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[gromacs.git] / src / gromacs / analysisdata / dataframe.h

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/*! \file
 * \brief
 * Declares classes for accessing data frame information.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \inpublicapi
 * \ingroup module_analysisdata
 */
#ifndef GMX_ANALYSISDATA_DATAFRAME_H
#define GMX_ANALYSISDATA_DATAFRAME_H

#include <vector>

#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/flags.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/real.h"

namespace gmx
{

/*! \brief
 * Value type for representing a single value in analysis data objects.
 *
 * Default copy constructor and assignment operator are used and work as
 * intended.
 *
 * Methods in this class do not throw.
 *
 * Non-const methods are provided for use within the library only; currently
 * it is not possible to access a non-const AnalysisDataValue through the
 * public interface.
 *
 * \inpublicapi
 * \ingroup module_analysisdata
 */
class AnalysisDataValue
{
public:
    /*! \brief
     * Constructs an unset value.
     */
    AnalysisDataValue() : value_(0.0), error_(0.0) {}
    /*! \brief
     * Constructs a value object with the given value.
     *
     * The constructed object is marked as set and present.
     */
    explicit AnalysisDataValue(real value) : value_(value), error_(0.0)
    {
        flags_.set(efSet);
        flags_.set(efPresent);
    }

    /*! \brief
     * Direct access to the value.
     *
     * Assigning a value to this does not mark the value as set; setValue()
     * must be used for this.
     */
    real& value() { return value_; }
    /*! \brief
     * Direct access to the error estimate.
     *
     * Assigning a value to this does not mark the error estimate as set;
     * setValue() must be used for this.
     */
    real& error() { return error_; }
    //! Returns the value for this value.
    real value() const { return value_; }
    //! Returns the error estimate for this value, or zero if not set.
    real error() const { return error_; }
    /*! \brief
     * Returns whether this value has been set.
     *
     * If this method returns false, the return value of value() and
     * error() are undefined.
     */
    bool isSet() const { return flags_.test(efSet); }
    /*! \brief
     * Returns whether the error estimate for this value has been set.
     *
     * If this method returns false, but isSet() returns true, error()
     * returns zero.
     */
    bool hasError() const { return flags_.test(efErrorSet); }
    /*! \brief
     * Returns whether this value has been marked as present.
     *
     * If this method returns false, it is up to the source data to define
     * whether isSet() may return true.
     */
    bool isPresent() const { return flags_.test(efPresent); }

    //! Clears and unsets this value.
    void clear() { *this = AnalysisDataValue(); }
    //! Sets this value.
    void setValue(real value, bool bPresent = true)
    {
        value_ = value;
        flags_.set(efSet);
        flags_.set(efPresent, bPresent);
    }
    //! Sets this value and its error estimate.
    void setValue(real value, real error, bool bPresent = true)
    {
        value_ = value;
        error_ = error;
        flags_.set(efSet);
        flags_.set(efErrorSet);
        flags_.set(efPresent, bPresent);
    }
    //! Set only error estimate for this value.
    void setError(real error)
    {
        error_ = error;
        flags_.set(efErrorSet);
    }

private:
    //! Possible flags for \a flags_.
    enum Flag : uint64_t
    {
        efSet      = 1 << 0, //!< Value has been set.
        efErrorSet = 1 << 1, //!< Error estimate has been set.
        efPresent  = 1 << 2  //!< Value is set as present.
    };

    //! Value for this value.
    real value_;
    //! Error estimate for this value, zero if not set.
    real error_;
    //! Status flags for thise value.
    FlagsTemplate<Flag> flags_;
};

//! Shorthand for reference to an array of data values.
typedef ArrayRef<const AnalysisDataValue> AnalysisDataValuesRef;


/*! \brief
 * Value type for storing frame-level information for analysis data.
 *
 * Default copy constructor and assignment operator are used and work as
 * intended.
 * Typically new objects of this type are only constructed internally by the
 * library and in classes that are derived from AbstractAnalysisData.
 *
 * Methods in this class do not throw, but may contain asserts for incorrect
 * usage.
 *
 * Note that it is not possible to change the contents of an initialized
 * object, except by assigning a new object to replace it completely.
 *
 * \inpublicapi
 * \ingroup module_analysisdata
 */
class AnalysisDataFrameHeader
{
public:
    /*! \brief
     * Constructs an invalid frame header.
     *
     * Return values of other methods than isValid() are unspecified for
     * the constructed object.
     */
    AnalysisDataFrameHeader();
    /*! \brief
     * Constructs a frame header from given values.
     *
     * \param[in] index  Index of the frame. Must be >= 0.
     * \param[in] x      x coordinate for the frame.
     * \param[in] dx     Error estimate for x.
     */
    AnalysisDataFrameHeader(int index, real x, real dx);

    /*! \brief
     * Returns whether the frame header corresponds to a valid frame.
     *
     * If returns false, return values of other methods are not specified.
     */
    bool isValid() const { return index_ >= 0; }
    /*! \brief
     * Returns zero-based index of the frame.
     *
     * The return value is >= 0 for valid frames.
     * Should not be called for invalid frames.
     */
    int index() const
    {
        GMX_ASSERT(isValid(), "Tried to access invalid frame header");
        return index_;
    }
    /*! \brief
     * Returns the x coordinate for the frame.
     *
     * Should not be called for invalid frames.
     */
    real x() const
    {
        GMX_ASSERT(isValid(), "Tried to access invalid frame header");
        return x_;
    }
    /*! \brief
     * Returns error in the x coordinate for the frame (if applicable).
     *
     * All data do not provide error estimates.
     * Typically returns zero in those cases.
     *
     * Should not be called for invalid frames.
     */
    real dx() const
    {
        GMX_ASSERT(isValid(), "Tried to access invalid frame header");
        return dx_;
    }

private:
    int  index_;
    real x_;
    real dx_;
};


/*! \cond libinternal */
/*! \libinternal \brief
 * Value type for internal indexing of point sets.
 *
 * This class contains the necessary data to split an array of
 * AnalysisDataValue objects into point sets.  It is always specified in the
 * context of an array of AnalysisDataValues: the point set specified by this
 * class contains valueCount() values, starting from the array index
 * valueOffset().
 * The value at location valueOffset() corresponds to column firstColumn().
 * It is not necessary for code using the analysis data framework to know of
 * this class, but it is declared in a public header to allow using it in other
 * types.
 *
 * Default copy constructor and assignment operator are used and work as
 * intended.
 * Typically new objects of this type are only constructed internally by the
 * library and in classes that are derived from AbstractAnalysisData.
 *
 * Methods in this class do not throw, but may contain asserts for incorrect
 * usage.
 *
 * Note that it is not possible to change the contents of an initialized
 * object, except by assigning a new object to replace it completely.
 *
 * \inlibraryapi
 * \ingroup module_analysisdata
 */
class AnalysisDataPointSetInfo
{
public:
    //! Construct point set data object with the given values.
    AnalysisDataPointSetInfo(int valueOffset, int valueCount, int dataSetIndex, int firstColumn) :
        valueOffset_(valueOffset),
        valueCount_(valueCount),
        dataSetIndex_(dataSetIndex),
        firstColumn_(firstColumn)
    {
        GMX_ASSERT(valueOffset >= 0, "Negative value offsets are invalid");
        GMX_ASSERT(valueCount >= 0, "Negative value counts are invalid");
        GMX_ASSERT(dataSetIndex >= 0, "Negative data set indices are invalid");
        GMX_ASSERT(firstColumn >= 0, "Negative column indices are invalid");
    }

    //! Returns the offset of the first value in the referenced value array.
    int valueOffset() const { return valueOffset_; }
    //! Returns the number of values in this point set.
    int valueCount() const { return valueCount_; }
    //! Returns the data set index for this point set.
    int dataSetIndex() const { return dataSetIndex_; }
    //! Returns the index of the first column in this point set.
    int firstColumn() const { return firstColumn_; }

private:
    int valueOffset_;
    int valueCount_;
    int dataSetIndex_;
    int firstColumn_;
};

//! Shorthand for reference to an array of point set data objects.
typedef ArrayRef<const AnalysisDataPointSetInfo> AnalysisDataPointSetInfosRef;

//! \endcond


/*! \brief
 * Value type wrapper for non-mutable access to a set of data column values.
 *
 * Default copy constructor and assignment operator are used and work as
 * intended.
 * Typically new objects of this type are only constructed internally by the
 * library and in classes that are derived from AbstractAnalysisData.
 *
 * Methods in this class do not throw, but may contain asserts for incorrect
 * usage.
 *
 * The design of the interfaces is such that all objects of this type should be
 * valid, i.e., header().isValid() should always return true.
 *
 * Note that it is not possible to change the contents of an initialized
 * object, except by assigning a new object to replace it completely.
 *
 * \inpublicapi
 * \ingroup module_analysisdata
 */
class AnalysisDataPointSetRef
{
public:
    /*! \brief
     * Constructs a point set reference from given values.
     *
     * \param[in] header       Header for the frame.
     * \param[in] pointSetInfo Information about the point set.
     * \param[in] values       Values for each column.
     *
     * The first element of the point set should be found from \p values
     * using the offset in \p pointSetInfo.
     */
    AnalysisDataPointSetRef(const AnalysisDataFrameHeader&  header,
                            const AnalysisDataPointSetInfo& pointSetInfo,
                            const AnalysisDataValuesRef&    values);
    /*! \brief
     * Constructs a point set reference from given values.
     *
     * \param[in] header      Header for the frame.
     * \param[in] values      Values for each column.
     *
     * The first element in \p values should correspond to the first
     * column.
     */
    AnalysisDataPointSetRef(const AnalysisDataFrameHeader&        header,
                            const std::vector<AnalysisDataValue>& values);
    /*! \brief
     * Constructs a point set reference to a subset of columns.
     *
     * \param[in] points      Point set to use as source.
     * \param[in] firstColumn First column index to include.
     * \param[in] columnCount Number of columns to include.
     *
     * Creates a point set that contains \p columnCount columns starting
     * from \p firstColumn from \p points, or a subset if all requested
     * columns are not present in \p points.  If the requested column range
     * and the range in \p points do not intersect, the result has
     * columnCount() == 0.
     *
     * \p firstColumn is relative to the whole data set, i.e., not relative
     * to points.firstColumn().
     *
     * Mainly intended for internal use.
     */
    AnalysisDataPointSetRef(const AnalysisDataPointSetRef& points, int firstColumn, int columnCount);

    /*! \brief
     * Returns the frame header for the frame of this point set.
     */
    const AnalysisDataFrameHeader& header() const { return header_; }
    //! \copydoc AnalysisDataFrameHeader::index()
    int frameIndex() const { return header_.index(); }
    //! \copydoc AnalysisDataFrameHeader::x()
    real x() const { return header_.x(); }
    //! \copydoc AnalysisDataFrameHeader::dx()
    real dx() const { return header_.dx(); }
    //! Returns zero-based index of the dataset that this set is part of.
    int dataSetIndex() const { return dataSetIndex_; }
    //! Returns zero-based index of the first column included in this set.
    int firstColumn() const { return firstColumn_; }
    //! Returns the number of columns included in this set.
    int columnCount() const { return ssize(values()); }
    //! Returns zero-based index of the last column included in this set (inclusive).
    int lastColumn() const { return firstColumn_ + columnCount() - 1; }
    /*! \brief
     * Returns reference container for all values.
     *
     * First value in the returned container corresponds to firstColumn().
     */
    const AnalysisDataValuesRef& values() const { return values_; }
    /*! \brief
     * Returns data value for a column in this set.
     *
     * \param[in] i  Zero-based column index relative to firstColumn().
     *     Should be >= 0 and < columnCount().
     */
    real y(int i) const
    {
        GMX_ASSERT(i >= 0 && i < columnCount(), "Out of range data access");
        return values()[i].value();
    }
    /*! \brief
     * Returns error estimate for a column in this set if applicable.
     *
     * \param[in] i  Zero-based column index relative to firstColumn().
     *     Should be >= 0 and < columnCount().
     *
     * Currently, this method returns zero if the source data does not
     * specify errors.
     */
    real dy(int i) const
    {
        GMX_ASSERT(i >= 0 && i < columnCount(), "Out of range data access");
        return values()[i].error();
    }
    /*! \brief
     * Returns whether a column is present in this set.
     *
     * \param[in] i  Zero-based column index relative to firstColumn().
     *     Should be >= 0 and < columnCount().
     *
     * If present(i) returns false, it is depends on the source data
     * whether y(i) and/or dy(i) are defined.
     */
    bool present(int i) const
    {
        GMX_ASSERT(i >= 0 && i < columnCount(), "Out of range data access");
        return values()[i].isPresent();
    }
    /*! \brief
     * Returns true if all points in this point set are present.
     *
     * That is, if present() would return true for all points.
     */
    bool allPresent() const;

private:
    AnalysisDataFrameHeader header_;
    int                     dataSetIndex_;
    int                     firstColumn_;
    AnalysisDataValuesRef   values_;
};


/*! \brief
 * Value type wrapper for non-mutable access to a data frame.
 *
 * Default copy constructor and assignment operator are used and work as
 * intended.
 * Typically new objects of this type are only constructed internally by the
 * library and in classes that are derived from AbstractAnalysisData.
 *
 * Methods in this class do not throw, but may contain asserts for incorrect
 * usage.
 *
 * Note that it is not possible to change the contents of an initialized
 * object, except by assigning a new object to replace it completely.
 *
 * \inpublicapi
 * \ingroup module_analysisdata
 */
class AnalysisDataFrameRef
{
public:
    /*! \brief
     * Constructs an invalid frame reference.
     *
     * Return values of other methods than isValid() are unspecified for
     * the constructed object.
     */
    AnalysisDataFrameRef();
    /*! \brief
     * Constructs a frame reference from given values.
     *
     * \param[in] header      Header for the frame.
     * \param[in] values      Values for each column.
     * \param[in] pointSets   Point set data.
     */
    AnalysisDataFrameRef(const AnalysisDataFrameHeader&      header,
                         const AnalysisDataValuesRef&        values,
                         const AnalysisDataPointSetInfosRef& pointSets);
    /*! \brief
     * Constructs a frame reference from given values.
     *
     * \param[in] header      Header for the frame.
     * \param[in] values      Values for each column.
     * \param[in] pointSets   Point set data.
     */
    AnalysisDataFrameRef(const AnalysisDataFrameHeader&               header,
                         const std::vector<AnalysisDataValue>&        values,
                         const std::vector<AnalysisDataPointSetInfo>& pointSets);
    /*! \brief
     * Constructs a frame reference to a subset of columns.
     *
     * \param[in] frame       Frame to use as source.
     * \param[in] firstColumn First column index to include.
     * \param[in] columnCount Number of columns to include.
     *
     * Creates a frame reference that contains \p columnCount columns
     * starting from \p firstColumn from \p frame, or a subset if all
     * requested columns are not present in \p frame.
     *
     * Mainly intended for internal use.
     */
    AnalysisDataFrameRef(const AnalysisDataFrameRef& frame, int firstColumn, int columnCount);

    /*! \brief
     * Returns whether the object refers to a valid frame.
     *
     * If returns false, return values of other methods are not specified.
     */
    bool isValid() const { return header().isValid(); }
    //! Returns the header for this frame.
    const AnalysisDataFrameHeader& header() const { return header_; }
    //! \copydoc AnalysisDataFrameHeader::index()
    int frameIndex() const { return header().index(); }
    //! \copydoc AnalysisDataFrameHeader::x()
    real x() const { return header().x(); }
    //! \copydoc AnalysisDataFrameHeader::dx()
    real dx() const { return header().dx(); }
    /*! \brief
     * Returns the number of point sets for this frame.
     *
     * Returns zero for an invalid frame.
     */
    int pointSetCount() const { return ssize(pointSets_); }
    /*! \brief
     * Returns point set reference for a given point set.
     *
     * Should not be called for invalid frames.
     */
    AnalysisDataPointSetRef pointSet(int index) const
    {
        GMX_ASSERT(isValid(), "Invalid data frame accessed");
        GMX_ASSERT(index >= 0 && index < pointSetCount(), "Out of range data access");
        return AnalysisDataPointSetRef(header_, pointSets_[index], values_);
    }
    /*! \brief
     * Convenience method for accessing a column value in simple data.
     *
     * \copydetails AnalysisDataPointSetRef::y()
     */
    real y(int i) const { return singleColumnValue(i).value(); }
    /*! \brief
     * Convenience method for accessing error for a column value in simple
     * data.
     *
     * \copydetails AnalysisDataPointSetRef::dy()
     */
    real dy(int i) const { return singleColumnValue(i).error(); }
    /*! \brief
     * Convenience method for accessing present status for a column in
     * simple data.
     *
     * \copydetails AnalysisDataPointSetRef::present()
     */
    bool present(int i) const { return singleColumnValue(i).isPresent(); }
    /*! \brief
     * Returns true if all points in this frame are present.
     */
    bool allPresent() const;

private:
    //! Helper method for accessing single columns in simple data.
    const AnalysisDataValue& singleColumnValue(int i) const
    {
        GMX_ASSERT(isValid(), "Invalid data frame accessed");
        GMX_ASSERT(pointSets_.size() == 1U && pointSets_[0].firstColumn() == 0,
                   "Convenience method not available for multiple point sets");
        GMX_ASSERT(i >= 0 && i < ssize(values_), "Out of range data access");
        return values_[i];
    }

    AnalysisDataFrameHeader      header_;
    AnalysisDataValuesRef        values_;
    AnalysisDataPointSetInfosRef pointSets_;
};

} // namespace gmx

#endif