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/*! \internal \file
* \brief
* This header also defines ::gmx_ana_selcollection_t, which is used in the old
* C code for handling selection collections.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_SELECTIONCOLLECTION_IMPL_H
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
+#include <boost/scoped_ptr.hpp>
+
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/utility/uniqueptr.h"
-#include "../onlinehelp/helptopicinterface.h"
-#include "../options/options.h"
-#include "../utility/uniqueptr.h"
-#include "indexutil.h"
#include "poscalc.h"
-#include "selection.h" // For gmx::SelectionList
-#include "selectioncollection.h"
+#include "selelem.h"
+
+struct gmx_sel_mempool_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
namespace gmx
{
+
//! Smart pointer for managing an internal selection data object.
typedef gmx_unique_ptr<internal::SelectionData>::type SelectionDataPointer;
//! Container for storing a list of selections internally.
typedef std::vector<SelectionDataPointer> SelectionDataList;
-}
+
+class SelectionParserSymbolTable;
+
+} // namespace gmx
/*! \internal \brief
* Information for a collection of selections.
*/
struct gmx_ana_selcollection_t
{
- /** Root of the selection element tree. */
- struct t_selelem *root;
+ //! Position calculation collection used for selection position evaluation.
+ gmx::PositionCalculationCollection pcc;
+ //! Root of the selection element tree.
+ gmx::SelectionTreeElementPointer root;
/*! \brief
* Array of compiled selections.
*
char **varstrs;
/** Topology for the collection. */
- t_topology *top;
+ t_topology *top;
/** Index group that contains all the atoms. */
- struct gmx_ana_index_t gall;
- /** Position calculation collection used for selection position evaluation. */
- gmx::PositionCalculationCollection pcc;
+ gmx_ana_index_t gall;
/** Memory pool used for selection evaluation. */
- struct gmx_sel_mempool_t *mempool;
- /** Parser symbol table. */
- struct gmx_sel_symtab_t *symtab;
+ gmx_sel_mempool_t *mempool;
+ //! Parser symbol table.
+ boost::scoped_ptr<gmx::SelectionParserSymbolTable> symtab;
//! Root of help topic tree (NULL is no help yet requested).
- gmx::HelpTopicPointer rootHelp;
+ gmx::HelpTopicPointer rootHelp;
};
namespace gmx
{
-class MessageStringCollector;
+class ExceptionInitializer;
/*! \internal \brief
* Private implemention class for SelectionCollection.
* Does not throw.
*/
void clearSymbolTable();
- /*! \brief
- * Helper function that runs the parser once the tokenizer has been
- * initialized.
- *
- * \param[in,out] scanner Scanner data structure.
- * \param[in] maxnr Maximum number of selections to parse
- * (if -1, parse as many as provided by the user).
- * \returns Vector of parsed selections.
- * \throws std::bad_alloc if out of memory.
- * \throws InvalidInputError if there is a parsing error.
- *
- * Used internally to implement parseFromStdin(), parseFromFile() and
- * parseFromString().
- */
- SelectionList runParser(void *scanner, int maxnr);
/*! \brief
* Replace group references by group contents.
*
* \param[in] root Root of selection tree to process.
* \param errors Object for reporting any error messages.
+ * \throws std::bad_alloc if out of memory.
*
* Recursively searches the selection tree for unresolved external
* references. If one is found, finds the referenced group in
- * \a _grps and replaces the reference with a constant element that
+ * \a grps_ and replaces the reference with a constant element that
* contains the atoms from the referenced group. Any failures to
* resolve references are reported to \p errors.
- *
- * Does not throw currently, but this is subject to change when more
- * underlying code is converted to C++.
*/
- void resolveExternalGroups(struct t_selelem *root,
- MessageStringCollector *errors);
+ void resolveExternalGroups(const gmx::SelectionTreeElementPointer &root,
+ ExceptionInitializer *errors);
//! Internal data, used for interfacing with old C code.
- gmx_ana_selcollection_t _sc;
- //! Options object for setting global properties on the collection.
- Options _options;
+ gmx_ana_selcollection_t sc_;
//! Default reference position type for selections.
- std::string _rpost;
+ std::string rpost_;
//! Default output position type for selections.
- std::string _spost;
+ std::string spost_;
+ //! Largest atom index needed by the selections for evaluation.
+ int maxAtomIndex_;
/*! \brief
* Debugging level for the collection.
*
* - 3: like 1, also print the tree after evaluation
* - 4: combine 2 and 3
*/
- int _debugLevel;
+ int debugLevel_;
//! Whether setIndexGroups() has been called.
- bool _bExternalGroupsSet;
+ bool bExternalGroupsSet_;
//! External index groups (can be NULL).
- gmx_ana_indexgrps_t *_grps;
+ gmx_ana_indexgrps_t *grps_;
};
-/*! \internal \brief
+/*! \internal
+ * \brief
* Implements selection evaluation.
*
* This class is used to implement SelectionCollection::evaluate() and
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff