Public Member Functions | List of all members
MatchRequest Class Reference
Inheritance diagram for MatchRequest:
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Collaboration diagram for MatchRequest:
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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 

Definition at line 64 of file PT_match.cxx.

MatchRequest::~MatchRequest ( )

Definition at line 72 of file PT_match.cxx.

Member Function Documentation

PT_local& MatchRequest::get_PT_local ( ) const

Definition at line 76 of file PT_match.cxx.

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

bool MatchRequest::hit_limit_reached ( ) const

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

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 
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,
Mismatches mismatch,
int  height 
int MatchRequest::allowed_mismatches ( ) const

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

Definition at line 94 of file PT_match.cxx.

References MismatchWeights::get().

Referenced by Mismatches::count_weighted().

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