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/*****************************************************************************\
* Filename : intronmodel.hh
* Authors : Emmanouil Stafilarakis, Mario Stanke
*
* Description: Intron Model Header File
*
*
* Date | Author | Changes
*------------|-----------------------|----------------------------------------
* 10.11.2001 | Stafilarakis Emm. | Creation of the file
* 31.05.2002 | Mario Stanke | static data members
\******************************************************************************/
#ifndef _INTRONMODEL_HH
#define _INTRONMODEL_HH
#include "statemodel.hh"
/**
* @memo The intron model class.
*
* @doc
*
* @authors Emmanouil Stafilarakis, Mario Stanke
*/
class IntronModel : public StateModel {
public:
IntronModel();
~IntronModel();
StateType getStateType () const {
return itype;
}
/**
* Build all needed probabilities from the given
* gene set.
*
* @param annoseq A single linked list annotated sequences
*/
void buildModel( const AnnoSequence* annoseq, int parIndex );
void registerPars( Parameters* parameters);
/**
* Print the wanted probabilities in files.
* The names of the files should be given with
* the Properties object /IntronModel/outfile
*/
void printProbabilities( int parIndex, BaseCount *bc, const char* suffix = NULL );
void initAlgorithms(Matrix<Double>&, int);
virtual void updateToLocalGCEach( Matrix<Double>& trans, int cur);
void viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int,
AlgorithmVariant, OptionListItem&);
Double emiProbUnderModel (int begin, int end) const;
Double seqProb (int left, int right) const;
static Double dSSProb (int base, bool forwardStrand);
static Double aSSProb (int base, bool forwardStrand);
static void init();
static void resetPars() {
initSnippetProbs();
initAlgorithmsCalled = false;
}
static void updateToLocalGC(int from = -1, int to = -1);
static void readProbabilities(int parIndex);
static void readAllParameters();
static void updateParameters(int idx);
static void storeGCPars(int idx);
static Integer getD() {return d;}
static double getMAL() {return mal.doubleValue();}
static void resetModelCount(){introncount = 0;};
static double getGeoProb(){return geoProb;}
static Double getAssMotifProbThreshold(double q) {return assMotif->getProbThreshold(q);}
static double getMeanIntrLen();
private:
static void initSnippetProbs();
void processSequence( const char* start, const char* end);
/**
*
*/
void buildProbabilities ( const AnnoSequence* annoseq );
void buildLenDist ( const AnnoSequence* annoseq );
void processASS ( const char* dna, int pos, Boolean withMotif=true);
void processDSS ( const char* dna, int pos );
void makeDSSProbs ( );
void storeIntronLengths ( const AnnoSequence* annoseq);
void printLengthQuantiles();
void initCountVars ( );
void readSpliceSites ();
public:
static Integer k;
static PatMMGroup emiprobs;
static PatMMGroup *GCemiprobs;
static BinnedMMGroup dssBinProbs;
static BinnedMMGroup assBinProbs;
static vector<Double> lenDist;
private:
StateType itype;
Integer gweight;
char* codon;
static int beginOfBioIntron, endOfBioIntron;
static vector<Integer> emicount;
static vector<Integer> intlencount;
static Integer introns; // number of introns
static Integer introns_d; // number of introns of length <= d
static Integer d;
static Integer minwindowcount;
static double slope_of_bandwidth;
static Double patpseudo;
static Double probShortIntron; // probability that intron is at most d long
static Double *GCprobShortIntron; // array for each GC content class
static Double mal; // mean additional length (if longer than d)
static Double *GCmal; // array for each GC content class
static Integer introncount;
static Integer gesbasen;
// variables related to splicing
static Integer c_ass;
static Integer c_dss;
static vector<Integer> asscount;
static vector<Integer> dsscount;
static Integer ass_upwindow_size;
static vector<Double> assprobs;
static vector<Double> dssprobs;
static Motif *assMotif; // basecounts of the window before the ass
static Motif *GCassMotif; // array of Motifs, one for each GC content class
static Boolean hasSpliceSites;
static Double asspseudo; // pseudocount for patterns in acceptor splice sites
static Double dsspseudo; // pseudocount for patterns in donor splice sites
static Double dssneighborfactor; // taken from the prob of the neighbor patterns
static Integer ass_motif_memory; // order of the markov chain in the ass upstream motif
static Integer ass_motif_radius; // radius of the pooling window in the ass upstream motif
static double non_gt_dss_prob;
static double non_ag_ass_prob;
static SnippetProbs *snippetProbs, *rSnippetProbs;
static bool initAlgorithmsCalled, haveSnippetProbs;
static int lastParIndex; // GC-index of current parameter set
static Integer verbosity;
static double geoProb;
static int ass_outside; // Constant::ass_upwindow_size + Constant::ass_start + ASS_MIDDLE;
};
class IntronModelError : public ProjectError {
public:
IntronModelError(string msg) : ProjectError(msg) {}
};
#endif // _INTRONMODEL_HH
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