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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.
//
#include <RDGeneral/export.h>
#ifndef __RD_DISCRETE_VALUE_VECT_20050124__
#define __RD_DISCRETE_VALUE_VECT_20050124__
#include <boost/smart_ptr.hpp>
#include <string>
#include <cstring>
#include <cstdint>
namespace RDKit {
// we require 32bit unsigneds using the std::uint32_t type:
const unsigned int BITS_PER_INT = 32;
//! a class for efficiently storing vectors of discrete values
class RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect {
public:
typedef boost::shared_array<std::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);
auto *data = new std::uint32_t[d_numInts];
memset(static_cast<void *>(data), 0, d_numInts * sizeof(std::uint32_t));
d_data.reset(data);
}
//! Copy constructor
DiscreteValueVect(const DiscreteValueVect &other);
DiscreteValueVect &operator=(const DiscreteValueVect &other);
//! constructor from a pickle
DiscreteValueVect(const std::string &pkl) {
initFromText(pkl.c_str(), static_cast<unsigned int>(pkl.size()));
}
//! constructor from a pickle
DiscreteValueVect(const char *pkl, const unsigned int len) {
initFromText(pkl, len);
}
~DiscreteValueVect() = default;
//! 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 accommodate
*/
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 std::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);
};
RDKIT_DATASTRUCTS_EXPORT unsigned int computeL1Norm(
const DiscreteValueVect &v1, const DiscreteValueVect &v2);
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect
operator+(const DiscreteValueVect &p1, const DiscreteValueVect &p2);
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect
operator-(const DiscreteValueVect &p1, const DiscreteValueVect &p2);
} // namespace RDKit
#endif
RDKit::DiscreteValueVect
a class for efficiently storing vectors of discrete values
Definition DiscreteValueVect.h:24
RDKit::DiscreteValueVect::size
unsigned int size() const
returns the length
Definition DiscreteValueVect.h:84
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const std::string &pkl)
constructor from a pickle
Definition DiscreteValueVect.h:55
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const DiscreteValueVect &other)
Copy constructor.
RDKit::DiscreteValueVect::toString
std::string toString() const
returns a binary string representation (pickle)
RDKit::DiscreteValueVect::getVal
unsigned int getVal(unsigned int i) const
return the value at an index
RDKit::DiscreteValueVect::getLength
unsigned int getLength() const
returns the length
RDKit::DiscreteValueVect::DiscreteValueType
DiscreteValueType
used to define the possible range of the values
Definition DiscreteValueVect.h:29
RDKit::DiscreteValueVect::TWOBITVALUE
@ TWOBITVALUE
Definition DiscreteValueVect.h:31
RDKit::DiscreteValueVect::SIXTEENBITVALUE
@ SIXTEENBITVALUE
Definition DiscreteValueVect.h:34
RDKit::DiscreteValueVect::FOURBITVALUE
@ FOURBITVALUE
Definition DiscreteValueVect.h:32
RDKit::DiscreteValueVect::EIGHTBITVALUE
@ EIGHTBITVALUE
Definition DiscreteValueVect.h:33
RDKit::DiscreteValueVect::~DiscreteValueVect
~DiscreteValueVect()=default
RDKit::DiscreteValueVect::getTotalVal
unsigned int getTotalVal() const
returns the sum of all the elements in the vect
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:38
RDKit::DiscreteValueVect::operator&
DiscreteValueVect operator&(const DiscreteValueVect &other) const
support dvv3 = dvv1&dvv2
RDKit::DiscreteValueVect::operator=
DiscreteValueVect & operator=(const DiscreteValueVect &other)
RDKit::DiscreteValueVect::DATA_SPTR
boost::shared_array< std::uint32_t > DATA_SPTR
Definition DiscreteValueVect.h:26
RDKit::DiscreteValueVect::getValueType
DiscreteValueType getValueType() const
return the type of value being stored
Definition DiscreteValueVect.h:93
RDKit::DiscreteValueVect::operator-=
DiscreteValueVect & operator-=(const DiscreteValueVect &other)
RDKit::DiscreteValueVect::getData
const std::uint32_t * getData() const
return a pointer to our raw data storage
RDKit::DiscreteValueVect::getNumInts
unsigned int getNumInts() const
returns the size of our storage
Definition DiscreteValueVect.h:96
RDKit::DiscreteValueVect::operator[]
int operator[](unsigned int idx) const
support indexing using []
Definition DiscreteValueVect.h:69
RDKit::DiscreteValueVect::getNumBitsPerVal
unsigned int getNumBitsPerVal() const
return the number of bits used to store each value
Definition DiscreteValueVect.h:90
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const char *pkl, const unsigned int len)
constructor from a pickle
Definition DiscreteValueVect.h:59
RDKit::DiscreteValueVect::setVal
void setVal(unsigned int i, unsigned int val)
set the value at an index
RDKit::DiscreteValueVect::operator+=
DiscreteValueVect & operator+=(const DiscreteValueVect &other)
export.h
RDKIT_DATASTRUCTS_EXPORT
#define RDKIT_DATASTRUCTS_EXPORT
Definition export.h:81
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::computeL1Norm
RDKIT_DATASTRUCTS_EXPORT unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2)
RDKit::operator-
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect operator-(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::operator+
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect operator+(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::BITS_PER_INT
const unsigned int BITS_PER_INT
Definition DiscreteValueVect.h:21