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33 * Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData.
35 * \author Teemu Murtola <teemu.murtola@cbr.su.se>
37 * \ingroup module_analysisdata
39 #ifndef GMX_ANALYSISDATA_ARRAYDATA_H
40 #define GMX_ANALYSISDATA_ARRAYDATA_H
46 #include "../fatalerror/gmxassert.h"
48 #include "abstractdata.h"
54 * Abstract base class for data objects that present in-memory data.
56 * This class implements a subclass of AbstractAnalysisData that presents an
57 * in-memory array through the AbstractAnalysisData interface. Subclasses
58 * should initialize the in-memory array through the provided protected member
62 * \ingroup module_analysisdata
64 class AbstractAnalysisArrayData : public AbstractAnalysisData
67 virtual ~AbstractAnalysisArrayData();
69 virtual bool getDataWErr(int index, real *x, real *dx,
70 const real **y, const real **dy,
71 const bool **present = 0) const;
72 virtual bool requestStorage(int nframes = -1);
75 * Returns the number of rows in the data array.
77 * This function is identical to frameCount(), except that frameCount()
78 * returns 0 before valuesReady() has been called.
80 int rowCount() const { return _nrows; }
81 //! Returns true if values have been allocated.
82 bool isAllocated() const { return !_value.empty(); }
83 //! Returns the x value of the first frame.
84 real xstart() const { return _xstart; }
85 //! Returns the step between frame x values.
86 real xstep() const { return _xstep; }
87 //! Returns the x value of a row.
88 real xvalue(int row) const
90 GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
91 return xstart() + row * xstep();
93 //! Returns a given array element.
94 real value(int row, int col) const
96 GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
97 GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
98 GMX_ASSERT(isAllocated(), "Data array not allocated");
99 return _value[row * columnCount() + col];
103 AbstractAnalysisArrayData();
106 * Sets the number of columns in the data array.
108 * Cannot be called after allocateValues().
110 void setColumnCount(int ncols);
112 * Sets the number of rows in the data array.
114 * Cannot be called after allocateValues().
116 void setRowCount(int nrows);
118 * Allocates memory for the values.
120 * setColumnCount() and setRowCount() must have been called.
122 void allocateValues();
124 * Sets the values reported as x values for frames.
126 void setXAxis(real start, real step);
127 //! Returns a reference to a given array element.
128 real &value(int row, int col)
130 GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
131 GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
132 GMX_ASSERT(isAllocated(), "Data array not allocated");
133 return _value[row * columnCount() + col];
136 * Sets the value of an element in the array.
138 void setValue(int row, int col, real val)
140 value(row, col) = val;
143 * Notifies modules of the data.
145 * This function should be called once the values in the array
146 * have been initialized. The values should not be changed after this
147 * function has been called.
152 * Copies the contents into a new object.
154 * \param[in] src Object to copy data from.
155 * \param[in,out] dest Empty array data object to copy data to.
157 * \p dest should not have previous contents.
159 static void copyContents(const AbstractAnalysisArrayData *src,
160 AbstractAnalysisArrayData *dest);
164 std::vector<real> _value;
169 // Copy and assign disallowed by base.
173 * Simple in-memory data array.
175 * This class simply exposes the protected functions of
176 * AbstractAnalysisArrayData to allow construction of simple in-memory data
177 * arrays for input into data modules.
180 * \ingroup module_analysisdata
182 class AnalysisArrayData : public AbstractAnalysisArrayData
185 AnalysisArrayData() {}
187 // TODO: These statements cause Doxygen to generate confusing
189 using AbstractAnalysisArrayData::setColumnCount;
190 using AbstractAnalysisArrayData::setRowCount;
191 using AbstractAnalysisArrayData::allocateValues;
192 using AbstractAnalysisArrayData::setXAxis;
193 using AbstractAnalysisArrayData::value;
194 using AbstractAnalysisArrayData::setValue;
195 using AbstractAnalysisArrayData::valuesReady;
197 // Copy and assign disallowed by base.