BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioHmm.h
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00001 #ifndef BIOHMM_H
00002 #define BIOHMM_H
00003 
00004 #include "BioProteinSequence.h"
00005 #include "BioAminoAcidLibrary.h"
00006 #include "BioDnaSequence.h"
00007 #include "BioClustal.h"
00008 #include "BioOutputStream.h"
00009 #include <vector>
00010 #include <algorithm>
00011 
00012 using namespace std;
00013 
00014 class BioHmm
00015 {
00016   private:
00017     vector<char> h_states, o_states;
00018     vector<float> ini_prob;
00019     vector<vector<float> > trans, emit;
00020     
00021   public:
00022     BioHmm();
00023     ~BioHmm();
00024     BioHmm(vector<char>hs,vector<char>os,vector<float> init, vector<vector<float> > tr, vector<vector<float> > em);
00025     BioHmm(BioClustal bc);
00026     vector<char> getObservableStates(BioClustal bc);
00027     vector<float> getInitialStateProbabilities(BioClustal bc);
00028     void showProfile();
00029 };
00030 
00031 #endif
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