DiscreteValueVect.h
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//
// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef __RD_DISCRETE_VALUE_VECT_20050124__
#define __RD_DISCRETE_VALUE_VECT_20050124__
#include <boost/smart_ptr.hpp>
#include <string>
#include <cstring>
#include <boost/cstdint.hpp>
namespace RDKit{
// we require 32bit unsigneds using the boost::uint32_t type:
const unsigned int BITS_PER_INT=32;
//! a class for efficiently storing vectors of discrete values
class DiscreteValueVect {
public:
typedef boost::shared_array<boost::uint32_t> DATA_SPTR;
//! used to define the possible range of the values
typedef enum {
ONEBITVALUE=0,
TWOBITVALUE,
FOURBITVALUE,
EIGHTBITVALUE,
SIXTEENBITVALUE,
} DiscreteValueType;
//! initialize with a particular type and size
DiscreteValueVect(DiscreteValueType valType, unsigned int length) : d_type(valType), d_length(length) {
d_bitsPerVal = (1 << static_cast<unsigned int>(valType));
d_valsPerInt = BITS_PER_INT/d_bitsPerVal;
d_numInts = (length + d_valsPerInt -1)/d_valsPerInt;
d_mask = ((1<<d_bitsPerVal) -1);
boost::uint32_t *data = new boost::uint32_t[d_numInts];
memset(static_cast<void *>(data),0,d_numInts*sizeof(boost::uint32_t));
d_data.reset(data);
}
//! Copy constructor
DiscreteValueVect(const DiscreteValueVect& other);
//! constructor from a pickle
DiscreteValueVect(const std::string pkl){
initFromText(pkl.c_str(),pkl.size());
};
//! constructor from a pickle
DiscreteValueVect(const char *pkl,const unsigned int len){
initFromText(pkl,len);
};
~DiscreteValueVect() {}
//! return the value at an index
unsigned int getVal(unsigned int i) const;
//! support indexing using []
int operator[] (unsigned int idx) const { return getVal(idx); };
//! set the value at an index
/*!
NOTE: it is an error to have val > the max value this
DiscreteValueVect can accomodate
*/
void setVal(unsigned int i, unsigned int val);
//! returns the sum of all the elements in the vect
unsigned int getTotalVal() const;
//! returns the length
unsigned int getLength() const;
//! returns the length
unsigned int size() const { return getLength(); };
//! return a pointer to our raw data storage
const boost::uint32_t *getData() const;
//! return the number of bits used to store each value
unsigned int getNumBitsPerVal() const {
return d_bitsPerVal;
}
//! return the type of value being stored
DiscreteValueType getValueType() const {
return d_type;
}
//! returns the size of our storage
unsigned int getNumInts() const {
return d_numInts;
}
//! support dvv3 = dvv1&dvv2
/*!
operator& returns the minimum value for each element.
e.g.:
[0,1,2,0] & [0,1,1,1] -> [0,1,1,0]
*/
DiscreteValueVect operator& (const DiscreteValueVect &other) const;
//! support dvv3 = dvv1|dvv2
/*!
operator& returns the maximum value for each element.
e.g.:
[0,1,2,0] | [0,1,1,1] -> [0,1,2,1]
*/
DiscreteValueVect operator| (const DiscreteValueVect &other) const;
//DiscreteValueVect operator^ (const DiscreteValueVect &other) const;
//DiscreteValueVect operator~ () const;
DiscreteValueVect& operator+=(const DiscreteValueVect &other);
DiscreteValueVect& operator-=(const DiscreteValueVect &other);
//! returns a binary string representation (pickle)
std::string toString() const;
private:
DiscreteValueType d_type;
unsigned int d_bitsPerVal;
unsigned int d_valsPerInt;
unsigned int d_numInts;
unsigned int d_length;
unsigned int d_mask;
DATA_SPTR d_data;
void initFromText(const char *pkl,const unsigned int len);
};
unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2);
DiscreteValueVect operator+ (const DiscreteValueVect& p1,
const DiscreteValueVect& p2);
DiscreteValueVect operator- (const DiscreteValueVect& p1,
const DiscreteValueVect& p2);
}
#endif
RDKit::DiscreteValueVect::getVal
unsigned int getVal(unsigned int i) const
return the value at an index
RDKit::DiscreteValueVect::getNumInts
unsigned int getNumInts() const
returns the size of our storage
Definition: DiscreteValueVect.h:96
RDKit::DiscreteValueVect::DiscreteValueType
DiscreteValueType
used to define the possible range of the values
Definition: DiscreteValueVect.h:28
RDKit::DiscreteValueVect::DATA_SPTR
boost::shared_array< boost::uint32_t > DATA_SPTR
Definition: DiscreteValueVect.h:25
RDKit::DiscreteValueVect::getData
const boost::uint32_t * getData() const
return a pointer to our raw data storage
RDKit::DiscreteValueVect::SIXTEENBITVALUE
Definition: DiscreteValueVect.h:33
RDKit::DiscreteValueVect::operator|
DiscreteValueVect operator|(const DiscreteValueVect &other) const
support dvv3 = dvv1|dvv2
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(DiscreteValueType valType, unsigned int length)
initialize with a particular type and size
Definition: DiscreteValueVect.h:37
RDKit::DiscreteValueVect::FOURBITVALUE
Definition: DiscreteValueVect.h:31
RDKit::DiscreteValueVect::size
unsigned int size() const
returns the length
Definition: DiscreteValueVect.h:80
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const std::string pkl)
constructor from a pickle
Definition: DiscreteValueVect.h:51
RDKit::DiscreteValueVect::toString
std::string toString() const
returns a binary string representation (pickle)
RDKit::DiscreteValueVect::EIGHTBITVALUE
Definition: DiscreteValueVect.h:32
RDKit::DiscreteValueVect::setVal
void setVal(unsigned int i, unsigned int val)
set the value at an index
RDKit::DiscreteValueVect
a class for efficiently storing vectors of discrete values
Definition: DiscreteValueVect.h:23
RDKit::DiscreteValueVect::operator-=
DiscreteValueVect & operator-=(const DiscreteValueVect &other)
RDKit::DiscreteValueVect::operator+=
DiscreteValueVect & operator+=(const DiscreteValueVect &other)
RDKit::DiscreteValueVect::getLength
unsigned int getLength() const
returns the length
RDKit::DiscreteValueVect::operator[]
int operator[](unsigned int idx) const
support indexing using []
Definition: DiscreteValueVect.h:65
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const char *pkl, const unsigned int len)
constructor from a pickle
Definition: DiscreteValueVect.h:55
RDKit::DiscreteValueVect::TWOBITVALUE
Definition: DiscreteValueVect.h:30
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::operator-
DiscreteValueVect operator-(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::DiscreteValueVect::~DiscreteValueVect
~DiscreteValueVect()
Definition: DiscreteValueVect.h:59
RDKit::DiscreteValueVect::ONEBITVALUE
Definition: DiscreteValueVect.h:29
RDKit::operator+
DiscreteValueVect operator+(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::DiscreteValueVect::operator&
DiscreteValueVect operator&(const DiscreteValueVect &other) const
support dvv3 = dvv1&dvv2
RDKit::DiscreteValueVect::getNumBitsPerVal
unsigned int getNumBitsPerVal() const
return the number of bits used to store each value
Definition: DiscreteValueVect.h:86
RDKit::BITS_PER_INT
const unsigned int BITS_PER_INT
Definition: DiscreteValueVect.h:20
RDKit::DiscreteValueVect::getTotalVal
unsigned int getTotalVal() const
returns the sum of all the elements in the vect
RDKit::computeL1Norm
unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2)
RDKit::DiscreteValueVect::getValueType
DiscreteValueType getValueType() const
return the type of value being stored
Definition: DiscreteValueVect.h:91