BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
Overlap/BioProteinSequenceAlignment.h
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00001 #ifndef BIOPROTEINSEQUENCEALIGNMENT_H
00002 #define BIOPROTEINSEQUENCEALIGNMENT_H
00003 
00004 #include <iostream>
00005 #include <fstream>
00006 #include <sstream>
00007 #include <string>
00008 #include <vector>
00009 #include "BioUtilities.h"
00010 #include "BioProteinSequence.h"
00011 #include "BioSwissProt.h"
00012 #include "BioFasta.h"
00013 #include "BioProteinSubstitutionMatrix.h"
00014 #include "BioMultipleFasta.h"
00015 #include "BioLenPos.h"
00016 #include "BioMatrix.h"
00017 
00018 class BioProteinSequenceAlignment
00019 {
00020 protected:
00021                 /*VARIABLES*/
00022                 string seq1_,seq2_; /* These variables holds the sequences to be aligned*/
00023     
00024                 string outSeq1_,outSeq2_;  /* These varables holds the ouput aligned sequences*/
00025    
00026       string seqName1_,seqName2_; /* These variables holds the Sequence Names */
00027       
00028                 static string aminoAcidSeq_; /* This String Holds the AminoAcid names in a most comman way of its usage*/
00029     
00030                 int gapPenalty; /* This varible is used to Set the Gap Penality in sequnce alignment process (in substitution matrix) */
00031     
00032                 int gapExtn; /* This variable is used to set the Gap Extention Penality in seqquence alignment process*/
00033     
00034                 BioMatrix substitutionMatrix; /* This 2D array holds the Substitutionmatrix elements used for the currrent alignment*/
00035 //              vector < vector < int > > tempMatrix; /* This is a temporary 2D variable used for most convenetianal way data transfer*/
00036                 BioMatrix scoringMatrix;
00037                 //int** accumMatrix;
00038       int status;
00039     
00040         /*FUNCTIONS*/
00041                 void formScoringMatrix();
00042     
00043       int getAccValMov(long,long,int);
00044 
00045       void init();
00046       
00047       BioProteinSequenceAlignment();
00048 //      ~BioProteinSequenceAlignment(){ delete seq1_, seq2_, outSeq1_, outSeq2_, seqName1_, seqName2_; };
00049     
00050                 BioProteinSequenceAlignment(BioProteinSequence,BioProteinSequence,string mat="BLOSUM62",int GP=-11,int extn=-9999);
00051                 BioProteinSequenceAlignment(BioProteinSequence,BioProteinSequence,string,string,int GP=-11,int extn=-9999);
00052                 BioProteinSequenceAlignment(BioProteinSequence,BioProteinSequence,int MS,int MMS,int GP=-11,int extn=-9999);
00053                 BioProteinSequenceAlignment(BioProteinSequence,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
00054                 BioProteinSequenceAlignment(BioProteinSequence,string,string,string,int GP=-11,int extn=-9999);
00055                 BioProteinSequenceAlignment(BioProteinSequence,string,int MS,int MMS,int GP=-11,int extn=-9999);
00056 
00057      BioProteinSequenceAlignment(BioSwissProt,BioSwissProt,string mat="BLOSUM62",int GP=-11,int extn=-9999);
00058      BioProteinSequenceAlignment(BioSwissProt,BioSwissProt,string,string,int GP=-11,int extn=-9999);
00059      BioProteinSequenceAlignment(BioSwissProt,BioSwissProt,int MS,int MMS,int GP=-11,int extn=-9999);
00060      BioProteinSequenceAlignment(BioSwissProt,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
00061      BioProteinSequenceAlignment(BioSwissProt,string,string,string,int GP=-11,int extn=-9999);
00062      BioProteinSequenceAlignment(BioSwissProt,string,int MS,int MMS,int GP=-11,int extn=-9999);
00063 
00064         
00065      BioProteinSequenceAlignment(const BioFasta&,const BioFasta&,const string& mat="BLOSUM62",const int& GP=-11,const int& extn=-9999);
00066      BioProteinSequenceAlignment(BioFasta,BioFasta,string,string,int GP=-11,int extn=-9999);
00067      BioProteinSequenceAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-11,int extn=-9999);
00068      BioProteinSequenceAlignment(BioFasta,string,string mat="BLOSUM62",int GP=-11,int extn=-9999);
00069      BioProteinSequenceAlignment(BioFasta,string,string,string,int GP=-11,int extn=-9999);
00070      BioProteinSequenceAlignment(BioFasta,string,int MS,int MMS,int GP=-11,int extn=-9999);
00071 
00072         
00073      BioProteinSequenceAlignment(const string&,const string&,const string& mat="BLOSUM62",int GP=-11,int extn=-9999);
00074      BioProteinSequenceAlignment(const string&,const string&,const string&,const string&,int GP=-11,int extn=-9999);
00075         BioProteinSequenceAlignment(const string&,const string&,int MS,int MMS,int GP=-11,int extn=-9999);
00076                 
00077 public:
00078    void setSequence1(BioProteinSequence);
00079    void setSequence2(BioProteinSequence);
00080 
00081         void setSequence1(BioSwissProt);
00082         void setSequence2(BioSwissProt);
00083 
00084    void setSequence1(BioFasta);
00085         void setSequence2(BioFasta);
00086 
00087         void setSequence1(const string&);
00088    void setSequence2(const string&);
00089 
00090    void setGapPenalty(int GP=-11,int extn=-9999);
00091         void setSubstitutionMatrix(const string&);
00092         void setSubstitutionMatrix(const string&,const string&);
00093         void setMatchMisMatchScore(int MS=1,int MMS=0);
00094 
00095         void showScoringMatrix(ostream & = cout);
00096 
00097 };
00098 
00099 #endif
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