WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / RNAforester / src / alignment.h

diff --git a/binaries/src/ViennaRNA/RNAforester/src/alignment.h b/binaries/src/ViennaRNA/RNAforester/src/alignment.h
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/RNAforester/src/alignment.h
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+/*
+  Copyright by Matthias Hoechsmann (C) 2002-2004
+  =====================================                                   
+  You may use, copy and distribute this file freely as long as you
+  - do not change the file,
+  - leave this copyright notice in the file,
+  - do not make any profit with the distribution of this file
+  - give credit where credit is due
+  You are not allowed to copy or distribute this file otherwise
+  The commercial usage and distribution of this file is prohibited
+  Please report bugs and suggestions to <mhoechsm@TechFak.Uni-Bielefeld.DE>
+*/
+
+#ifndef _ALIGNMENT_H_
+#define _ALIGNMENT_H_
+
+#include <cassert>
+#include <list>
+
+#include "types.h"
+#include "algebra.h"
+#include "ppforest.h"
+#include "ppforestali.h"
+
+template<class R,class L,class AL>
+class Alignment
+{
+private:
+       struct CSFPair
+       {
+               Uint i;
+               Uint j;
+               Uint k;
+               Uint l;
+
+               CSFPair(Uint i, Uint j, Uint k, Uint l) : i(i),j(j),k(k),l(l) {};
+       };
+
+       R *m_mtrx;
+       Ulong *m_rowStart;
+    Ulong m_mtrxSize;
+
+    PPForest<L> *m_ppfx;
+    PPForest<L> *m_ppfy;
+
+    const Algebra<R,L> *m_alg;
+    const RNA_Algebra<R,L> *m_rnaAlg;
+
+    R m_localOptimum;
+    R m_localSubOptimum;
+    std::list<CSFPair> m_localAlis;        // holds which alignments are already produced by getOptLocalAlignment
+    double m_suboptimalsPercent;            // percentage is stores as a value between 0 and 1
+
+    inline R getMtrxVal(Ulong i,Ulong j) const          
+      {
+       assert(m_rowStart[i]+j<m_mtrxSize);
+       return m_mtrx[m_rowStart[i]+j];
+      };
+
+    inline void setMtrxVal(Ulong i,Ulong j,R val)
+      {
+       assert(m_rowStart[i]+j<m_mtrxSize);
+
+       m_mtrx[m_rowStart[i]+j]=val;
+       
+       m_localOptimum=m_alg->choice(m_localOptimum,val);   // here we calculate local similarity on the fly
+      };
+
+    void calculateLocal(const PPForest<L> *ppfx, const PPForest<L> *ppfy,const Algebra<R,L> &alg, bool noSpeedup=false);
+    void calculateGlobal(const PPForest<L> *ppfx, const PPForest<L> *ppfy,const Algebra<R,L> &alg, bool noSpeedup=false);
+    Uint backtrack(PPForestAli<L,AL> &ppf,Uint i, Uint j, Uint k, Uint l, Uint &node);
+public:    
+    Alignment(const PPForest<L> *ppfx, const PPForest<L> *ppfy,const Algebra<R,L> &alg, bool local, bool noSpeedup=false);
+    Alignment(const PPForest<L> *ppfx, const PPForest<L> *ppfy,const RNA_Algebra<R,L> &rnaAlg);
+    ~Alignment();
+    
+    R getGlobalOptimum();
+
+    /** This function should only be used in conjunction with
+        *  similarity based algebras
+        */
+    double getGlobalOptimumRelative();
+
+    inline R getLocalOptimum(){return m_localSubOptimum;};
+    R getSILOptimum();
+    void getOptGlobalAlignment(PPForestAli<L,AL> &ppfali);
+
+    void resetOptLocalAlignment(int suboptimalsPercent=100);
+    bool nextLocalSuboptimum();
+    void getOptLocalAlignment(PPForestAli<L,AL> &ppfali,Uint &xbasepos, Uint &ybasepos);
+    void getOptSILAlignment(PPForestAli<L,AL> &ppfali,Uint &ybasepos);
+};
+
+#endif