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

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

diff --git a/binaries/src/ViennaRNA/RNAforester/src/treeedit.h b/binaries/src/ViennaRNA/RNAforester/src/treeedit.h
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/RNAforester/src/treeedit.h
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+/*
+  Copyright by Matthias Hoechsmann (C) 2002
+  =====================================                                   
+  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 _TREE_EDIT_H_
+#define _TREE_EDIT_H_
+
+#include <cassert>
+#include <list>
+
+#include "types.h"
+#include "algebra.h"
+#include "ppforestsz.h"
+//#include "ppforestali.h"
+
+template<class R,class L>
+class Mapping
+{
+    R *m_mtrxTD;
+       R *m_mtrxFD;
+    Ulong *m_rowStartTD;
+       Ulong *m_rowStartFD;
+    Ulong m_mtrxSizeTD;
+       Ulong m_mtrxSizeFD;
+       R m_optimum;
+
+    PPForestSZ<L> *m_ppfx;
+    PPForestSZ<L> *m_ppfy;
+    const SZAlgebra<R,L> *m_alg;
+
+    inline R getMtrxTDVal(Ulong i,Ulong j) const          
+      {
+               assert(m_rowStartTD[i]+j<m_mtrxSizeTD);
+               return m_mtrxTD[m_rowStartTD[i]+j];
+      };
+
+    inline void setMtrxTDVal(Ulong i,Ulong j,R val)
+      {
+               assert(m_rowStartTD[i]+j<m_mtrxSizeTD);
+               m_mtrxTD[m_rowStartTD[i]+j]=val;
+      };
+
+   inline R getMtrxFDVal(Ulong i,Ulong j) const          
+      {
+               assert(m_rowStartFD[i]+j<m_mtrxSizeFD);
+               return m_mtrxFD[m_rowStartFD[i]+j];
+      };
+
+    inline void setMtrxFDVal(Ulong i,Ulong j,R val)
+      {
+               assert(m_rowStartFD[i]+j<m_mtrxSizeFD);
+               m_mtrxFD[m_rowStartFD[i]+j]=val;
+      };
+
+//    Uint backtrack(PPForestAli<L,AL> &ppf,Uint i, Uint j, Uint k, Uint l, Uint &node);
+public:    
+       Mapping(const PPForestSZ<L> *ppfx, const PPForestSZ<L> *ppfy,const SZAlgebra<R,L> &alg);
+    ~Mapping();
+    
+       R getGlobalOptimum() {return m_optimum;};
+};
+
+#endif