shortcuts.cpp File Reference

#include <ncbi_pch.hpp>
#include "read_blast_result.hpp"
#include <objects/seqloc/Seq_point.hpp>

Include dependency graph for shortcuts.cpp:

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Functions
string	GetRRNAtype (const CRNA_ref &rna)
string	Get3type (const CRNA_ref &rna)
string	get_title (const CBioseq &seq)
EMyFeatureType	get_my_seq_type (const CBioseq &seq)
string	get_trna_string (const CSeq_feat &feat)
string	GetRNAname (const CSeq_feat &feat)
EMyFeatureType	get_my_feat_type (const CSeq_feat &feat, const LocMap &loc_map)
string	GetStringDescr (const CBioseq &bioseq)
string	printed_range (const TSeqPos from2, const TSeqPos to2)
string	printed_range (const CSeq_feat &feat)
string	printed_range (const CSeq_loc &seq_interval)
string	printed_ranges (const CSeq_loc &seq_interval)
string	printed_range (const CBioseq &seq)
string	printed_range (const TSimpleSeqs::iterator &ext_rna)
string	printed_range (const TSimplePair &apair)
string	printed_range (const TSimpleSeq &ext_rna)
string	printed_range (const TSimpleSeqs::iterator &ext_rna, const TSimpleSeqs::iterator &end)
string	printed_range (const TSimpleSeqs::iterator &ext_rna, TSimpleSeqs &seqs)

Function Documentation

Get3type()

string Get3type

(

const CRNA_ref &

rna

)

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()

EMyFeatureType get_my_feat_type	(	const CSeq_feat &	feat,
		const LocMap &	loc_map
	)

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()

EMyFeatureType get_my_seq_type

(

const CBioseq &

seq

)

Definition at line 176 of file shortcuts.cpp.

References eMyFeatureType_hypo_CDS, eMyFeatureType_normal_CDS, eMyFeatureType_unknown, get_title(), GetStringDescr(), NcbiCerr, NcbiEndl, CReadBlastApp::PrintDetails(), and type.

Referenced by CReadBlastApp::overlaps_prot_na().

get_title()

string get_title

(

const CBioseq &

seq

)

Definition at line 159 of file shortcuts.cpp.

References CBioseq_Base::CanGetDescr(), CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), and ITERATE.

Referenced by get_my_seq_type(), and CReadBlastApp::overlaps_prot_na().

get_trna_string()

string get_trna_string

(

const CSeq_feat &

feat

)

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().

GetRNAname()

string GetRNAname

(

const CSeq_feat &

feat

)

Definition at line 229 of file shortcuts.cpp.

References CRNA_ref_Base::CanGetExt(), CRNA_ref_Base::CanGetType(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetName(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::IsName(), and CSeqFeatData_Base::IsRna().

Referenced by CReadBlastApp::overlaps_prot_na().

GetRRNAtype()

string GetRRNAtype

(

const CRNA_ref &

rna

)

Definition at line 101 of file shortcuts.cpp.

References rna, and type.

Referenced by CReadBlastApp::CheckMissingRibosomalRNA(), CReadBlastApp::CollectSimpleSeqs(), and CReadBlastApp::overlaps_na().

GetStringDescr()

string GetStringDescr

(

const CBioseq &

bioseq

)

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().

printed_range() [1/9]

string printed_range

(

const CBioseq &

seq

)

Definition at line 367 of file shortcuts.cpp.

References CReadBlastApp::getGenomicLocation(), and printed_range().

printed_range() [2/9]

string printed_range

(

const CSeq_feat &

feat

)

Definition at line 328 of file shortcuts.cpp.

References CSeq_feat_Base::GetLocation(), and printed_range().

printed_range() [3/9]

string printed_range

(

const CSeq_loc &

seq_interval

)

Definition at line 333 of file shortcuts.cpp.

References eExtreme_Positional, CSeq_loc::GetStart(), CSeq_loc::GetStop(), and printed_range().

printed_range() [4/9]

string printed_range	(	const TSeqPos	from2,
		const TSeqPos	to2
	)

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]

string printed_range

(

const TSimplePair &

apair

)

Definition at line 384 of file shortcuts.cpp.

References TSimplePair::from, printed_range(), and TSimplePair::to.

printed_range() [6/9]

string printed_range

(

const TSimpleSeq &

ext_rna

)

Definition at line 391 of file shortcuts.cpp.

References eNa_strand_plus, TSimpleSeq::exons, and printed_range().

printed_range() [7/9]

string printed_range

(

const TSimpleSeqs::iterator &

ext_rna

)

Definition at line 372 of file shortcuts.cpp.

References printed_range().

printed_range() [8/9]

string printed_range	(	const TSimpleSeqs::iterator &	ext_rna,
		const TSimpleSeqs::iterator &	end
	)

Definition at line 408 of file shortcuts.cpp.

References printed_range().

printed_range() [9/9]

string printed_range	(	const TSimpleSeqs::iterator &	ext_rna,
		TSimpleSeqs &	seqs
	)

Definition at line 414 of file shortcuts.cpp.

References printed_range().

printed_ranges()

string printed_ranges

(

const CSeq_loc &

seq_interval

)

Definition at line 341 of file shortcuts.cpp.

References ConstBegin(), CReadBlastApp::less_pair(), NON_CONST_ITERATE, and printed_range().

Referenced by CReadBlastApp::printOverlapReport().