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

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

diff --git a/binaries/src/ViennaRNA/RNAforester/src/rnaforestsz.h b/binaries/src/ViennaRNA/RNAforester/src/rnaforestsz.h
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/RNAforester/src/rnaforestsz.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 _RNA_FORESTSZ_H_
+#define _RNA_FORESTSZ_H_
+
+#include <iostream>
+
+#include "ppforestsz.h"
+#include "rna_alphabet.h"
+
+using namespace std;
+
+
+// RNAForestSZ
+
+class RNAForestSZ : public PPForestSZ<RNA_Alphabet>
+{
+ private:
+  string m_name;
+  string m_baseStr;
+  string m_viennaStr;
+
+//  void showLabel(ostream &s,RNA_Alphabet a); // virtual function of PPForest
+//  void makeLabel(RNA_Alphabet &a,char c);
+    void buildForest(Uint &pos, Uint &node);
+ public:
+  RNAForestSZ(const string &baseStr, const string &viennaStr, const string &name);
+
+  const string& getName() const {return m_name;};
+  const string& getBaseStr() const {return m_baseStr;};
+  const string& getViennaStr() const {return m_viennaStr;};
+
+//  void plot2d(const string &filename_prefix, const list<pair<Uint,Uint> > &regions, const RNAFuncs::SquigglePlotOptions &sqOptions);
+};
+
+#endif
+
+