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/*! \internal \file
* \brief
* This is an implementation header: there should be no need to use it outside
* this directory.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_SELELEM_H
#include <boost/shared_ptr.hpp>
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/selection/indexutil.h"
#include "gromacs/utility/common.h"
+#include "gromacs/utility/real.h"
-#include "indexutil.h"
#include "selvalue.h"
struct gmx_ana_poscalc_t;
/** Defines the arithmetic operation of gmx::SelectionTreeElement objects with type \ref SEL_ARITHMETIC. */
typedef enum
{
- ARITH_PLUS, /**< + */
- ARITH_MINUS, /**< - */
- ARITH_NEG, /**< Unary - */
- ARITH_MULT, /**< * */
- ARITH_DIV, /**< / */
- ARITH_EXP /**< ^ (to power) */
+ ARITH_PLUS, /**< Addition (`+`) */
+ ARITH_MINUS, /**< Subtraction (`-`) */
+ ARITH_NEG, /**< Unary `-` */
+ ARITH_MULT, /**< Multiplication (`*`) */
+ ARITH_DIV, /**< Division (`/`) */
+ ARITH_EXP /**< Power (`^`) */
} e_arithmetic_t;
/** Returns a string representation of the type of a gmx::SelectionTreeElement. */
* The element (or one of its children) is dynamic.
*/
#define SEL_DYNAMIC 16
+/*! \brief
+ * The element may contain atom indices in an unsorted order.
+ */
+#define SEL_UNSORTED 32
/*! \brief
* Mask that covers the flags that describe the number of values.
*/
namespace gmx
{
+class ExceptionInitializer;
+
/*! \brief
* Function pointer for evaluating a gmx::SelectionTreeElement.
*/
-typedef void (*sel_evalfunc)(struct gmx_sel_evaluate_t *data,
+typedef void (*sel_evalfunc)(struct gmx_sel_evaluate_t *data,
const SelectionTreeElementPointer &sel,
- gmx_ana_index_t *g);
+ gmx_ana_index_t *g);
/*! \internal \brief
* Represents an element of a selection expression.
void setName(const char *name) { name_ = (name != NULL ? name : ""); }
//! \copydoc setName(const char *)
void setName(const std::string &name) { name_ = name; }
+ /*! \brief
+ * Sets the name of a root element if it is missing.
+ *
+ * \param[in] selectionText Full selection text to use as a fallback.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * If index groups have not yet been set and the selection is a result
+ * of a group reference, the name may still be empty after this call.
+ *
+ * Strong exception safety guarantee.
+ */
+ void fillNameIfMissing(const char *selectionText);
+
+ /*! \brief
+ * Checks that this element and its children do not contain unsupported
+ * elements with unsorted atoms.
+ *
+ * \param[in] bUnsortedAllowed Whether this element's parents allow it
+ * to have unsorted atoms.
+ * \param errors Object for reporting any error messages.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Errors are reported as nested exceptions in \p errors.
+ */
+ void checkUnsortedAtoms(bool bUnsortedAllowed,
+ ExceptionInitializer *errors) const;
+ /*! \brief
+ * Resolves an unresolved reference to an index group.
+ *
+ * \param[in] grps Index groups to use to resolve the reference.
+ * \param[in] natoms Maximum number of atoms the selections can evaluate to
+ * (zero if the topology/atom count is not set yet).
+ * \throws std::bad_alloc if out of memory.
+ * \throws InconsistentInputError if the reference cannot be
+ * resolved.
+ */
+ void resolveIndexGroupReference(gmx_ana_indexgrps_t *grps, int natoms);
+ /*! \brief
+ * Checks that an index group has valid atom indices.
+ *
+ * \param[in] natoms Maximum number of atoms the selections can evaluate to.
+ * \throws std::bad_alloc if out of memory.
+ * \throws InconsistentInputError if there are invalid atom indices.
+ */
+ void checkIndexGroup(int natoms);
//! Type of the element.
e_selelem_t type;
/** Sets the value type of a gmx::SelectionTreeElement. */
void
_gmx_selelem_set_vtype(const gmx::SelectionTreeElementPointer &sel,
- e_selvalue_t vtype);
+ e_selvalue_t vtype);
/** Frees the memory allocated for a selection method. */
void
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