MatchRequest Class Reference

Inheritance diagram for MatchRequest:

Collaboration diagram for MatchRequest:

Public Member Functions
	MatchRequest (PT_local &locs, int probe_length)
	~MatchRequest ()
PT_local &	get_PT_local () const
bool	hit_limit_reached () const
int	accept_N_mismatches (int ambig) const
bool	add_hit (const DataLoc &at, const Mismatches &mismatch)
bool	add_hits_for_children (POS_TREE2 *pt, const Mismatches &mismatch)
bool	collect_hits_for (const char *probe, POS_TREE2 *pt, Mismatches &mismatch, int height)
int	allowed_mismatches () const
double	get_mismatch_weight (char probe, char seq) const

Detailed Description

Definition at line 53 of file PT_match.cxx.

Constructor & Destructor Documentation

MatchRequest::MatchRequest ( PT_local &  locs, int  probe_length  )

inlineexplicit

Definition at line 64 of file PT_match.cxx.

MatchRequest::~MatchRequest ( )

inline

Definition at line 72 of file PT_match.cxx.

Member Function Documentation

PT_local& MatchRequest::get_PT_local ( ) const

inline

Definition at line 76 of file PT_match.cxx.

Referenced by add_hit(), and Mismatches::get_PT_local().

bool MatchRequest::hit_limit_reached ( ) const

inline

Definition at line 78 of file PT_match.cxx.

Referenced by add_hit(), add_hits_for_children(), and collect_hits_for().

int MatchRequest::accept_N_mismatches ( int  ambig ) const

inline

Definition at line 84 of file PT_match.cxx.

References pt_assert.

Referenced by Mismatches::accepted(), and add_hit().

bool MatchRequest::add_hit	(	const DataLoc &	at,
		const Mismatches &	mismatch
	)

Definition at line 140 of file PT_match.cxx.

References accept_N_mismatches(), aisc_link(), AbsLoc::get_abs_pos(), Mismatches::get_ambig(), AbsLoc::get_name(), Mismatches::get_plain(), get_PT_local(), DataLoc::get_rel_pos(), Mismatches::get_weighted(), hit_limit_reached(), probe_struct_global::main_probe, psg, and probe_struct_global::reversed.

Referenced by add_hits_for_children(), and collect_hits_for().

bool MatchRequest::add_hits_for_children	(	POS_TREE2 *	pt,
		const Mismatches &	mismatch
	)

go down the tree to chains and leafs; copy names, positions and mismatches in locs structure

Definition at line 160 of file PT_match.cxx.

References Mismatches::accepted(), add_hit(), ChainIteratorStage2::at(), POS_TREE2::get_type(), hit_limit_reached(), PT2_CHAIN, PT2_LEAF, PT2_NODE, pt_assert, PT_BASES, PT_QU, and PT_read_son().

Referenced by collect_hits_for().

bool MatchRequest::collect_hits_for	(	const char *	probe,
		POS_TREE2 *	pt,
		Mismatches &	mismatch,
		int	height
	)

search down the tree to find matching species for the given probe

Definition at line 210 of file PT_match.cxx.

References Mismatches::accepted(), add_hit(), add_hits_for_children(), ChainIteratorStage2::at(), Mismatches::count_versus(), Mismatches::count_weighted(), POS_TREE2::get_type(), hit_limit_reached(), PT2_CHAIN, PT2_LEAF, PT2_NODE, pt_assert, PT_BASES, PT_QU, and PT_read_son().

Referenced by probe_match().

int MatchRequest::allowed_mismatches ( ) const

inline

Definition at line 93 of file PT_match.cxx.

Referenced by Mismatches::accepted(), and probe_match().

double MatchRequest::get_mismatch_weight ( char  probe, char  seq  ) const

inline

Definition at line 94 of file PT_match.cxx.

References MismatchWeights::get().

Referenced by Mismatches::count_weighted().

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

• PROBE/PT_match.cxx