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enum ECoreDataType { eUndefined = 0 , eSubmit , eEntry , eTbl } enum EProblem {Definition at line 168 of file read_blast_result.hpp.
◆ EProblem Enumerator eOverlap eCompleteOverlap ePartial eFrameShift eMayBeNotFrameShift eRnaOverlap eTRNAMissing eTRNABadStrand eTRNAComMismatch eTRNAMismatch eTRNAAbsent eRemoveOverlap eTRNAUndefStrand eShortProtein eRelFrameShift eTRNAProblems eAllProblemsDefinition at line 135 of file read_blast_result.hpp.
◆ addProblems() ◆ diagName() ◆ Get3type()Definition at line 115 of file shortcuts.cpp.
References CTrna_ext_Base::C_Aa::e_Iupacaa, CTrna_ext_Base::C_Aa::e_Ncbi8aa, CTrna_ext_Base::C_Aa::e_Ncbieaa, CTrna_ext_Base::C_Aa::e_Ncbistdaa, ERR_POST, Error(), let1_2_let3(), MSerial_AsnText, NCBI_USER_THROW, NcbiCerr, NcbiEndl, rna, and type.
Referenced by CReadBlastApp::CollectSimpleSeqs(), and CReadBlastApp::overlaps_na().
◆ get_my_feat_type()Definition at line 246 of file shortcuts.cpp.
References CTrna_ext_Base::CanGetAa(), CRNA_ref_Base::CanGetExt(), CRNA_ref_Base::CanGetPseudo(), CRNA_ref_Base::CanGetType(), eMyFeatureType_atypical_tRNA, eMyFeatureType_miscRNA, eMyFeatureType_normal_tRNA, eMyFeatureType_pseudo_tRNA, eMyFeatureType_rRNA, eMyFeatureType_unknown, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_rRNA, CRNA_ref_Base::eType_tRNA, CTrna_ext_Base::GetAa(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), GetLocusTag(), CTrna_ext_Base::C_Aa::GetNcbieaa(), CRNA_ref_Base::GetPseudo(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::GetTRNA(), CRNA_ref_Base::GetType(), CTrna_ext_Base::C_Aa::IsNcbieaa(), CSeqFeatData_Base::IsRna(), CRNA_ref_Base::C_Ext::IsTRNA(), NcbiCerr, NcbiEndl, and CReadBlastApp::PrintDetails().
Referenced by CReadBlastApp::overlaps_prot_na().
◆ get_my_seq_type() ◆ get_parent_seqset()Definition at line 379 of file read_blast_result_lib.cpp.
References CBioseq_set_Base::CanGetSeq_set(), CBioseq::GetParentEntry(), CSeq_entry::GetParentEntry(), CSeq_entry_Base::GetSet(), GetStringDescr(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), NcbiCerr, NULL, CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
Referenced by CReadBlastApp::get_nucleotide_seq(), CReadBlastApp::overlaps(), CReadBlastApp::overlaps_prot_na(), and CReadBlastApp::short_proteins().
◆ get_title() ◆ get_trna_string()Definition at line 197 of file shortcuts.cpp.
References CTrna_ext_Base::CanGetAa(), CRNA_ref_Base::CanGetExt(), CRNA_ref_Base::CanGetPseudo(), CRNA_ref_Base::CanGetType(), CRNA_ref_Base::eType_tRNA, CTrna_ext_Base::GetAa(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CTrna_ext_Base::C_Aa::GetNcbieaa(), CRNA_ref_Base::GetPseudo(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::GetTRNA(), CRNA_ref_Base::GetType(), CTrna_ext_Base::C_Aa::IsNcbieaa(), CSeqFeatData_Base::IsRna(), and CRNA_ref_Base::C_Ext::IsTRNA().
Referenced by CReadBlastApp::overlaps_prot_na().
◆ GetLocationString() [1/2] ◆ GetLocationString() [2/2]template<typename interval_type >
◆ GetLocusTag()Definition at line 328 of file read_blast_result_lib.cpp.
References map_checker< Container >::end(), f, map_checker< Container >::find(), GetLocationString(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::IsSetLocus_tag(), NcbiCerr, NcbiEndl, and CReadBlastApp::PrintDetails().
Referenced by get_my_feat_type(), CReadBlastApp::overlaps_prot_na(), and CReadBlastApp::RemoveProblems().
◆ GetRNAname() ◆ GetRRNAtype() ◆ GetStringDescr()Definition at line 309 of file shortcuts.cpp.
References CSeq_id::eFormat_FastA, CReadBlastApp::getLocusTag(), CSeq_id::GetStringDescr(), and result.
Referenced by CReadBlastApp::addLocation(), CReadBlastApp::AnalyzeSeqs(), CReadBlastApp::AnalyzeSeqsViaBioseqs(), CReadBlastApp::CollectSimpleSeqs(), CReadBlastApp::CopyInfoFromGenesToProteins(), CReadBlastApp::fit_blast(), get_my_seq_type(), get_parent_seqset(), CReadBlastApp::getGenomicInterval(), CReadBlastApp::getGenomicLocation(), CReadBlastApp::hasGenomicInterval(), CReadBlastApp::hasGenomicLocation(), CReadBlastApp::hasProblems(), CReadBlastApp::overlaps(), CReadBlastApp::overlaps_prot_na(), CReadBlastApp::ReadBlast(), CReadBlastApp::RemoveProblems(), CReadBlastApp::reportProblems(), CReadBlastApp::skip_to_valid_seq_cand(), and CReadBlastApp::skip_toprot().
◆ let1_2_let3() string let1_2_let3 ( char let1 ) ◆ printed_range() [1/9] ◆ printed_range() [2/9] ◆ printed_range() [3/9] ◆ printed_range() [4/9]Definition at line 320 of file shortcuts.cpp.
References r().
Referenced by CReadBlastApp::addLoctoSimpleSeq(), CReadBlastApp::CollectRNAFeatures(), CReadBlastApp::CollectSimpleSeqs(), CReadBlastApp::find_overlap(), CReadBlastApp::FixStrands(), CReadBlastApp::get_neighboring_sequences(), printed_range(), printed_ranges(), CReadBlastApp::printOverlapReport(), CReadBlastApp::ReadRRNA2(), CReadBlastApp::short_proteins(), CReadBlastApp::simple_overlaps(), and CReadBlastApp::ugly_simple_overlaps_call().
◆ printed_range() [5/9] ◆ printed_range() [6/9] ◆ printed_range() [7/9] string printed_range ( const TSimpleSeqs::iterator & ext_rna ) ◆ printed_range() [8/9] string printed_range ( const TSimpleSeqs::iterator & ext_rna, const TSimpleSeqs::iterator & end ) ◆ printed_range() [9/9] ◆ printed_ranges() ◆ s_GetFormat() ◆ USING_SCOPE() [1/2] ◆ USING_SCOPE() [2/2]RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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