BioUtilities.h File Reference

#include <fstream>
#include <vector>
#include <string>
#include <sstream>
#include <algorithm>
#include <cmath>
#include <cstdlib>
#include <iostream>
#include "BioMatrix.h"

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Functions
string	toString (const vector< int > &x)
vector< string >	extractDataBlock (ifstream &fin, const string &startStr, const string &endStr)
bool	checkFloat (string val)
vector< int >	processString (string indexstr)
string	rightTrim (const string &a)
string	leftTrim (const string &a)
string	parseStr (const string &st, const string &fill)
void	reverseLargeString (string &st)
vector< int >	getUniqueVectorElements (vector< int >)
vector< float >	getUniqueVectorElements (vector< float >)
vector< char >	getUniqueVectorElements (vector< char >)
vector< string >	getUniqueVectorElements (vector< string >)
vector< string >	removeVectorElements (vector< string >, string)
void	printVector (vector< string >, char c='\t')
vector< string >	splitString (string s, char c='\t')
void	BioGetChar ()
void	BioClear ()
int	stringToInt (const string &)
long	stringToLong (const string &)
float	stringToFloat (const string &)
double	stringToDouble (const string &)
string	toString (const int &)
string	toString (const long &)
string	toString (const float &)
string	toString (const double &)
string	toUpperCase (const string &s)
string	toLowerCase (const string &s)
string	reverseString (const string &s)
string	replaceString (string st, string p1, string rep="", int noRep=-1)
void	align (string, int, int, ostream &=cout)
void	alignLines (string, ostream &=cout, unsigned int len=67)
float	roundNumber (float number, float dec)
int	delimiter (string, char, string &, int z=0)
string	rmBlank (const string &x)
float	toDegrees (const float rad_)
float	toRadians (const float th_)
float	distance (const float x1, const float y1, const float z1, const float x2, const float y2, const float z2)
float	angle (const float, const float, const float, const float, const float, const float, const float, const float, const float)
float	torsion (const float, const float, const float, const float, const float, const float, const float, const float, const float, const float, const float, const float)
float	angleBetweenDirectionCosines (float l1, float m1, float n1, float l2, float m2, float n2)
float	angleBetweenDirectionCosines (BioMatrix &x1, BioMatrix &x2)
float	determinant (float, float, float, float, float, float, float, float, float)
float	BioDeterminant3by3 (BioMatrix &)
BioMatrix	BioInverse3by3 (BioMatrix &)
void	breakLines (string &s, ostream &=cout)
void	BioShowInBrowser (string fileName_, string browser_="c:/Program\\ Files/Internet\\ Explorer/IEXPLORE.exe")
void	BioShowDnaSubstitutionMatrix (ostream &os=cout)
void	BioShowProteinSubstitutionMatrix (ostream &os=cout)
void	BioShowAcidicAminoAcids (ostream &os=cout)
void	BioShowBasicAminoAcids (ostream &os=cout)
void	BioShowPolarAminoAcids (ostream &os=cout)
void	BioShowNonPolarAminoAcids (ostream &os=cout)
void	BioShowAminoAcidAmbiguityCode (ostream &os=cout)
void	BioShowNucleicAcidAmbiguityCode (ostream &os=cout)
void	BioShowFTKs (ostream &os=cout)
void	BioShowFTQs (ostream &os=cout)
void	BioShowNucleicAcidProperties (ostream &os=cout)
void	BioShowAminoAcidProperties (ostream &os=cout)
void	BioShowSpaceGroupNames (ostream &os=cout)
void	BioShowStandardCodonTable (ostream &os=cout)
void	BioShowAmbiguousRestrictionEnzymes (ostream &os=cout)
void	BioShowUnAmbiguousRestrictionEnzymes (ostream &os=cout)
void	BioShowUniqueAmbiguousRestrictionEnzymes (ostream &os=cout)
void	BioShowUniqueUnAmbiguousRestrictionEnzymes (ostream &os=cout)
Variables
const double	PI = 3.14285714285714

---

Function Documentation

void align	(	string	,
		int	,
		int	,
		ostream &	= cout
	)

void alignLines	(	string	,
		ostream &	= cout,
		unsigned int	len = 67
	)

float angle	(	const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float
	)

float angleBetweenDirectionCosines	(	float	l1,
		float	m1,
		float	n1,
		float	l2,
		float	m2,
		float	n2
	)

float angleBetweenDirectionCosines	(	BioMatrix &	x1,
		BioMatrix &	x2
	)

void BioClear

(

)

float BioDeterminant3by3

(

BioMatrix &

)

void BioGetChar

(

)

BioMatrix BioInverse3by3

(

BioMatrix &

)

void BioShowAcidicAminoAcids

(

ostream &

os = cout

)

void BioShowAmbiguousRestrictionEnzymes

(

ostream &

os = cout

)

void BioShowAminoAcidAmbiguityCode

(

ostream &

os = cout

)

void BioShowAminoAcidProperties

(

ostream &

os = cout

)

void BioShowBasicAminoAcids

(

ostream &

os = cout

)

void BioShowDnaSubstitutionMatrix

(

ostream &

os = cout

)

void BioShowFTKs

(

ostream &

os = cout

)

void BioShowFTQs

(

ostream &

os = cout

)

void BioShowInBrowser	(	string	fileName_,
		string	browser_ = "c:/Program\\ Files/Internet\\ Explorer/IEXPLORE.exe"
	)

void BioShowNonPolarAminoAcids

(

ostream &

os = cout

)

void BioShowNucleicAcidAmbiguityCode

(

ostream &

os = cout

)

void BioShowNucleicAcidProperties

(

ostream &

os = cout

)

void BioShowPolarAminoAcids

(

ostream &

os = cout

)

void BioShowProteinSubstitutionMatrix

(

ostream &

os = cout

)

void BioShowSpaceGroupNames

(

ostream &

os = cout

)

void BioShowStandardCodonTable

(

ostream &

os = cout

)

void BioShowUnAmbiguousRestrictionEnzymes

(

ostream &

os = cout

)

void BioShowUniqueAmbiguousRestrictionEnzymes

(

ostream &

os = cout

)

void BioShowUniqueUnAmbiguousRestrictionEnzymes

(

ostream &

os = cout

)

void breakLines	(	string &	s,
		ostream &	= cout
	)

bool checkFloat

(

string

val

)

int delimiter	(	string	,
		char	,
		string &	,
		int	z = 0
	)

float determinant	(	float	,
		float	,
		float	,
		float	,
		float	,
		float	,
		float	,
		float	,
		float
	)

float distance	(	const float	x1,
		const float	y1,
		const float	z1,
		const float	x2,
		const float	y2,
		const float	z2
	)

vector<string> extractDataBlock	(	ifstream &	fin,
		const string &	startStr,
		const string &	endStr
	)

vector<int> getUniqueVectorElements

(

vector< int >

)

vector<float> getUniqueVectorElements

(

vector< float >

)

vector<char> getUniqueVectorElements

(

vector< char >

)

vector<string> getUniqueVectorElements

(

vector< string >

)

string leftTrim

(

const string &

a

)

string parseStr	(	const string &	st,
		const string &	fill
	)

void printVector	(	vector< string >	,
		char	c = '\t'
	)

vector<int> processString

(

string

indexstr

)

vector<string> removeVectorElements	(	vector< string >	,
		string
	)

string replaceString	(	string	st,
		string	p1,
		string	rep = "",
		int	noRep = -1
	)

void reverseLargeString

(

string &

st

)

string reverseString

(

const string &

s

)

string rightTrim

(

const string &

a

)

string rmBlank

(

const string &

x

)

float roundNumber	(	float	number,
		float	dec
	)

vector<string> splitString	(	string	s,
		char	c = '\t'
	)

double stringToDouble

(

const string &

)

float stringToFloat

(

const string &

)

int stringToInt

(

const string &

)

long stringToLong

(

const string &

)

float toDegrees

(

const float

rad_

)

string toLowerCase

(

const string &

s

)

float toRadians

(

const float

th_

)

float torsion	(	const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float	,
		const float
	)

string toString

(

const vector< int > &

x

)

string toString

(

const int &

)

string toString

(

const long &

)

string toString

(

const float &

)

string toString

(

const double &

)

string toUpperCase

(

const string &

s

)

---

Variable Documentation

const double PI = 3.14285714285714