/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \file
* \brief
* Declares gmx::AbstractAnalysisArrayData and gmx::AnalysisArrayData.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_analysisdata
*/
#ifndef GMX_ANALYSISDATA_ARRAYDATA_H
#define GMX_ANALYSISDATA_ARRAYDATA_H
-#include <cstddef>
-
-#include "../fatalerror/gmxassert.h"
+#include <vector>
-#include "abstractdata.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
* This class implements a subclass of AbstractAnalysisData that presents an
* in-memory array through the AbstractAnalysisData interface. Subclasses
* should initialize the in-memory array through the provided protected member
- * functions.
+ * functions. This class provides public accessor methods for read access to
+ * the data.
+ *
+ * Public accessor methods in this class do not throw, but assert if data is
+ * accessed before it is available.
+ *
+ * \todo
+ * Add support for multiple data sets.
*
* \inlibraryapi
* \ingroup module_analysisdata
public:
virtual ~AbstractAnalysisArrayData();
- virtual bool getDataWErr(int index, real *x, real *dx,
- const real **y, const real **dy,
- const bool **present = 0) const;
- virtual bool requestStorage(int nframes = -1);
-
- protected:
- AbstractAnalysisArrayData();
+ virtual int frameCount() const
+ {
+ return bReady_ ? rowCount_ : 0;
+ }
/*! \brief
* Returns the number of rows in the data array.
* This function is identical to frameCount(), except that frameCount()
* returns 0 before valuesReady() has been called.
*/
- int rowCount() const { return _nrows; }
+ int rowCount() const { return rowCount_; }
+ //! Returns true if values have been allocated.
+ bool isAllocated() const { return !value_.empty(); }
+ //! Returns the x value of the first frame.
+ real xstart() const { return xvalue_[0]; }
+ //! Returns the step between frame x values.
+ real xstep() const
+ {
+ GMX_ASSERT(bUniformX_, "Accessing x step for non-uniform data");
+ return xstep_;
+ }
+ //! Returns the x value of a row.
+ real xvalue(int row) const
+ {
+ GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
+ return xvalue_[row];
+ }
+ //! Returns a given array element.
+ const AnalysisDataValue &value(int row, int col) const
+ {
+ GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
+ GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
+ GMX_ASSERT(isAllocated(), "Data array not allocated");
+ return value_[row * columnCount() + col];
+ }
+
+ protected:
+ /*! \brief
+ * Initializes an empty array data object.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ AbstractAnalysisArrayData();
+
/*! \brief
* Sets the number of columns in the data array.
*
+ * \param[in] ncols Number of columns in the data.
+ *
* Cannot be called after allocateValues().
+ *
+ * See AbstractAnalysisData::setColumnCount() for exception behavior.
*/
void setColumnCount(int ncols);
/*! \brief
* Sets the number of rows in the data array.
*
+ * \param[in] rowCount Number of rows in the data.
+ *
* Cannot be called after allocateValues().
+ *
+ * Does not throw.
*/
- void setRowCount(int nrows);
+ void setRowCount(int rowCount);
/*! \brief
* Allocates memory for the values.
*
+ * \throws std::bad_alloc if memory allocation fails.
+ *
* setColumnCount() and setRowCount() must have been called.
+ *
+ * Strong exception safety guarantee.
*/
void allocateValues();
- //! Returns the x value of the first frame.
- real xstart() const { return _xstart; }
- //! Returns the step between frame x values.
- real xstep() const { return _xstep; }
/*! \brief
* Sets the values reported as x values for frames.
+ *
+ * \param[in] start x value for the first frame.
+ * \param[in] step Step between x values of successive frames.
+ *
+ * Must not be called after valuesReady().
+ * Any values set with setXAxisValue() are overwritten.
+ *
+ * Does not throw.
*/
void setXAxis(real start, real step);
- //! Returns a reference to a given array element.
- real &value(int row, int col)
- {
- GMX_ASSERT(row >= 0 && row < _nrows, "Row index out of range");
- GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
- GMX_ASSERT(_value != NULL, "Data array not allocated");
- return _value[row * columnCount() + col];
- }
- //! Returns a given array element.
- const real &value(int row, int col) const
- {
- GMX_ASSERT(row >= 0 && row < _nrows, "Row index out of range");
- GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
- GMX_ASSERT(_value != NULL, "Data array not allocated");
- return _value[row * columnCount() + col];
- }
/*! \brief
- * Sets the value of an element in the array.
+ * Sets a single value reported as x value for frames.
+ *
+ * \param[in] row Row/frame for which to set the value.
+ * \param[in] value x value for the frame specified by \p row.
+ *
+ * Must not be called after valuesReady().
+ *
+ * Does not throw.
*/
- void setValue(int row, int col, real val)
+ void setXAxisValue(int row, real value);
+ //! Returns a reference to a given array element.
+ AnalysisDataValue &value(int row, int col)
{
- value(row, col) = val;
+ GMX_ASSERT(row >= 0 && row < rowCount(), "Row index out of range");
+ GMX_ASSERT(col >= 0 && col < columnCount(), "Column index out of range");
+ GMX_ASSERT(isAllocated(), "Data array not allocated");
+ return value_[row * columnCount() + col];
}
/*! \brief
* Notifies modules of the data.
*
+ * \throws unspecified Any exception thrown by attached data modules
+ * in data notification methods.
+ *
* This function should be called once the values in the array
- * have been initialized. The values should not be changed after this
+ * have been initialized. The values should not be changed after this
* function has been called.
*/
void valuesReady();
*
* \param[in] src Object to copy data from.
* \param[in,out] dest Empty array data object to copy data to.
+ * \throws std::bad_alloc if memory allocation for \p dest fails.
*
* \p dest should not have previous contents.
*/
static void copyContents(const AbstractAnalysisArrayData *src,
- AbstractAnalysisArrayData *dest);
+ AbstractAnalysisArrayData *dest);
private:
- int _nrows;
- real *_value;
- real _xstart;
- real _xstep;
- bool _bReady;
+ virtual AnalysisDataFrameRef tryGetDataFrameInternal(int index) const;
+ virtual bool requestStorageInternal(int nframes);
+
+ int rowCount_;
+ AnalysisDataPointSetInfo pointSetInfo_;
+ std::vector<AnalysisDataValue> value_;
+ std::vector<real> xvalue_;
+ real xstep_;
+ bool bUniformX_;
+ bool bReady_;
// Copy and assign disallowed by base.
};
/*! \brief
* Simple in-memory data array.
*
- * This class simply exposes the protected functions of
- * AbstractAnalysisArrayData to allow construction of simple in-memory data
- * arrays for input into data modules.
+ * This class is a simple alternative to AnalysisData for in-memory data arrays
+ * that are constructed in-place.
+ *
+ * Public accessor methods in this class do not throw, but assert if data is
+ * accessed before it is available.
+ *
+ * \if libapi
+ * This class exposes the protected functions of AbstractAnalysisArrayData for
+ * users.
+ * \endif
*
* \inpublicapi
* \ingroup module_analysisdata
class AnalysisArrayData : public AbstractAnalysisArrayData
{
public:
+ /*! \brief
+ * Initializes an empty array data object.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
AnalysisArrayData() {}
// TODO: These statements cause Doxygen to generate confusing
// documentation.
- using AbstractAnalysisArrayData::rowCount;
using AbstractAnalysisArrayData::setColumnCount;
using AbstractAnalysisArrayData::setRowCount;
using AbstractAnalysisArrayData::allocateValues;
- using AbstractAnalysisArrayData::xstart;
- using AbstractAnalysisArrayData::xstep;
using AbstractAnalysisArrayData::setXAxis;
+ using AbstractAnalysisArrayData::setXAxisValue;
using AbstractAnalysisArrayData::value;
- using AbstractAnalysisArrayData::setValue;
using AbstractAnalysisArrayData::valuesReady;
// Copy and assign disallowed by base.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff