable::x_DoImportFeaturesFromClipboard ( const wxString &  workDir)
private

◆ x_DoImportFeaturesFromFile()

CIRef< IEditCommand > CImportFeatTable::x_DoImportFeaturesFromFile ( const wxString &  workDir,
const string format_id = kEmptyStr 
)
private

◆ x_FindLocalBioseq_Handle()

CBioseq_Handle CImportFeatTable::x_FindLocalBioseq_Handle ( const objects::CSeq_feat &  feat,
const objects::CTSE_Handle &  tseh 
) const
private

◆ x_GatherAdditionalChanges()

CIRef< IEditCommand > CImportFeatTable::x_GatherAdditionalChanges ( CIRef< IEditCommand > &  start_cmd)
private

◆ x_GetFixedId()

CSeq_id_Handle CImportFeatTable::x_GetFixedId ( const objects::CSeq_id &  id,
const objects::CTSE_Handle &  tseh 
) const
private

◆ xPostProcessAnnot()

void CImportFeatTable::xPostProcessAnnot ( objects::CSeq_annot &  annot,
unsigned int startingLocusTagNumber,
unsigned int startingFeatureId,
const string locus_tag,
bool  euk 
)
private

Definition at line 715 of file import_feat_table.cpp.

References cleanup().

Referenced by AddSeqAnnotToSeqEntry().

Member Data Documentation

◆ m_Error

string CImportFeatTable::m_Error
private

◆ m_is_gff

bool CImportFeatTable::m_is_gff
private

◆ m_OffsetForId

map<string, int> CImportFeatTable::m_OffsetForId
private

Definition at line 106 of file import_feat_table.hpp.

Referenced by x_DoImportCDS().

◆ m_Seh

objects::CSeq_entry_Handle CImportFeatTable::m_Seh
private

The documentation for this class was generated from the following files:
Modified on Mon Jul 22 05:04:12 2024 by modify_doxy.py rev. 669887