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/*! \file
* \brief
* Declares gmx::SelectionCollection.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_SELECTIONCOLLECTION_H
#define GMX_SELECTION_SELECTIONCOLLECTION_H
+#include <cstdio>
+
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
-
-#include "../utility/common.h"
-#include "selection.h" // For gmx::SelectionList
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
struct gmx_ana_indexgrps_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
namespace gmx
{
/*! \brief
* Initializes options for setting global properties on the collection.
*
- * \returns Initialized options object.
- * \throws std::bad_alloc if out of memory.
+ * \param[in,out] options Options object to initialize.
+ * \throws std::bad_alloc if out of memory.
*
- * The returned options can be used to set the default position types
- * (see setReferencePosType() and setOutputPosType()) and debugging
- * options.
+ * Adds options to \p options that can be used to set the default
+ * position types (see setReferencePosType() and setOutputPosType())
+ * and debugging flags.
*/
- Options &initOptions();
+ void initOptions(Options *options);
/*! \brief
* Sets the default reference position handling for a selection
*
* \param[in] grps Index groups to use for the selections.
* \throws std::bad_alloc if out of memory.
- * \throws InvalidInputError if a group reference cannot be resolved.
+ * \throws InconsistentInputError if a group reference cannot be resolved.
*
* Only the first call to this method can have a non-NULL \p grps.
* At this point, any selections that have already been provided are
* searched for references to external groups, and the references are
* replaced by the contents of the groups. If any referenced group
* cannot be found in \p grps (or if \p grps is NULL and there are any
- * references), InvalidInputError is thrown.
+ * references), InconsistentInputError is thrown.
*
* The selection collection keeps a reference to \p grps until this
* method is called with a NULL \p grps.
* (if -1, parse as many as provided by the user).
* \param[in] bInteractive Whether the parser should behave
* interactively.
- * \param[out] output Vector to which parsed selections are appended.
+ * \param[in] context Context to print for interactive input.
+ * \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error
* (an interactive parser only throws this if too few selections
* are provided and the user forced the end of input).
*
- * Parsed selections are appended to \p output without clearing it
- * first. If parsing fails, \p output is not modified.
- *
- * The objects returned in \p output remain valid for the lifetime of
+ * The returned objects remain valid for the lifetime of
* the selection collection.
* Some information about the selections only becomes available once
* compile() has been called; see \ref Selection.
+ *
+ * The string provided to \p context should be such that it can replace
+ * the three dots in "Specify selections ...:". It can be empty.
*/
- void parseFromStdin(int count, bool bInteractive,
- SelectionList *output);
+ SelectionList parseFromStdin(int count, bool bInteractive,
+ const std::string &context);
/*! \brief
* Parses selection(s) from a file.
*
* \param[in] filename Name of the file to parse selections from.
- * \param[out] output Vector to which parsed selections are appended.
+ * \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error.
*
- * Parsed selections are appended to \p output without clearing it
- * first. If parsing fails, \p output is not modified.
- *
- * The objects returned in \p output remain valid for the lifetime of
+ * The returned objects remain valid for the lifetime of
* the selection collection.
* Some information about the selections only becomes available once
* compile() has been called; see \ref Selection.
*/
- void parseFromFile(const std::string &filename,
- SelectionList *output);
+ SelectionList parseFromFile(const std::string &filename);
/*! \brief
* Parses selection(s) from a string.
*
* \param[in] str String to parse selections from.
- * \param[out] output Vector to which parsed selections are appended.
+ * \returns Vector of parsed selections.
* \throws std::bad_alloc if out of memory.
* \throws InvalidInputError if there is a parsing error.
*
- * Parsed selections are appended to \p output without clearing it
- * first. If parsing fails, \p output is not modified.
- *
- * The objects returned in \p output remain valid for the lifetime of
+ * The returned objects remain valid for the lifetime of
* the selection collection.
* Some information about the selections only becomes available once
* compile() has been called; see \ref Selection.
*/
- void parseFromString(const std::string &str,
- SelectionList *output);
+ SelectionList parseFromString(const std::string &str);
/*! \brief
* Prepares the selections for evaluation and performs optimizations.
*
private:
class Impl;
- PrivateImplPointer<Impl> _impl;
+ PrivateImplPointer<Impl> impl_;
/*! \brief
* Needed for the compiler to freely modify the collection.
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff