src/gromacs/analysisdata/arraydata.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \inpublicapi
  41  * \ingroup module_analysisdata
  42  */
  43 #ifndef GMX_ANALYSISDATA_ARRAYDATA_H
  44 #define GMX_ANALYSISDATA_ARRAYDATA_H
  45
  46 #include <vector>
  47
  48 #include "gromacs/analysisdata/abstractdata.h"
  49 #include "gromacs/analysisdata/dataframe.h"
  50 #include "gromacs/utility/gmxassert.h"
  51
  52 namespace gmx
  53 {
  54
  55 /*! \brief
  56  * Abstract base class for data objects that present in-memory data.
  57  *
  58  * This class implements a subclass of AbstractAnalysisData that presents an
  59  * in-memory array through the AbstractAnalysisData interface.  Subclasses
  60  * should initialize the in-memory array through the provided protected member
  61  * functions.  This class provides public accessor methods for read access to
  62  * the data.
  63  *
  64  * Public accessor methods in this class do not throw, but assert if data is
  65  * accessed before it is available.
  66  *
  67  * \todo
  68  * Add support for multiple data sets.
  69  *
  70  * \inlibraryapi
  71  * \ingroup module_analysisdata
  72  */
  73 class AbstractAnalysisArrayData : public AbstractAnalysisData
  74 {
  75     public:
  76         virtual ~AbstractAnalysisArrayData();
  77
  78         virtual int frameCount() const
  79         {
  80             return bReady_ ? rowCount_ : 0;
  81         }
  82
  83         /*! \brief
  84          * Returns the number of rows in the data array.
  85          *
  86          * This function is identical to frameCount(), except that frameCount()
  87          * returns 0 before valuesReady() has been called.
  88          */
  89         int rowCount() const { return rowCount_; }
  90         //! Returns true if values have been allocated.
  91         bool isAllocated() const { return !value_.empty(); }
  92         //! Returns the x value of the first frame.
  93         real xstart() const { return xvalue_[0]; }
  94         //! Returns the step between frame x values.
  95         real xstep() const
  96         {
  97             GMX_ASSERT(bUniformX_, "Accessing x step for non-uniform data");
  98             return xstep_;
  99         }
 100         //! Returns the x value of a row.
 101         real xvalue(int row) const
 102         {
 103             GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
 104             return xvalue_[row];
 105         }
 106         //! Returns a given array element.
 107         const AnalysisDataValue &value(int row, int col) const
 108         {
 109             GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
 110             GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
 111             GMX_ASSERT(isAllocated(), "Data array not allocated");
 112             return value_[row * columnCount() + col];
 113         }
 114
 115     protected:
 116         /*! \brief
 117          * Initializes an empty array data object.
 118          *
 119          * \throws std::bad_alloc if out of memory.
 120          */
 121         AbstractAnalysisArrayData();
 122
 123         /*! \brief
 124          * Sets the number of columns in the data array.
 125          *
 126          * \param[in] ncols  Number of columns in the data.
 127          *
 128          * Cannot be called after allocateValues().
 129          *
 130          * See AbstractAnalysisData::setColumnCount() for exception behavior.
 131          */
 132         void setColumnCount(int ncols);
 133         /*! \brief
 134          * Sets the number of rows in the data array.
 135          *
 136          * \param[in] rowCount  Number of rows in the data.
 137          *
 138          * Cannot be called after allocateValues().
 139          *
 140          * Does not throw.
 141          */
 142         void setRowCount(int rowCount);
 143         /*! \brief
 144          * Allocates memory for the values.
 145          *
 146          * \throws std::bad_alloc if memory allocation fails.
 147          *
 148          * setColumnCount() and setRowCount() must have been called.
 149          *
 150          * Strong exception safety guarantee.
 151          */
 152         void allocateValues();
 153         /*! \brief
 154          * Sets the values reported as x values for frames.
 155          *
 156          * \param[in] start  x value for the first frame.
 157          * \param[in] step   Step between x values of successive frames.
 158          *
 159          * Must not be called after valuesReady().
 160          * Any values set with setXAxisValue() are overwritten.
 161          *
 162          * Does not throw.
 163          */
 164         void setXAxis(real start, real step);
 165         /*! \brief
 166          * Sets a single value reported as x value for frames.
 167          *
 168          * \param[in] row    Row/frame for which to set the value.
 169          * \param[in] value  x value for the frame specified by \p row.
 170          *
 171          * Must not be called after valuesReady().
 172          *
 173          * Does not throw.
 174          */
 175         void setXAxisValue(int row, real value);
 176         //! Returns a reference to a given array element.
 177         AnalysisDataValue &value(int row, int col)
 178         {
 179             GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
 180             GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
 181             GMX_ASSERT(isAllocated(), "Data array not allocated");
 182             return value_[row * columnCount() + col];
 183         }
 184         /*! \brief
 185          * Notifies modules of the data.
 186          *
 187          * \throws    unspecified Any exception thrown by attached data modules
 188          *      in data notification methods.
 189          *
 190          * This function should be called once the values in the array
 191          * have been initialized.  The values should not be changed after this
 192          * function has been called.
 193          */
 194         void valuesReady();
 195
 196         /*! \brief
 197          * Copies the contents into a new object.
 198          *
 199          * \param[in]     src  Object to copy data from.
 200          * \param[in,out] dest Empty array data object to copy data to.
 201          * \throws std::bad_alloc if memory allocation for \p dest fails.
 202          *
 203          * \p dest should not have previous contents.
 204          */
 205         static void copyContents(const AbstractAnalysisArrayData *src,
 206                                  AbstractAnalysisArrayData       *dest);
 207
 208     private:
 209         virtual AnalysisDataFrameRef tryGetDataFrameInternal(int index) const;
 210         virtual bool requestStorageInternal(int nframes);
 211
 212         int                            rowCount_;
 213         AnalysisDataPointSetInfo       pointSetInfo_;
 214         std::vector<AnalysisDataValue> value_;
 215         std::vector<real>              xvalue_;
 216         real                           xstep_;
 217         bool                           bUniformX_;
 218         bool                           bReady_;
 219
 220         // Copy and assign disallowed by base.
 221 };
 222
 223 /*! \brief
 224  * Simple in-memory data array.
 225  *
 226  * This class is a simple alternative to AnalysisData for in-memory data arrays
 227  * that are constructed in-place.
 228  *
 229  * Public accessor methods in this class do not throw, but assert if data is
 230  * accessed before it is available.
 231  *
 232  * \if libapi
 233  * This class exposes the protected functions of AbstractAnalysisArrayData for
 234  * users.
 235  * \endif
 236  *
 237  * \inpublicapi
 238  * \ingroup module_analysisdata
 239  */
 240 class AnalysisArrayData : public AbstractAnalysisArrayData
 241 {
 242     public:
 243         /*! \brief
 244          * Initializes an empty array data object.
 245          *
 246          * \throws std::bad_alloc if out of memory.
 247          */
 248         AnalysisArrayData() {}
 249
 250         // TODO: These statements cause Doxygen to generate confusing
 251         // documentation.
 252         using AbstractAnalysisArrayData::setColumnCount;
 253         using AbstractAnalysisArrayData::setRowCount;
 254         using AbstractAnalysisArrayData::allocateValues;
 255         using AbstractAnalysisArrayData::setXAxis;
 256         using AbstractAnalysisArrayData::setXAxisValue;
 257         using AbstractAnalysisArrayData::value;
 258         using AbstractAnalysisArrayData::valuesReady;
 259
 260         // Copy and assign disallowed by base.
 261 };
 262
 263 } // namespace gmx
 264
 265 #endif