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added the Rtreemix package and removed the bim package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@28790 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 16/11/2007 21:25:16
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+#ifndef _REPLACELEDA_HH
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+#define _REPLACELEDA_HH
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+
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+typedef unsigned int uint;
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+
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+#include "Array.hh"
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+#include "Graph.hh"
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+#include "List.hh"
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+#include "Map.hh"
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+#include "Matrix.hh"
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+#include "Queue.hh"
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+#include "Vector.hh"
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+
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+#include <fstream>
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+#include <climits>
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+
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+
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+namespace replaceleda {
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+
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+    const double DBL_MAX = 1.79769313486231470e+308;
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+    
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+
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+    typedef mmatrix<int> integer_matrix;
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+    typedef mmatrix<double> matrix;
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+    
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+    typedef mvector<int> integer_vector;
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+    typedef mvector<double> vector;
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+
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+    typedef std::string string;
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+
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+    typedef int integer;    
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+
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+//    template<class T>
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+    bool member(std::set<node> s, node e);
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+    bool member(std::set<edge> s, edge e);    
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+
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+//    template <class T>
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+    std::vector<int> permute(std::vector<int> v);
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+
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+//    template <class T>
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+    list<int> permute(list<int> l);
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+
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+    graph *graph_of(node n);
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+
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+    graph *graph_of(edge e);
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+
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+    node source(edge e);
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+
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+    node target(edge e);
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+
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+    void mydfs(graph &G, list<edge> &cycle, std::set<node> &unseen, std::set<node> &on_path, node v);
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+    bool Is_Acyclic(graph &G, list<edge> &cycle);
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+
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+    void CopyGraph(graph &g1, graph &g2);
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+    void CopyGraph(GRAPH<node, edge>  &g_target, graph &g_source);
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+
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+    //split string
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+    std::vector<replaceleda::string> strsplit(replaceleda::string inputstr, replaceleda::string splitseq);
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+
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+    //does something like the formated output in C
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+    replaceleda::string tostring(replaceleda::string inputstr, ...);
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+
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+    //from Matrix.hh
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+    //template <class T>
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+    std::ostream& operator<< (std::ostream &os, mmatrix<double> &m);
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+    std::ostream& operator<< (std::ostream &os, mmatrix<int> &m);
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+
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+//    template <class T>
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+    std::istream& operator>> (std::istream &is, mmatrix<double> &m);
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+    std::istream& operator>> (std::istream &is, mmatrix<int> &m);
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+   
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+//    template<class T>
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+    mmatrix<double> transpose(mmatrix<double> &m);
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+    mmatrix<int> transpose(mmatrix<int> &m);
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+
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+    std::ostream& operator<< (std::ostream &os, std::set<node> s);
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+
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+    //from Vector.hh    
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+//    template <class T>
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+    std::ostream& operator<< (std::ostream &os, mvector<double> v);
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+    std::ostream& operator<< (std::ostream &os, mvector<int> v);
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+    
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+//    template <class T>
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+    std::istream& operator>> (std::istream &is, mvector<double> &v);    
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+    std::istream& operator>> (std::istream &is, mvector<int> &v);    
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+
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+    std::ostream& operator<< (std::ostream &os, graph &g);
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+
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+    void printGraph (graph &g, edge_array<double>  &weights);
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+
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+}
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+
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+//#include "replaceleda.cc"
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+
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+#endif // _REPLACELEDA_HH