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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 <boost/scoped_ptr.hpp>
-#include "../legacyheaders/typedefs.h"
+#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 "../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
{
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;
+ gmx_ana_index_t gall;
/** Memory pool used for selection evaluation. */
- struct gmx_sel_mempool_t *mempool;
+ 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.
*
* \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
* 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(const gmx::SelectionTreeElementPointer &root,
- MessageStringCollector *errors);
+ ExceptionInitializer *errors);
//! Internal data, used for interfacing with old C code.
gmx_ana_selcollection_t sc_;
std::string rpost_;
//! Default output position type for selections.
std::string spost_;
+ //! Largest atom index needed by the selections for evaluation.
+ int maxAtomIndex_;
/*! \brief
* Debugging level for the collection.
*
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