BioUtilities.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : A Programming Language for Biologist
Version 1.0 (19th December 2001)
Dr. Prasad, B.V.L.S.
Contact: prasadbvls@helixgenomics.com
Version 1.1 (23th January 2003)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/

#ifndef BIOUTILITIES_H
#define BIOUTILITIES_H

using namespace std;

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

/*****************************************************************************
 *
 * COMMENTARY on Each Class/Concept: Hows and Whys :
 *
 * BioUtilities:
 *              As the name suggests, this file holds some  global functions
 *              which have been most frequently and most extensivly used to 
 *              write efficient file parsers, converters etc... and some 
 *              very primitive functions like distance, angle, torsion etc.
 * *************************************************************************/

const double PI = 3.14285714285714;

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 );

// REVERSING THE GIVEN LARGE STRING
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();

//float getPreciseFloat(double& d);
//float getPreciseFloat(double& d, int pre);

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);            
// Delimiter Needs some explanation:
// 1st Argument [string] : string which has to be parsed 
// 2nd Argument [char  ] : delimiter character, ex: ';','.'etc
// 3rd Argument [string&]: return string till the delimiter
// 4th Argument [int   ] : Position in the 1st Argument String, from where 
//                      the parsing should start.
// int Return Value: This give the position of the delimiter and 
// this return integer value can be used to parse the whole string for 
// multiple delimiters within  the string by using recurrence technique.
// This delimiter function is especially useful in Fasta Format for reading
// the First Line with ';' as delimiter to identify the seqId.

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);

#endif