MatchingOligo Class Reference

Public Member Functions
	MatchingOligo (const Oligo &oligo_)
int	dangling () const
char	dangling_char () const
MatchingOligo	bind_against (char c, const Splits &splits) const
MatchingOligo	dont_bind_rest () const
int	domainLength () const
bool	domainSeen () const
bool	domainPossible () const
bool	completely_bound () const
int	calc_centigrade_pos (const PT_tprobes *tprobe, const PT_pdc *const pdc) const
bool	centigrade_pos_out_of_reach (const PT_tprobes *tprobe, const PT_pdc *const pdc, const Splits &splits) const
const Oligo &	get_oligo () const

Detailed Description

Definition at line 105 of file PT_new_design.cxx.

Constructor & Destructor Documentation

MatchingOligo::MatchingOligo ( const Oligo &  oligo_ )

inlineexplicit

Definition at line 183 of file PT_new_design.cxx.

Member Function Documentation

int MatchingOligo::dangling ( ) const

inline

Definition at line 192 of file PT_new_design.cxx.

References pt_assert, and Oligo::size().

Referenced by completely_bound(), dangling_char(), and domainPossible().

char MatchingOligo::dangling_char ( ) const

inline

Definition at line 198 of file PT_new_design.cxx.

References Oligo::at(), dangling(), and pt_assert.

Referenced by bind_against().

MatchingOligo MatchingOligo::bind_against ( char  c, const Splits &  splits  ) const

inline

Definition at line 203 of file PT_new_design.cxx.

References Splits::check(), dangling_char(), MaxBond::get_max_bond(), is_std_base_or_N(), max, PT_A, pt_assert, PT_BASES, and PT_N.

MatchingOligo MatchingOligo::dont_bind_rest ( ) const

inline

Definition at line 226 of file PT_new_design.cxx.

int MatchingOligo::domainLength ( ) const

inline

Definition at line 232 of file PT_new_design.cxx.

Referenced by domainPossible().

bool MatchingOligo::domainSeen ( ) const

inline

Definition at line 234 of file PT_new_design.cxx.

Referenced by calc_centigrade_pos(), centigrade_pos_out_of_reach(), and domainPossible().

bool MatchingOligo::domainPossible ( ) const

inline

Definition at line 235 of file PT_new_design.cxx.

References dangling(), domainLength(), domainSeen(), and pt_assert.

bool MatchingOligo::completely_bound ( ) const

inline

Definition at line 240 of file PT_new_design.cxx.

References dangling().

Referenced by calc_centigrade_pos().

int MatchingOligo::calc_centigrade_pos ( const PT_tprobes *  tprobe, const PT_pdc *const  pdc  ) const

inline

Definition at line 242 of file PT_new_design.cxx.

References completely_bound(), domainSeen(), dt_bondssum::dt, and pt_assert.

Referenced by centigrade_pos_out_of_reach().

bool MatchingOligo::centigrade_pos_out_of_reach ( const PT_tprobes *  tprobe, const PT_pdc *const  pdc, const Splits &  splits  ) const

inline

Definition at line 253 of file PT_new_design.cxx.

References calc_centigrade_pos(), and domainSeen().

const Oligo& MatchingOligo::get_oligo ( ) const

inline

Definition at line 263 of file PT_new_design.cxx.

---

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

• PROBE/PT_new_design.cxx