NCBI C++ ToolKit
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CProSplignTrimmer Class Reference

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Public Member Functions

 CProSplignTrimmer (const CProteinAlignText &alignment_text)
 CProSplignTrimmer implementation. More...
 
size_t RestoreFivePrime (size_t beg) const
 checks if alignment ends should be restored beyond 'beg' or 'end' returns new flanking coord or 'beg'/'end' if no restoring ) More...
 
size_t RestoreThreePrime (size_t end) const
 
int CutFromLeft (CNPiece pc, const CProSplignOutputOptionsExt &options) const
 trim flanks with positives dropoff over a cutoff, iterative flank 'good pieces' should not be dropped completely applied inside an exon only More...
 
int CutFromRight (CNPiece pc, const CProSplignOutputOptionsExt &options) const
 trim right flank with positives dropoff over a cutoff, iterative 'pc' should not be dropped completely returns new pc.end applied inside an exon only More...
 

Private Attributes

const CProteinAlignTextm_alignment_text
 
string m_posit
 

Detailed Description

Definition at line 71 of file Info.cpp.

Constructor & Destructor Documentation

◆ CProSplignTrimmer()

CProSplignTrimmer::CProSplignTrimmer ( const CProteinAlignText alignment_text)

Member Function Documentation

◆ CutFromLeft()

int CProSplignTrimmer::CutFromLeft ( CNPiece  pc,
const CProSplignOutputOptionsExt options 
) const

trim flanks with positives dropoff over a cutoff, iterative flank 'good pieces' should not be dropped completely applied inside an exon only

trim left flank with positives dropoff over a cutoff, iterative 'pc' should not be dropped completely returns new pc.beg applied inside an exon only

Definition at line 1181 of file Info.cpp.

References _ASSERT, CNPiece::beg, CNPiece::end, GAP_CHAR, CProSplignOutputOptions::GetCutFlanksWithPositDrop(), CProSplignOutputOptions::GetCutFlanksWithPositDropoff(), CProSplignOutputOptions::GetCutFlanksWithPositGapRatio(), CProSplignOutputOptions::GetCutFlanksWithPositMaxLen(), CProSplignOutputOptions::GetCutFlanksWithPositWindow(), CProteinAlignText::GetDNA(), CProteinAlignText::GetProtein(), INTRON_CHAR, m_alignment_text, m_posit, POSIT_CHAR, prot, and window_size.

Referenced by FindGoodParts().

◆ CutFromRight()

int CProSplignTrimmer::CutFromRight ( CNPiece  pc,
const CProSplignOutputOptionsExt options 
) const

◆ RestoreFivePrime()

size_t CProSplignTrimmer::RestoreFivePrime ( size_t  beg) const

checks if alignment ends should be restored beyond 'beg' or 'end' returns new flanking coord or 'beg'/'end' if no restoring )

Definition at line 1088 of file Info.cpp.

References _ASSERT, GAP_CHAR, CProteinAlignText::GetDNA(), CProteinAlignText::GetProtein(), i, int, INTRON_CHAR, INTRON_OR_GAP, m_alignment_text, m_posit, and POSIT_CHAR.

Referenced by FindGoodParts().

◆ RestoreThreePrime()

size_t CProSplignTrimmer::RestoreThreePrime ( size_t  end) const

Member Data Documentation

◆ m_alignment_text

const CProteinAlignText& CProSplignTrimmer::m_alignment_text
private

Definition at line 88 of file Info.cpp.

Referenced by CutFromLeft(), CutFromRight(), RestoreFivePrime(), and RestoreThreePrime().

◆ m_posit

string CProSplignTrimmer::m_posit
private

The documentation for this class was generated from the following file:
Modified on Sun Feb 25 03:03:30 2024 by modify_doxy.py rev. 669887