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

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

diff --git a/binaries/src/ViennaRNA/RNAforester/src/ppforestali.h b/binaries/src/ViennaRNA/RNAforester/src/ppforestali.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 _PPFORESTALI_H_
+#define _PPFORESTALI_H_
+
+//#include "alignment.h"
+#include "ppforest.h"
+
+//template<class R,class L,class AL>
+//class Alignment;
+
+/** PPForestAli is the Base class of forest Alignemnts.
+ *  The pure virtual functions must be implemented when 
+ *  inherited to allow the construction of alignments.
+ */
+
+template <class L,class AL>
+class PPForestAli : public PPForest<AL>
+{
+public:
+  typedef typename PPForest<AL>::size_type size_type;
+
+  //private:
+public:
+       /** @name Interface functions for alignment construction */
+       //@{ 
+
+       virtual void makeRepLabel(size_type node,L a, L b) = 0;
+       virtual void makeDelLabel(size_type node,L a) = 0;
+       virtual void makeInsLabel(size_type node,L b) = 0;
+
+       //@}
+
+public:
+       PPForestAli() : PPForest<AL>(){};
+       PPForestAli(size_type size) : PPForest<AL>(size) {};
+
+       //  virtual ~PPForestAli(){};
+};
+
+#endif