Realigner Class Reference

Public Member Functions
	Realigner (const char *ali_source_, const char *ali_dest_, size_t ali_len_)
size_t	get_needed_dest_alilen () const
void	set_failure (const char *reason)
void	clear_failure ()
const char *	failure () const
char *	realign_seq (TransTables &allowed, const char *const source, size_t source_len, const char *const dest, size_t dest_len, bool cutoff_dna)

Detailed Description

Definition at line 833 of file TranslateRealign.cxx.

Constructor & Destructor Documentation

Realigner::Realigner ( const char *  ali_source_, const char *  ali_dest_, size_t  ali_len_  )

inline

Definition at line 892 of file TranslateRealign.cxx.

References clear_failure().

Member Function Documentation

size_t Realigner::get_needed_dest_alilen ( ) const

inline

Definition at line 901 of file TranslateRealign.cxx.

Referenced by ALI_realign_marked().

void Realigner::set_failure ( const char *  reason )

inline

Definition at line 903 of file TranslateRealign.cxx.

Referenced by ALI_realign_marked().

void Realigner::clear_failure ( )

inline

Definition at line 904 of file TranslateRealign.cxx.

References NULp.

Referenced by ALI_realign_marked(), and Realigner().

const char* Realigner::failure ( ) const

inline

Definition at line 906 of file TranslateRealign.cxx.

Referenced by ALI_realign_marked(), and realign_seq().

char* Realigner::realign_seq ( TransTables &  allowed, const char *const  source, size_t  source_len, const char *const  dest, size_t  dest_len, bool  cutoff_dna  )

inline

Definition at line 908 of file TranslateRealign.cxx.

References ali_assert, ARB_alloc(), buffer, RealignAttempt::failed(), failure(), GBS_global_string(), RealignAttempt::get_remaining_tables(), TransTables::is_subset_of(), NULp, and unalign().

Referenced by ALI_realign_marked().

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The documentation for this class was generated from the following file:

• SL/ALILINK/TranslateRealign.cxx