/usr/include/libMems-1.6/libMems/HomologyHMM/homology.h is in libmems-1.6-dev 1.6.0+4725-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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/* Generated from file homology.xml (author: Aaron Darling) on Mon Jul 16 11:09:12 EST 2007 */
/*
This file is a work based on HMMoC VERSION, a hidden Markov model compiler.
Copyright (C) 2006 by Gerton Lunter, Oxford University.
HMMoC and works based on it are free software; you can redistribute
it and/or modify it under the terms of the GNU General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
HMMOC is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with HMMoC; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
#ifndef _homology_h_
#define _homology_h_
#include "dptables.h"
#include "algebras.h"
#include <vector>
#include <iostream>
#include <string>
#include <algorithm>
using std::vector;
using std::cout;
#include <map>
using std::map;
struct Params;
//void run(std::string& sequence, std::string& prediction, double goHomologous = 0.004, double goUnrelated = 0.004, std::vector<double>* emitHomologous = NULL, std::vector<double>* emitUnrelated = NULL);
void run(std::string& sequence, std::string& prediction, const Params& params );
// Here go the state memory clique typedefs:
typedef States<bfloat,2> Statesblock2;
typedef States<bfloat,1> Statesblock1;
typedef States<bfloat,1> Statesblock3;
class HomologyDPTable {
public:
// If true, this class' destructor will delete the DP arrays
bool isInCharge;
// Pointers to arrays containing ids of states and transitions
const std::string* const stateId;
const std::string* const emissionId;
const std::string* const transitionId;
const std::string* const transitionFrom;
const std::string* const transitionTo;
const std::string* const transitionProb;
const std::string* const transitionEmit;
const std::string* const outputId;
// The actual DP tables, and total sequence lengths (which determine size of DP arrays) follow:
int iLen;
DPTable<Statesblock2,1> StateMemoryblock2;
DPTable<Statesblock1,0> StateMemoryblock1;
DPTable<Statesblock3,0> StateMemoryblock3;
// Member functions:
public:
// Default copy constructor is used; user has to set isInCharge appropriately afterwards!
HomologyDPTable(int iLen);
~HomologyDPTable();
// returns probability from DP table, given position and int or std::string state identifier
bfloat getProb(int iState ,int ) const;
bfloat getProb(const std::string sState ,int ) const;
// converts std::string identifier (for state, transition or emission) into integer id
static int getId(const std::string& sState);
static const std::string& getTransitionId(int id);
static const std::string& getEmissionId(int id);
static const std::string& getStateId(int id);
static const std::string& getOutputId(int id);
static void _cleanup() { getId("_cleanup_"); }
};
// give a name to the real type used for this HMM
typedef bfloat HomologyReal;
// define type for a 'short' real -- usually double, but can be logspace for efficiency
typedef double HomologyShortReal;
class HomologyBaumWelch {
public:
// Default copy constructor is used.
// Void constructor:
HomologyBaumWelch() { resetCounts(); }
// Not calling resetCounts() across calls allows to aggregate results over multiple datasets
void resetCounts();
void scaleCounts(bfloat scale);
// Translate an identifier (string or integer) to the index into their corresponding Baum-Welch counter array (below)
// Which array is used for any particular emission/transition depends on its order signature - see documentation for details
int transitionIndex(int intId) const { return atransitionIdx[intId]; }
int transitionIndex(string strId) const;
int emissionIndex(int intId) const { return aemissionIdx[intId]; }
int emissionIndex(string strId) const;
// Now follow, in triplets (one for each order signature):
// Transition or emission counters;
// Array of identifiers; and
// Dimension of array (number of counters).
bfloat transitionBaumWelchCount0[8];
static int transitionIdentifier0[8];
static const int transitionDimension0 = 8;
bfloat emissionBaumWelchCount0[1];
static int emissionIdentifier0[1];
static const int emissionDimension0 = 1;
bfloat emissionBaumWelchCount1[8][2];
static int emissionIdentifier1[2];
static const int emissionDimension1 = 2;
private:
static int atransitionIdx[8];
static int aemissionIdx[3];
static map<const std::string,int> mId;
};
class Path {
//protected:
public:
vector<int> transitions;
public:
unsigned int size() const { // Number of transitions in path
return transitions.size();
}
int transition(int i) const { // i-th transition
return transitions[i];
}
virtual double prob(int) const = 0; // i-th transition*emission probability:
virtual const vector<int>& emission(int) const = 0; // i-th emission vector
virtual int fromState(int) const = 0; // State at from-end of i-th transition
virtual int toState(int) const = 0; // State at to-end of i-th transition
virtual int nextFrom(int) const = 0; // index of next sibling, -1 if no more (always -1 for simple paths)
virtual int nextTo(int) const = 0; // index of child (always i+1 for simple paths), or -1 if no more
virtual ~Path() {}
};
ostream& operator<<(ostream& os, const Path& p);
class SimplePath: public Path {
public:
vector<double> probs;
vector<vector<int> > emissions;
vector<int> froms;
vector<int> tos;
public:
void addEdge(int transition, double prob, vector<int>& emission, int from, int to);
double prob(int index) const;
int nextFrom(int index) const;
int nextTo(int index) const;
const vector<int>& emission(int index) const;
int fromState(int index) const;
int toState(int index) const;
void reverse();
};
struct Params {
double iStartHomologous;
double iGoHomologous;
double iGoUnrelated;
double iGoStopFromUnrelated;
double iGoStopFromHomologous;
double aEmitHomologous[8];
double aEmitUnrelated[8];
};
bfloat Forward(HomologyDPTable** ppOutTable,Params iPar,char *aSeq,int iLen);
bfloat Backward(HomologyBaumWelch& bw,HomologyDPTable* pInTable,HomologyDPTable** ppOutTable,Params iPar,char *aSeq,int iLen);
bfloat Viterbi_recurse(HomologyDPTable** ppOutTable,Params iPar,char *aSeq,int iLen);
Path& Viterbi_trace(HomologyDPTable* pInTable,Params iPar,char *aSeq,int iLen);
#endif // _homology_h_
/* --- end of HMMoC-generated file --- */
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