da/d1b/_bio_dna_sequence_overlap_alignment_8h_source.html

00001 #ifndef BIODNASEQUENCEOVERLAPALIGNMENT_H
00002 #define BIODNASEQUENCEOVERLAPALIGNMENT_H
00003
00004 #include <iostream>
00005 #include <fstream>
00006 #include <string>
00007 #include <sstream>
00008 #include "BioUtilities.h"
00009 #include "BioDnaSequence.h"
00010 #include "BioGenBank.h"
00011 #include "BioFasta.h"
00012 #include "BioEmbl.h"
00013 #include "BioDnaSequenceAlignment.h"
00014
00015 class BioDnaSequenceOverlapAlignment : public BioDnaSequenceAlignment
00016 {
00017         int threshold;
00018
00019         void formAccumulationMatrix();
00020
00021         void backTrack();
00022
00023         void show(ostream & = cout);
00024
00025  public:
00026         BioDnaSequenceOverlapAlignment();
00027                 BioDnaSequenceOverlapAlignment(BioDnaSequence,BioDnaSequence,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00028                 BioDnaSequenceOverlapAlignment(BioDnaSequence,string,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00029                 BioDnaSequenceOverlapAlignment(BioDnaSequence,BioDnaSequence,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00030                 BioDnaSequenceOverlapAlignment(BioDnaSequence,string,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00031                 BioDnaSequenceOverlapAlignment(BioDnaSequence,BioDnaSequence,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00032                 BioDnaSequenceOverlapAlignment(BioDnaSequence,string,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00033
00034                 BioDnaSequenceOverlapAlignment(BioGenBank,BioGenBank,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00035                 BioDnaSequenceOverlapAlignment(BioGenBank,string,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00036                 BioDnaSequenceOverlapAlignment(BioGenBank,BioGenBank,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00037                 BioDnaSequenceOverlapAlignment(BioGenBank,string,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00038                 BioDnaSequenceOverlapAlignment(BioGenBank,BioGenBank,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00039         BioDnaSequenceOverlapAlignment(BioGenBank,string,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00040
00041                 BioDnaSequenceOverlapAlignment(BioFasta,BioFasta,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00042                 BioDnaSequenceOverlapAlignment(BioFasta,string,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00043                 BioDnaSequenceOverlapAlignment(BioFasta,BioFasta,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00044                 BioDnaSequenceOverlapAlignment(BioFasta,string,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00045                 BioDnaSequenceOverlapAlignment(BioFasta,BioFasta,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00046                 BioDnaSequenceOverlapAlignment(BioFasta,string,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00047
00048                 BioDnaSequenceOverlapAlignment(BioEmbl,BioEmbl,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00049                 BioDnaSequenceOverlapAlignment(BioEmbl,string,string,string MatName,int GP=-11,int extn=-9999,int TH=10);
00050                 BioDnaSequenceOverlapAlignment(BioEmbl,BioEmbl,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00051                 BioDnaSequenceOverlapAlignment(BioEmbl,string,string MatName="IDENTITY",int GP=-11,int extn=-9999,int TH=10);
00052                 BioDnaSequenceOverlapAlignment(BioEmbl,BioEmbl,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00053                 BioDnaSequenceOverlapAlignment(BioEmbl,string,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00054
00055                 BioDnaSequenceOverlapAlignment(string,string,string,string,int GP=-11,int extn=-9999,int TH=10);
00056                 BioDnaSequenceOverlapAlignment(string,string,string,int GP=-11,int extn=-9999,int TH=10);
00057                 BioDnaSequenceOverlapAlignment(string,string,int MS,int MMS,int GP=-11,int extn=-9999,int TH=10);
00058
00059         void setThreshold(int);
00060
00061         void showAccumulationMatrix(ostream & = cout);
00062
00063         void showAlignment(ostream & = cout);
00064
00065             long getNumberOfIdentities();
00066     float getIdentity();
00067     float getScore();
00068
00069     string getAlignedSequence1();
00070     string getAlignedSequence2();
00071
00072
00073 };
00074
00075 #endif