codon.h File Reference

#include <map>
#include <string>
#include <iostream>

Go to the source code of this file.

Classes
class	codon
Functions
int	hashbase (char n)
int	hashcodon (char c[3])
int	hashcodon (const string &cc)
Variables
	N
	T
*ACU	R
*ACU	S
*ACU *AGU	I
*ACU *AGU	M
*ACU *AGU *AUU	Q
*ACU *AGU *AUU	H
*ACU *AGU *AUU *CAU	P
*ACU *AGU *AUU *CAU *CCU *CGU	L
*ACU *AGU *AUU *CAU *CCU *CGU *CUU	E
*ACU *AGU *AUU *CAU *CCU *CGU *CUU	D
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU	A
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU	G
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU	V
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU	Y
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU	C
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU	W
*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU *UGU	F

---

Function Documentation

int hashbase

(

char

n

)

convert base to integer A=>0, C=>1, G=>2, T,U=>3, S,W,R,Y,K,M,B,V,H,D,N => 4-14 regardless of case

Referenced by DNA::getcodeNuc(), hashcodon(), and Matrix::read().

int hashcodon

(

const string &

cc

)

References hashbase().

int hashcodon

(

char

c[3]

)

convert 3-letter codon to a integer from 0-63 for regular codon with letter from [ACGT] if codon length is 1 then return 64, 2 ten 65, other 66

References hashbase().

Referenced by codon::convert(), and codon::operator[]().

---

Variable Documentation

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU * A

Referenced by main().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU *UGU * C

Referenced by main(), and qcdir().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU * D

Referenced by qcdir().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU E

Referenced by Noschain::append(), fddeclump(), fitD(), fitS(), fsdeclump(), globalD(), globalS(), Noschain::intronsInside(), localS(), lsdeclump(), Noschain::Noschain(), overS(), pfitS(), pfsdeclump(), processAll(), srlocalS(), and srlsdeclump().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU *UGU *UUU * F

Referenced by fddeclump(), fsdeclump(), lsdeclump(), pfsdeclump(), print_align_header_n(), and srlsdeclump().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU * G

Referenced by main().

*ACU *AGU *AUU *CAU * H

Referenced by entropy(), bioseq::entropy(), main(), and operator<<().

*ACU *AGU *AUU * I

Referenced by Linkbox::bestChain(), Linkmatch::bestModel(), cmpEditMinusChainFirstFront(), cmpEditPlusChainFirstFront(), cmpEditPlusChainIdenticalFront(), Noschain::commonExons(), Noschain::commonIntrons(), compareMinusChainFirstBefore(), compareMinusChainIdenticalRight(), comparePlusChainFirstBefore(), comparePlusChainIdenticalLeft(), Linkmatch::removeChain(), and SIM4().

* ACU * AGU * AUU * CAU * CCU * CGU * CUU * GAU * GCU * GGU * GUU * UAU * UCU * UGU L

* ACU * AGU M

N

* ACU * AGU * AUU * CAU * CCU* P

*ACU *AGU *AUU Q

Referenced by main(), qcdir(), gentree::showAsObject(), and gentree::showAsTable().

*ACU *AGU *AUU *CAU *CCU *CGU * R

Referenced by Refreader::newRef(), LSDynaln::tracebackBW(), and LSDynaln::tracebackFW().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU * S

Referenced by print_align_blk(), and print_align_lat().

*ACU * T

Referenced by hatrees< T >::clusterArray(), main(), print_align_header_n(), hatrees< T >::readFromFile(), hatrees< T >::readFromMap(), hatrees< T >::showClusterByLine(), and hatrees< T >::showClusterIntId().

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU * V

* ACU * AGU * AUU * CAU * CCU * CGU * CUU * GAU * GCU * GGU * GUU * UAU * UCU W

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU * Y