genmodel 0.0.27 → 0.0.28

data/ext/Genmodel/BitVector.h

@@ -0,0 +1,172 @@
+//
+//  BitVector.h
+//  
+//
+//  Created by Mathieu Bouchard on 2014-03-03.
+//
+//
+
+#ifndef _BitVector_h
+#define _BitVector_h
+
+#include <stdint.h>
+#include <math.h>
+
+#include <string>
+#include <vector>
+#include <map>
+
+
+using namespace std;
+
+class BitVector
+{
+public:
+    BitVector(const BitVector& bit_vector);
+    BitVector() : bits(NULL), n(0), m(0), extra(0) { }
+    BitVector(size_t _size);
+    ~BitVector();
+    
+    bool operator[](size_t index) const;
+    BitVector operator&(const BitVector& bit_vector) const;
+    BitVector operator|(const BitVector& bit_vector) const;
+    BitVector operator^(const BitVector& bit_vector) const;
+    BitVector operator~() const;
+    BitVector& operator&=(const BitVector& bit_vector);
+    BitVector& operator|=(const BitVector& bit_vector);
+    BitVector& operator^=(const BitVector& bit_vector);
+    BitVector _and(const BitVector& bit_vector) const;
+    BitVector _or(const BitVector& bit_vector) const;
+    BitVector _xor(const BitVector& bit_vector) const;
+    BitVector _not() const;
+    BitVector& s_and(const BitVector& bit_vector) ;
+    BitVector& s_or(const BitVector& bit_vector);
+    BitVector& s_xor(const BitVector& bit_vector);
+    BitVector& s_not();
+    BitVector& operator=(const BitVector& bit_vector);
+    BitVector kronecker(const BitVector& bit_vector) const;
+    
+    bool is_zero() const;
+    bool is_one() const;
+    size_t sum() const;
+    //BitVector operator<<();
+    //BitVector operator>>();
+    
+    string to_s() const;
+    bool get(size_t index) const;
+    void set(size_t index, bool value);
+    void set(string val);
+    void random_fill();
+    void init(size_t _size);
+    size_t size() const;
+    void* Ptr();
+    
+private:
+    inline void set_extra();
+    uint64_t* bits;
+    size_t n;
+    size_t m;
+    uint64_t extra;
+};
+
+class BitIndex
+{
+public:
+    BitIndex(const BitVector& bit_vector);
+    ~BitIndex();
+    bool operator[](size_t _index) const;
+//private:
+    size_t* index;
+    size_t n;
+};
+
+class BitMatrix
+{
+public:
+    BitMatrix();
+    BitMatrix(size_t _m, size_t _n);
+    ~BitMatrix();
+    
+    void set_size(size_t _m, size_t _n);
+    void reset();
+    void seta(size_t index_i, size_t index_j, double val);
+    double geta(size_t index_i, size_t index_j) const;
+    void setrow(size_t index, const string& bit_str);
+    void setcol(size_t index, const string& bit_str);
+    double sum(const BitVector& col, const BitVector& row) const;
+    double sum_row(size_t i) const;
+    double sum_col(size_t i) const;
+    BitMatrix& operator+=(const BitMatrix& bit_matrix);
+    BitMatrix operator+(const BitMatrix& bit_matrix) const;
+    BitMatrix& operator-=(const BitMatrix& bit_matrix);
+    BitMatrix operator-(const BitMatrix& bit_matrix) const;
+    BitMatrix& operator=(const BitMatrix& bit_matrix);
+    BitMatrix copy() const;
+    BitMatrix operator*=(double m) const;
+    BitMatrix& operator*(double m);
+    BitMatrix add_m(const BitMatrix& bit_matrix, double m1) const; // C = A+m2*B
+    BitMatrix& s_add_m(const BitMatrix& bit_matrix, double m1); // A = A+m2*B
+    
+    void ComputeMaximalCliqueCoverage();
+    
+    size_t n; //nb_col
+    size_t m; //nb_row
+    BitVector* rows;
+    BitVector* cols;
+    
+private:
+    double** a_c;
+    double** a_r;
+};
+
+class BitHash
+{
+public:
+    BitHash() {name = "BitHash";}
+    BitHash(char* _name) {name = string(_name);}
+    ~BitHash() { }
+    
+    size_t id_for_oid(size_t _oid);
+    size_t oid_for_id(size_t _id);
+    
+    string name;
+    map<size_t,size_t> oid2id;
+    vector<size_t> id2oid;
+};
+
+class BitSet
+{
+public:
+    BitSet(	) {name = "BitSet";}
+    BitSet(char* _name) {name = string(_name);}
+    ~BitSet() { }
+    
+    void set(char* feature, char* item, bool value);
+    bool get(char* feature, char* item);
+    void set(size_t feature_id, size_t item_id, bool value);
+    bool get(size_t feature_id, size_t item_id);
+    void add_feature(char* _name, size_t _size);
+    
+    string name;
+    map<string, size_t> id_for_feature;
+    vector<map<string,size_t> > id_for_feature_item;
+    vector<BitVector> features;
+    vector<string> feature_names;
+};
+
+class BitModel
+{
+public:
+    BitModel() {name = "BitModel";}
+    BitModel(char* _name) {name = string(_name);}
+    
+    void add_set(char* _name);
+    BitSet& get_set(char* _name);
+    BitSet& get_set(size_t set_id);
+    
+    string name;
+    vector<BitSet> sets;
+    map<string, size_t> set_for_set_name;
+};
+
+#endif