BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioProteinSequence.h
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00001 /****************************************************************************
00002 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
00003 The BioBhasha : The Biologist's Programming Language 
00004 Version 1.0 (19th December 2001)
00005 Prasad, B.V.L.S.
00006 Contact: burrashiva@yahoo.com
00007 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
00008 *****************************************************************************/
00009 #ifndef BIOPROTEINSEQUENCE_H
00010 #define BIOPROTEINSEQUENCE_H
00011 
00012 #include "BioSequence.h"
00013 #include <string>
00014 
00015 class BioProteinSequence : public BioSequence
00016 {
00017         public: 
00018                 BioProteinSequence(const string&); 
00019                 BioProteinSequence();
00020           BioProteinSequence(const string& seqnam, const string& seq);
00021     
00022                 bool checkProteinSequence(); 
00023     void setSequence(const string& seqnam, const string& seq);
00024                 double getMolecularWeight();
00025     string  getAminoAcid(const long&);
00026         double getMolarExtinctionCoefficient();
00027         double getExtinctionCoefficient();
00028         double getProteinConcentration(double absorption);
00029 
00030         int getNumberOfBasicAminoAcids();
00031         int getNumberOfAcidicAminoAcids();
00032         int getNumberOfPolarAminoAcids();
00033         int getNumberOfNonPolarAminoAcids();
00034 
00035         vector <long >  getPositionsOfBasicAminoAcids();
00036         vector <long >  getPositionsOfAcidicAminoAcids();
00037         vector <long >  getPositionsOfPolarAminoAcids();
00038         vector <long >  getPositionsOfNonPolarAminoAcids();
00039 
00040         
00041         void  showPositionsOfBasicAminoAcids(ostream& os = cout);
00042         void  showPositionsOfAcidicAminoAcids(ostream& os = cout);
00043         void  showPositionsOfPolarAminoAcids(ostream& os = cout);
00044         void  showPositionsOfNonPolarAminoAcids(ostream& os = cout);
00045 
00046         void showHydropathyPlot(const int& windowSize, BioPostScript& ps);
00047 };
00048 
00049 BioProteinSequence BioGetRandomProteinSequence(const int& seqLength);
00050 #endif 
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