Augustus 3.4.0
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PP::Profile Class Reference

Public Member Functions

 Profile (string filename)
 
int getIntronIntraFreq (unsigned b, unsigned c, unsigned f)
 
int getIntronIntraFreqAtCol (unsigned b, unsigned c)
 
int getIntronInterFreq (unsigned b, unsigned n)
 
unsigned getIntronNumSeq ()
 
Position firstInRange (int blockno=0) const
 
int blockCount () const
 
int blockSize (int blockno) const
 
DistanceType interBlockDist (int blockno) const
 
Range interBlockRange (int blockno) const
 
Column getColumn (Position pos) const
 
string getName () const
 
string getInfoLine () const
 
ostream & write (ostream &) const
 
Block & operator[] (int blockno)
 
const Block & operator[] (int blockno) const
 
Double getGlobalThresh (bool complement, Position ppos) const
 

Friends

ostream & operator<< (ostream &strm, const Profile &P)
 
void initConstants ()
 

Member Function Documentation

◆ getIntronInterFreq()

int PP::Profile::getIntronInterFreq ( unsigned b,
unsigned n )
inline
Parameters
[in]bA block number
[in]nNumber of introns
Returns
The frequency of n introns in the inter-block section before block b. Return -1, if no inter-block intron profile exists before block b.

◆ getIntronIntraFreq()

int PP::Profile::getIntronIntraFreq ( unsigned b,
unsigned c,
unsigned f )
inline
Parameters
[in]bA block number
[in]cA block column
[in]fA frame in {0,1,2}
Returns
The frequency of introns after block column c and f residual nucleotides in block b

◆ getIntronIntraFreqAtCol()

int PP::Profile::getIntronIntraFreqAtCol ( unsigned b,
unsigned c )
inline
Parameters
[in]bA block number
[in]cA block column
Returns
The frequency of introns between block column c and c+1 in block b

◆ getIntronNumSeq()

unsigned PP::Profile::getIntronNumSeq ( )
inline
Returns
The number of protein sequences used to build an intron profile
The documentation for this class was generated from the following files:
Generated by doxygen 1.12.0