NCBI C++ ToolKit
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CBestIntron Class Reference

Search Toolkit Book for CBestIntron

#include "intron.hpp"
(Private to src/algo/align/prosplign.)

+ Collaboration diagram for CBestIntron:

Public Member Functions

 CBestIntron (int j, char amin, const CAlignInfo &prev, const CAlignInfo &cur, const CNSeq &nseq, const CProSplignScaledScoring &scoring)
 
void NucStep (const CProSplignScaledScoring scoring, const CSubstMatrix &matrix)
 
CHIntronScore GetBest (CHIntronScore sgt, CHIntronScore sgc, CHIntronScore sat, CHIntronScore sany)
 
CHIntronScore GetW1 (const CSubstMatrix &matrix)
 
CHIntronScore GetW2 ()
 
CHIntronScore Getw111 ()
 
CHIntronScore Getfv111 ()
 
CHIntronScore Getw012 ()
 
CHIntronScore Geth012 ()
 
CHIntronScore Getw021 ()
 
CHIntronScore Geth021 ()
 
CHIntronScore Geth000 ()
 
CHIntronScore Getv000 ()
 
CHIntronScore Getw000 ()
 
CHIntronScore Getfh000 ()
 
CHIntronScore Getfv000 ()
 

Public Attributes

CIntron gt
 
CIntron gc
 
CIntron at
 
CAnyIntron an
 
int gtcost
 
int gccost
 
int atcost
 
int anycost
 

Detailed Description

Definition at line 332 of file intron.hpp.

Constructor & Destructor Documentation

◆ CBestIntron()

CBestIntron::CBestIntron ( int  j,
char  amin,
const CAlignInfo prev,
const CAlignInfo cur,
const CNSeq nseq,
const CProSplignScaledScoring scoring 
)
inline

Member Function Documentation

◆ GetBest()

CHIntronScore CBestIntron::GetBest ( CHIntronScore  sgt,
CHIntronScore  sgc,
CHIntronScore  sat,
CHIntronScore  sany 
)
inline

Definition at line 356 of file intron.hpp.

References anycost, atcost, gccost, and gtcost.

Referenced by GetW1().

◆ Getfh000()

CHIntronScore CBestIntron::Getfh000 ( )
inline

Definition at line 393 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Getfv000()

CHIntronScore CBestIntron::Getfv000 ( )
inline

Definition at line 394 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Getfv111()

CHIntronScore CBestIntron::Getfv111 ( )
inline

Definition at line 385 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Geth000()

CHIntronScore CBestIntron::Geth000 ( )
inline

Definition at line 390 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Geth012()

CHIntronScore CBestIntron::Geth012 ( )
inline

Definition at line 387 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Geth021()

CHIntronScore CBestIntron::Geth021 ( )
inline

Definition at line 389 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Getv000()

CHIntronScore CBestIntron::Getv000 ( )
inline

Definition at line 391 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Getw000()

CHIntronScore CBestIntron::Getw000 ( )
inline

Definition at line 392 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Getw012()

CHIntronScore CBestIntron::Getw012 ( )
inline

Definition at line 386 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ Getw021()

CHIntronScore CBestIntron::Getw021 ( )
inline

Definition at line 388 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ GetW1()

CHIntronScore CBestIntron::GetW1 ( const CSubstMatrix matrix)
inline

Definition at line 381 of file intron.hpp.

References an, at, gc, GetBest(), CAnyIntron::GetW1(), CIntron::GetW1(), and gt.

Referenced by FindIGapIntrons().

◆ Getw111()

CHIntronScore CBestIntron::Getw111 ( )
inline

Definition at line 384 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ GetW2()

CHIntronScore CBestIntron::GetW2 ( )
inline

Definition at line 383 of file intron.hpp.

Referenced by FindIGapIntrons().

◆ NucStep()

void CBestIntron::NucStep ( const CProSplignScaledScoring  scoring,
const CSubstMatrix matrix 
)
inline

Definition at line 349 of file intron.hpp.

References an, at, gc, gt, CAnyIntron::NucStep(), and CIntron::NucStep().

Referenced by FindIGapIntrons().

Member Data Documentation

◆ an

CAnyIntron CBestIntron::an

Definition at line 335 of file intron.hpp.

Referenced by GetW1(), and NucStep().

◆ anycost

int CBestIntron::anycost

Definition at line 336 of file intron.hpp.

Referenced by CBestIntron(), and GetBest().

◆ at

CIntron CBestIntron::at

Definition at line 334 of file intron.hpp.

Referenced by CFIntron::Getlen(), GetW1(), and NucStep().

◆ atcost

int CBestIntron::atcost

Definition at line 336 of file intron.hpp.

Referenced by CBestIntron(), and GetBest().

◆ gc

CIntron CBestIntron::gc

Definition at line 334 of file intron.hpp.

Referenced by GetW1(), and NucStep().

◆ gccost

int CBestIntron::gccost

Definition at line 336 of file intron.hpp.

Referenced by CBestIntron(), and GetBest().

◆ gt

CIntron CBestIntron::gt

Definition at line 334 of file intron.hpp.

Referenced by GetW1(), and NucStep().

◆ gtcost

int CBestIntron::gtcost

Definition at line 336 of file intron.hpp.

Referenced by CBestIntron(), and GetBest().


The documentation for this class was generated from the following file:
Modified on Mon May 27 04:37:25 2024 by modify_doxy.py rev. 669887