/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, 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.
#ifndef GMX_SELECTION_SELECTIONCOLLECTION_H
#define GMX_SELECTION_SELECTIONCOLLECTION_H
+#include <cstdio>
+
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
-
-#include "../onlinehelp/helptopicinterface.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/classhelpers.h"
struct gmx_ana_indexgrps_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
namespace gmx
{
-class Options;
+class IOptionsContainer;
class SelectionCompiler;
class SelectionEvaluator;
+class TextInputStream;
+class TextOutputStream;
/*! \brief
* Collection of selections.
* initialization options.
*
* After setting the default values, one or more selections can be parsed with
- * one or more calls to parseFromStdin(), parseFromFile(), and/or
+ * one or more calls to parseInteractive(), parseFromStdin(), parseFromFile(), and/or
* parseFromString(). After all selections are parsed, the topology must be
* set with setTopology() unless requiresTopology() returns false (the topology
* can also be set earlier).
class SelectionCollection
{
public:
- /*! \brief
- * Creates a help tree for selections.
- *
- * \throws std::bad_alloc if out of memory.
- * \returns Root topic of the created selection tree.
- */
- static HelpTopicPointer createDefaultHelpTopic();
-
/*! \brief
* Creates an empty selection collection.
*
* position types (see setReferencePosType() and setOutputPosType())
* and debugging flags.
*/
- void initOptions(Options *options);
+ void initOptions(IOptionsContainer *options);
/*! \brief
* Sets the default reference position handling for a selection
* (if -1, parse as many as provided by the user).
* \param[in] bInteractive Whether the parser should behave
* interactively.
+ * \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
* 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.
+ */
+ SelectionList parseFromStdin(int count, bool bInteractive,
+ const std::string &context);
+ /*! \brief
+ * Parses selection(s) interactively using provided streams.
+ *
+ * \param[in] count Number of selections to parse
+ * (if -1, parse as many as provided by the user).
+ * \param[in] inputStream Stream to use for input.
+ * \param[in] outputStream Stream to use for output
+ * (if NULL, the parser runs non-interactively and does not
+ * produce any status messages).
+ * \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).
+ *
+ * Works the same as parseFromStdin(), except that the caller can
+ * provide streams to use instead of `stdin` and `stderr`.
+ *
+ * Mainly usable for unit testing interactive input.
*/
- SelectionList parseFromStdin(int count, bool bInteractive);
+ SelectionList parseInteractive(int count,
+ TextInputStream *inputStream,
+ TextOutputStream *outputStream,
+ const std::string &context);
/*! \brief
* Parses selection(s) from a file.
*