NCBI C++ ToolKit
Classes | Enumerations | Functions | Variables
gnomon_model.cpp File Reference
#include <ncbi_pch.hpp>
#include <algo/gnomon/gnomon_model.hpp>
#include <algo/gnomon/gnomon.hpp>
#include "gnomon_seq.hpp"
#include <algo/gnomon/id_handler.hpp>
#include <set>
#include <functional>
#include <corelib/ncbiutil.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqloc/Seq_id.hpp>
+ Include dependency graph for gnomon_model.cpp:

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class  CStreamState< T >
struct  SGFFrec
struct  Precedence


enum  EModelFileFormat { eGnomonFileFormat , eGFF3FileFormat , eASNFileFormat }


 USING_SCOPE (objects)
pair< int, intExonNumsForInterval (const CGeneModel &a, TSignedSeqRange &intersect)
CNcbiIstreamGetline (CNcbiIstream &is, string &line)
void Ungetline (CNcbiIstream &is)
CNcbiIstreamInputError (CNcbiIstream &is)
CNcbiOstreamoperator<< (CNcbiOstream &s, const setcontig &c)
CNcbiIstreamoperator>> (CNcbiIstream &is, const getcontig &c)
CNcbiOstreamoperator<< (CNcbiOstream &s, EModelFileFormat f)
CNcbiOstreamoperator<< (CNcbiOstream &os, const SGFFrec &r)
CNcbiIstreamoperator>> (CNcbiIstream &is, SGFFrec &res)
string BuildGFF3Gap (int &prev_pos, const CInDelInfo &indel)
string BuildGFF3Gap (int start, int end, const TInDels &indels)
void readGFF3Gap (const string &gap, TSignedSeqPos start, TSignedSeqPos end, TInDels &indels)
void CollectAttributes (const CAlignModel &a, map< string, string > &attributes)
TSignedSeqRange StringToRange (const string &s)
void ParseAttributes (map< string, string > &attributes, CAlignModel &a)
CNcbiOstreamprintGFF3 (CNcbiOstream &os, CAlignModel a)
TSignedSeqRange operator- (TSignedSeqRange a, TSignedSeqRange b)
CNcbiIstreamreadGFF3 (CNcbiIstream &is, CAlignModel &align)
CNcbiOstreamoperator<< (CNcbiOstream &s, const CGeneModel &a)
CNcbiOstreamoperator<< (CNcbiOstream &os, const CAlignModel &a)
CNcbiIstreamoperator>> (CNcbiIstream &is, CAlignModel &align)


CStreamState< pair< string, string > > line_buffer (make_pair(kEmptyStr, kEmptyStr))
CStreamState< stringcontig_stream_state (kEmptyStr)
CStreamState< EModelFileFormatmodel_file_format_state (eGFF3FileFormat)

Enumeration Type Documentation

◆ EModelFileFormat


Definition at line 1614 of file gnomon_model.cpp.

Function Documentation

◆ BuildGFF3Gap() [1/2]

string BuildGFF3Gap ( int prev_pos,
const CInDelInfo indel 

◆ BuildGFF3Gap() [2/2]

string BuildGFF3Gap ( int  start,
int  end,
const TInDels indels 

◆ CollectAttributes()

void CollectAttributes ( const CAlignModel a,
map< string, string > &  attributes 

◆ ExonNumsForInterval()

pair<int, int> ExonNumsForInterval ( const CGeneModel a,
TSignedSeqRange intersect 

Definition at line 1025 of file gnomon_model.cpp.

References a, CRange_Base::GetFrom(), and CRange_Base::GetTo().

Referenced by CGeneModel::HasCompatibleOverlap().

◆ Getline()

CNcbiIstream& Getline ( CNcbiIstream is,
string line 

Definition at line 1576 of file gnomon_model.cpp.

References line_buffer, and NcbiGetlineEOL().

Referenced by operator>>().

◆ InputError()

CNcbiIstream& InputError ( CNcbiIstream is)

Definition at line 1594 of file gnomon_model.cpp.

References ERR_POST, Error(), line_buffer, and Ungetline().

Referenced by operator>>(), and readGFF3().

◆ operator-()

Definition at line 2359 of file gnomon_model.cpp.

References a, and b.

◆ operator<<() [1/5]

CNcbiOstream& operator<< ( CNcbiOstream os,
const CAlignModel a 

Definition at line 2566 of file gnomon_model.cpp.

References a, eGFF3FileFormat, model_file_format_state, and printGFF3().

◆ operator<<() [2/5]

CNcbiOstream& operator<< ( CNcbiOstream os,
const SGFFrec r 

Definition at line 1643 of file gnomon_model.cpp.

References r().

◆ operator<<() [3/5]

CNcbiOstream& operator<< ( CNcbiOstream s,
const CGeneModel a 

Definition at line 2561 of file gnomon_model.cpp.

References a, and operator<<().

◆ operator<<() [4/5]

CNcbiOstream& operator<< ( CNcbiOstream s,
const setcontig c 

Definition at line 1605 of file gnomon_model.cpp.

References contig_stream_state, and setcontig::m_contig.

Referenced by operator<<().

◆ operator<<() [5/5]

CNcbiOstream& operator<< ( CNcbiOstream s,
EModelFileFormat  f 

Definition at line 1619 of file gnomon_model.cpp.

References f(), and model_file_format_state.

◆ operator>>() [1/3]

CNcbiIstream& operator>> ( CNcbiIstream is,
CAlignModel align 

Definition at line 2577 of file gnomon_model.cpp.

References eGFF3FileFormat, model_file_format_state, and readGFF3().

◆ operator>>() [2/3]

CNcbiIstream& operator>> ( CNcbiIstream is,
const getcontig c 

Definition at line 1609 of file gnomon_model.cpp.

References contig_stream_state, and getcontig::m_contig.

◆ operator>>() [3/3]

CNcbiIstream& operator>> ( CNcbiIstream is,
SGFFrec res 

◆ ParseAttributes()

void ParseAttributes ( map< string, string > &  attributes,
CAlignModel a 

◆ printGFF3()

CNcbiOstream& printGFF3 ( CNcbiOstream os,
CAlignModel  a 

◆ readGFF3()

CNcbiIstream& readGFF3 ( CNcbiIstream is,
CAlignModel align 

◆ readGFF3Gap()

void readGFF3Gap ( const string gap,
TSignedSeqPos  start,
TSignedSeqPos  end,
TInDels indels 

◆ StringToRange()

TSignedSeqRange StringToRange ( const string s)

Definition at line 1977 of file gnomon_model.cpp.

References NStr::SplitInTwo().

Referenced by ParseAttributes().

◆ Ungetline()

void Ungetline ( CNcbiIstream is)

Definition at line 1588 of file gnomon_model.cpp.

References line_buffer.

Referenced by InputError(), and readGFF3().


USING_SCOPE ( objects  )

Variable Documentation

◆ contig_stream_state

CStreamState<string> contig_stream_state(kEmptyStr) ( kEmptyStr  )

◆ line_buffer

CStreamState<pair<string,string> > line_buffer(make_pair(kEmptyStr, kEmptyStr)) ( make_pair(kEmptyStr, kEmptyStr )

Referenced by Getline(), InputError(), and Ungetline().

◆ model_file_format_state

Referenced by operator<<(), and operator>>().

Modified on Tue Apr 23 07:40:19 2024 by rev. 669887