NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Functions
read_blast_result.hpp File Reference
#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, TGenfoTranStr3
 
typedef map< string, TranStr3TranStrMap3
 
typedef map< string, TProblem_locTProblem_locs
 
typedef map< string, diagStrdiagMap
 
typedef map< long, long > parent_map
 
typedef map< string, CRef< CSeq_feat > > LocMap
 
typedef vector< TSimplePairTSimplePairs
 
typedef list< TSimpleSeqTSimpleSeqs
 
typedef vector< TExtRNATExtRNAtable
 

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_setget_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

Definition at line 204 of file read_blast_result.hpp.

◆ TranStr3

Definition at line 103 of file read_blast_result.hpp.

◆ 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

Enumerator
eUndefined 
eSubmit 
eEntry 
eTbl 

Definition at line 127 of file read_blast_result.hpp.

◆ 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 

Definition at line 135 of file read_blast_result.hpp.

Function Documentation

◆ addProblems()

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

Definition at line 844 of file problems.cpp.

References ITERATE, and n.

Referenced by CReadBlastApp::fit_blast().

◆ diagName()

string diagName ( const string type,
const string value 
)

Definition at line 839 of file problems.cpp.

References rapidjson::value.

Referenced by CReadBlastApp::match_na().

◆ Get3type()

string Get3type ( const CRNA_ref rna)

◆ get_my_feat_type()

EMyFeatureType get_my_feat_type ( const CSeq_feat feat,
const LocMap loc_map 
)

◆ get_my_seq_type()

EMyFeatureType get_my_seq_type ( const CBioseq seq)

◆ get_parent_seqset()

CBioseq_set::TSeq_set* get_parent_seqset ( const CBioseq seq)

◆ get_title()

string get_title ( const CBioseq seq)

◆ get_trna_string()

string get_trna_string ( const CSeq_feat feat)

◆ GetLocationString() [1/2]

string GetLocationString ( const CSeq_feat f)

◆ GetLocationString() [2/2]

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

Definition at line 232 of file locations.cpp.

References eNa_strand_plus, CReadBlastApp::getFromTo(), and label.

◆ GetLocusTag()

string GetLocusTag ( const CSeq_feat f,
const LocMap loc_map 
)

◆ GetRNAname()

string GetRNAname ( const CSeq_feat feat)

◆ GetRRNAtype()

string GetRRNAtype ( const CRNA_ref rna)

◆ GetStringDescr()

string GetStringDescr ( const CBioseq bioseq)

◆ let1_2_let3()

string let1_2_let3 ( char  let1)

Definition at line 409 of file read_blast_result_lib.cpp.

References int, NcbiCerr, and NcbiEndl.

Referenced by Get3type().

◆ 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)

◆ printed_range() [4/9]

string printed_range ( const TSeqPos  from2,
const TSeqPos  to2 
)

◆ 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)

◆ s_GetFormat()

ESerialDataFormat s_GetFormat ( const string name)

Definition at line 337 of file bss_info.cpp.

References eSerial_AsnBinary, eSerial_AsnText, eSerial_Xml, and THROW1_TRACE.

Referenced by CReadBlastApp::Run().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( ncbi  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( objects  )
Modified on Wed Jul 17 13:22:14 2024 by modify_doxy.py rev. 669887