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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \defgroup module_options Extensible Handling of Options
+/*! \defgroup module_options Extensible Handling of Options (options)
* \ingroup group_utilitymodules
* \brief
* Provides functionality for handling options.
* descriptions for individual options as well as for the whole set of options.
* These can then be used to write out help text.
*
+ * The sequence charts below provides an overview of how the options work from
+ * usage perspective. They include two fictional modules, A and B, that provide
+ * options, and a main routine that manages these. The first chart shows a
+ * typical initialization sequence, where the main routine creates an options
+ * object, and calls an initOptions() method in each module that can provide
+ * options (the modules may also request their submodules to add their own
+ * options). Each module uses gmx::Options::addOption() to add the options
+ * they require, and specify output variables into which the options values are
+ * stored.
+ * \msc
+ * main,
+ * options [ label="Options", URL="\ref gmx::Options" ],
+ * A [ label="module A" ],
+ * B [ label="module B" ];
+ *
+ * main box B [ label="main owns all objects" ];
+ * main => options [ label="create", URL="\ref gmx::Options::Options()" ];
+ * main => A [ label="initOptions()" ];
+ * A => options [ label="addOption()", URL="\ref gmx::Options::addOption()" ];
+ * ...;
+ * main << A;
+ * main => B [ label="initOptions()" ];
+ * B => options [ label="addOption()", URL="\ref gmx::Options::addOption()" ];
+ * ...;
+ * main << B;
+ * \endmsc
+ *
+ * After all options have been specified, they can be parsed. A parser splits
+ * the input into option-value pairs (one option may have multiple values), and
+ * passes these into the gmx::Options object, which is responsible for
+ * converting them into the appropriate types and storing the values into the
+ * variables provided in the calls to gmx::Options::addOption().
+ * \msc
+ * main,
+ * parser [ label="parser" ],
+ * options [ label="Options", URL="\ref gmx::Options" ],
+ * A [ label="module A" ],
+ * B [ label="module B" ];
+ *
+ * main => parser [ label="parse()" ];
+ * parser => options [ label="assign(string)" ];
+ * options -> A [ label="set variable" ];
+ * parser => options [ label="assign(string)" ];
+ * options -> B [ label="set variable" ];
+ * ...;
+ * \endmsc
+ *
+ * After all options have been parsed (possibly using multiple different
+ * parsers), gmx::Options::finish() is called. This performs final
+ * validation of the options and may further adjust the values stored in the
+ * output variables (see documentation on individual option types on when this
+ * may happen).
+ * \msc
+ * main,
+ * options [ label="Options", URL="\ref gmx::Options" ],
+ * A [ label="module A" ],
+ * B [ label="module B" ];
+ *
+ * main => options [ label="finish()", URL="\ref gmx::Options::finish()" ];
+ * options -> A [ label="set variable" ];
+ * options -> B [ label="set variable" ];
+ * ...;
+ * \endmsc
+ *
* Module \ref module_commandline implements classes that assign option values
* from command line and produce help for programs that use the command line
* parser.
* OptionsIterator to apply this visitor to the Options object.
* \endif
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
*/
/*! \file
* \brief
* Public API convenience header for handling of options.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_options
*/
#ifndef GMX_OPTIONS_H
#define GMX_OPTIONS_H
-#include "options/basicoptions.h"
-#include "options/filenameoption.h"
-#include "options/options.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/filenameoptionmanager.h"
+#include "gromacs/options/options.h"
#endif
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