#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbifile.hpp>
#include <serial/iterator.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Date.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <string>
#include <algorithm>
#include "tbl.hpp"

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Classes
struct	TGenfo

struct	distanceReportStr

struct	problemStr

struct	diagStr

struct	TProblem_loc

struct	hitStr

struct	blastStr

struct	perfectHitStr

struct	TExtRNA

struct	TSimplePair

struct	TSimpleSeq

class	CReadBlastApp

Typedefs
typedef map< CSeq_id::EAccessionInfo, TGenfo >	TranStr3

typedef map< string, TranStr3 >	TranStrMap3

typedef map< string, TProblem_loc >	TProblem_locs

typedef map< string, diagStr >	diagMap

typedef map< long, long >	parent_map

typedef map< string, CRef< CSeq_feat > >	LocMap

typedef vector< TSimplePair >	TSimplePairs

typedef list< TSimpleSeq >	TSimpleSeqs

typedef vector< TExtRNA >	TExtRNAtable

Enumerations
enum	ECoreDataType { eUndefined = 0 , eSubmit , eEntry , eTbl }

enum	EProblem { eOverlap = (1<<0) , eCompleteOverlap = (1<<1) , ePartial = (1<<2) , eFrameShift = (1<<3) , eMayBeNotFrameShift = (1<<4) , eRnaOverlap = (1<<5) , eTRNAMissing = (1<<6) , eTRNABadStrand = (1<<7) , eTRNAComMismatch = (1<<8) , eTRNAMismatch = (1<<9) , eTRNAAbsent = (1<<10) , eRemoveOverlap = (1<<11) , eTRNAUndefStrand = (1<<12) , eShortProtein = (1<<13) , eRelFrameShift = eFrameShift \| eMayBeNotFrameShift , eTRNAProblems , eAllProblems }

enum	EMyFeatureType { eMyFeatureType_unknown = 0 , eMyFeatureType_pseudo_tRNA , eMyFeatureType_atypical_tRNA , eMyFeatureType_normal_tRNA , eMyFeatureType_rRNA , eMyFeatureType_miscRNA , eMyFeatureType_hypo_CDS , eMyFeatureType_normal_CDS }

Functions
	USING_SCOPE (ncbi)

	USING_SCOPE (objects)

ESerialDataFormat	s_GetFormat (const string &name)

CBioseq_set::TSeq_set *	get_parent_seqset (const CBioseq &seq)

template<typename interval_type >
string	GetLocationString (const interval_type &loc)

string	GetLocationString (const CSeq_feat &f)

string	GetLocusTag (const CSeq_feat &f, const LocMap &loc_map)

int	addProblems (list< problemStr > &dest, const list< problemStr > &src)

string	GetStringDescr (const CBioseq &bioseq)

string	Get3type (const CRNA_ref &rna)

string	GetRRNAtype (const CRNA_ref &rna)

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	get_title (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)

string	let1_2_let3 (char let1)

string	diagName (const string &type, const string &value)

EMyFeatureType	get_my_seq_type (const CBioseq &seq)

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

string	get_trna_string (const CSeq_feat &feat)

string	GetRNAname (const CSeq_feat &feat)

Typedef Documentation

◆ diagMap

typedef map< string , diagStr > diagMap

Definition at line 207 of file read_blast_result.hpp.

◆ LocMap

typedef map< string, CRef < CSeq_feat > > LocMap

Definition at line 239 of file read_blast_result.hpp.

◆ parent_map

typedef map<long,long> parent_map

Definition at line 237 of file read_blast_result.hpp.

◆ TExtRNAtable

typedef vector<TExtRNA> TExtRNAtable

Definition at line 274 of file read_blast_result.hpp.

◆ TProblem_locs

typedef map<string, TProblem_loc> TProblem_locs

Definition at line 204 of file read_blast_result.hpp.

◆ TranStr3

typedef map<CSeq_id::EAccessionInfo, TGenfo > TranStr3

Definition at line 103 of file read_blast_result.hpp.

◆ TranStrMap3

typedef map<string, TranStr3> TranStrMap3

Definition at line 104 of file read_blast_result.hpp.

◆ TSimplePairs

typedef vector<TSimplePair> TSimplePairs

Definition at line 257 of file read_blast_result.hpp.

◆ TSimpleSeqs

typedef list<TSimpleSeq> TSimpleSeqs

Definition at line 272 of file read_blast_result.hpp.

Enumeration Type Documentation

◆ ECoreDataType

enum ECoreDataType

Enumerator
eUndefined
eSubmit
eEntry
eTbl

Definition at line 127 of file read_blast_result.hpp.

◆ EMyFeatureType

enum EMyFeatureType

Enumerator
eMyFeatureType_unknown
eMyFeatureType_pseudo_tRNA
eMyFeatureType_atypical_tRNA
eMyFeatureType_normal_tRNA
eMyFeatureType_rRNA
eMyFeatureType_miscRNA
eMyFeatureType_hypo_CDS
eMyFeatureType_normal_CDS

Definition at line 168 of file read_blast_result.hpp.

◆ EProblem

enum EProblem

Enumerator
eOverlap
eCompleteOverlap
ePartial
eFrameShift
eMayBeNotFrameShift
eRnaOverlap
eTRNAMissing
eTRNABadStrand
eTRNAComMismatch
eTRNAMismatch
eTRNAAbsent
eRemoveOverlap
eTRNAUndefStrand
eShortProtein
eRelFrameShift
eTRNAProblems
eAllProblems