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#ifndef __HMM_H__
#define __HMM_H__
extern "C" {
#include <float.h>
#include <structs.h>
#include <funcs.h>
#include <squid.h>
#include <msa.h>
#include <string.h>
}
#include <vector>
using namespace std;
class HMMHit {
public:
HMMHit(float s, double p, double e);
double getPValue() { return pvalue; };
void setPValue(double p) { pvalue = p; };
double getEValue() { return evalue; };
void setEValue(double e) { evalue = e; };
float getScore() { return score; };
void setScore(float s) { score = s; };
~HMMHit() { };
private:
double pvalue;
double evalue;
float score;
};
class HMMGlobalHit : public HMMHit {
public:
HMMGlobalHit(float s, double p, double e) : HMMHit(s, p, e) { };
private:
};
class HMMDomainHit : public HMMHit {
public:
HMMDomainHit(float s, double p, double e);
void setSeqFrom(int s) { seqfrom = s; };
int getSeqFrom() { return seqfrom; };
void setSeqTo(int s) { seqto = s; };
int getSeqTo() { return seqto; };
void setSeqLength(int s) { seqlen = s; };
int getSeqLength() { return seqlen; };
void setHMMFrom(int h) { hmmfrom = h; };
int getHMMFrom() { return hmmfrom; };
void setHMMTo(int h) { hmmto = h; };
int getHMMTo() { return hmmto; };
double getParentPValue() { return ppvalue; };
void setParentPValue(double p) { ppvalue = p; };
double getParentEValue() { return pevalue; };
void setParentEValue(double e) { pevalue = e; };
float getParentScore() { return pscore; };
void setParentScore(float s) { pscore = s; };
private:
int seqfrom, seqto, seqlen, hmmfrom, hmmto;
double ppvalue, pevalue;
float pscore;
};
class HMMReport {
public:
HMMReport() { };
void addGlobalHit(HMMGlobalHit *h);
HMMGlobalHit *getGlobalHit(int i);
int numGlobalHits() { return global.size(); };
void addDomainHit(HMMDomainHit *h);
HMMDomainHit *getDomainHit(int i);
int numDomainHits() { return domain.size(); };
~HMMReport();
private:
vector<HMMGlobalHit *> global;
vector<HMMDomainHit *> domain;
};
class HMM {
public:
HMM() { init(NULL, 0, 1); };
HMM(char *filename) { init(filename, 0, 1); };
HMM(char *filename, int df, int n2) { init(filename, df, n2); };
HMMReport *search(char *seq);
int train(char **seqs, int len);
int save(char *filename, int append, int binary);
int load(char *filename);
int modelLoaded() { return (model != NULL); };
int getDoForward() { return doForward; };
void setDoForward(int df) { doForward = df; };
int getDoNull2() { return doNull2; };
void setDoNull2(int n2) { doNull2 = n2; };
~HMM();
private:
void init(char *filename, int df, int n2);
struct threshold_s thresh;
struct plan7_s *model;
int doForward;
int doNull2;
};
#endif
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