da/d1d/_bio_dna_sequence_global_alignment_8h_source.html

00001 #ifndef BIODNASEQUENCEGLOBALALIGNMENT_H
00002 #define BIODNASEQUENCEGLOBALALIGNMENT_H
00003
00004 #include <iostream>
00005 #include <fstream>
00006 #include <string>
00007 #include <sstream>
00008 #include "BioUtilities.h"
00009 #include "BioDnaSequence.h"
00010 #include "BioFasta.h"
00011 #include "BioDnaSequenceAlignment.h"
00012
00013 class BioDnaSequenceGlobalAlignment : public BioDnaSequenceAlignment
00014 {
00015  private:
00016         void formAccumulationMatrix();
00017
00018         void backTrack();
00019
00020         void show(ostream & = cout);
00021  public:
00022     BioDnaSequenceGlobalAlignment();
00023     BioDnaSequenceGlobalAlignment(BioDnaSequence,BioDnaSequence,string,string MatName,int GP=-11,int extn=-9999);
00024     BioDnaSequenceGlobalAlignment(BioDnaSequence,string,string,string MatName,int GP=-11,int extn=-9999);
00025     BioDnaSequenceGlobalAlignment(BioDnaSequence,BioDnaSequence,string mat="IDENTITY",int GP=-11,int extn=-9999);
00026     BioDnaSequenceGlobalAlignment(BioDnaSequence,string,string mat="IDENTITY",int GP=-11,int extn=-9999);
00027     BioDnaSequenceGlobalAlignment(BioDnaSequence,BioDnaSequence,int MS,int MMS,int GP=-11,int extn=-9999);
00028     BioDnaSequenceGlobalAlignment(BioDnaSequence,string,int MS,int MMS,int GP=-11,int extn=-9999);
00029
00030
00031     BioDnaSequenceGlobalAlignment(BioFasta,BioFasta,string,string MatName,int GP=-11,int extn=-9999);
00032     BioDnaSequenceGlobalAlignment(BioFasta,string,string,string MatName,int GP=-11,int extn=-9999);
00033     BioDnaSequenceGlobalAlignment(BioFasta,BioFasta,string mat="IDENTITY",int GP=-11,int extn=-9999);
00034     BioDnaSequenceGlobalAlignment(BioFasta,string,string mat="IDENTITY",int GP=-11,int extn=-9999);
00035     BioDnaSequenceGlobalAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-11,int extn=-9999);
00036     BioDnaSequenceGlobalAlignment(BioFasta,string,int MS,int MMS,int GP=-11,int extn=-9999);
00037
00038
00039     BioDnaSequenceGlobalAlignment(string,string,string,string,int GP=-11,int extn=-9999);
00040     BioDnaSequenceGlobalAlignment(string,string,string mat="IDENTITY",int GP=-11,int extn=-9999);
00041     BioDnaSequenceGlobalAlignment(string,string,int MS,int MMS,int GP=-11,int extn=-9999);
00042
00043     void showAccumulationMatrix(ostream & = cout);
00044
00045     void showAlignment(ostream & = cout);
00046
00047     long getNumberOfIdentities();
00048     float getIdentity();
00049     float getScore();
00050
00051     string getAlignedSequence1();
00052     string getAlignedSequence2();
00053
00054 };
00055
00056 #endif