Removing old version of mafft to replace with the new

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / Globaldp.hpp

diff --git a/binaries/src/mafft/extensions/mxscarna_src/Globaldp.hpp b/binaries/src/mafft/extensions/mxscarna_src/Globaldp.hpp
deleted file mode 100644 (file)
index ba3e06f..0000000
--- a/binaries/src/mafft/extensions/mxscarna_src/Globaldp.hpp
+++ /dev/null
@@ -1,109 +0,0 @@
-////////////////////////////////////////////////////////////////
-// Globaldp.hpp
-// Global Alignment of two profile computed by SCARNA algorithm
-////////////////////////////////////////////////////////////////
-
-
-#ifndef __GLOBALDP_HPP__
-#define  __GLOBALDP_HPP__
-
-#include <string>
-#include <iostream>
-#include "nrutil.h"
-#include "Util.hpp"
-#include "Beta.hpp"
-#include "scarna.hpp"
-#include "StemCandidate.hpp"
-#include "MultiSequence.h"
-#include "Sequence.h"
-#include "BPPMatrix.hpp"
-
-using namespace ProbCons;
-using namespace std;
-namespace MXSCARNA {
-
-typedef std::vector<StemCandidate> stemcandidate;
-class Globaldp {
-private:
-    static double ribosum_matrix[16][16];
-
-    NRMat<float> VM, VG;
-    NRMat<int>   traceMI, traceMJ, traceGI, traceGJ;
-
-    const stemcandidate *pscs1, *pscs2;
-    const MultiSequence *seqs1, *seqs2;
-    std::vector<int> *matchPSCS1, *matchPSCS2;
-    SafeVector<BPPMatrix*> &BPPMatrices;
-    NRMat<float> posterior;
-    NRMat3d<int> countConp1, countConp2;
-    NRMat<int> countContConp1, countContConp2;
-    Trimat<float> *profileBPPMat1;
-    Trimat<float> *profileBPPMat2;
-    float multiDeltaScore;
-    float multiDeltaStacking;
-    float multiScore;
-    float multiStacking;
-    float multiPenalty;
-    
-    float scorePSCPair(const StemCandidate &sc1, const StemCandidate &sc2);
-    float wordSimilarity(const StemCandidate &sc1, const StemCandidate &sc2, int i, int j);
-    int   returnBasePairType(char s, char r);
-    float probabilityScore(const StemCandidate &sc1, const StemCandidate &sc2);
-    float stackingScore(const StemCandidate &sc1, const StemCandidate &sc2);
-    float distancePenalty(const StemCandidate &sc1, const StemCandidate &sc2);
-    float incrementalScorePSCPair(const StemCandidate &sc1, const StemCandidate &sc2);
-    float incrementalProbabilityScore(const StemCandidate &sc1, const StemCandidate &sc2);
-    float incrementalStackingScore(const StemCandidate &sc1, const StemCandidate &sc2);
-    float incrementalWordSimilarity(const StemCandidate &sc1, const StemCandidate &sc2, int i, int j);
-    Trimat<float>* makeProfileBPPMatrix(const MultiSequence *Sequences);
-
-    void Initialize();
-    void DP();
-    float traceBack();
-    void printMatch();
-public:
-
-    Globaldp(const stemcandidate *mypscs1, const stemcandidate *mypscs2, 
-            const MultiSequence *myseqs1, const MultiSequence *myseqs2,
-            std::vector<int> *matchPSCS1, std::vector<int> *matchPSCS2,
-            VF *myPosterior, SafeVector<BPPMatrix*> &myBPPMatrices,
-            float myMultiDeltaScore = MULTIDELTASCORE, float myMultiDeltaStacking = MULTIDELTASTACKING,
-            float myMultiScore = MULTISCORE, float myMultiStacking = MULTISTACKING,
-            float myMultiPenalty = MULTIPENALTY) 
-       : VM(mypscs1->size(), mypscs2->size()), 
-         VG(mypscs1->size(), mypscs2->size()),
-         traceMI(mypscs1->size(), mypscs2->size()),
-         traceMJ(mypscs1->size(), mypscs2->size()),
-         traceGI(mypscs1->size(), mypscs2->size()),
-         traceGJ(mypscs1->size(), mypscs2->size()),
-         pscs1(mypscs1), pscs2(mypscs2), 
-         seqs1(myseqs1), seqs2(myseqs2),
-         matchPSCS1(matchPSCS1), matchPSCS2(matchPSCS2), 
-         BPPMatrices(myBPPMatrices), posterior(myseqs1->GetSequence(0)->GetLength() + 1, myseqs2->GetSequence(0)->GetLength() + 1),
-         countConp1(WORDLENGTH, 17, mypscs1->size()+1), countConp2(WORDLENGTH, 17, mypscs2->size()+1),
-         countContConp1(0, 17, mypscs1->size()+1), countContConp2(0, 17, mypscs2->size()+1), 
-         multiDeltaScore(myMultiDeltaScore), multiDeltaStacking(myMultiDeltaStacking),
-         multiScore(myMultiScore), multiStacking(myMultiStacking), 
-         multiPenalty(myMultiPenalty) {
-       
-       VF::iterator myPosteriorPtr = myPosterior->begin();
-       for (int i = 0; i <= seqs1->GetSequence(0)->GetLength(); i++) {
-           for (int j = 0; j <= seqs2->GetSequence(0)->GetLength(); j++) {
-               posterior[i][j] = (*myPosteriorPtr)/(seqs1->GetSequence(0)->GetLength()*seqs2->GetSequence(0)->GetLength());
-               myPosteriorPtr++;
-           }
-       }
-    }
-
-
-                                                        
-    float Run();
-
-    void setMultiDeltaScore(float score) { multiDeltaScore = score; }
-    void setMultiDeltaStacking(float score) { multiDeltaStacking = score; }
-    void setMultiScore(float score) { multiScore = score; }
-    void setMultiStacking(float score) { multiStacking = score; }
-    void setMultiPenalty(float score) { multiPenalty = score; }
-};
-}
-#endif // __GLOBALDP_HPP__