To declare input data for the tool (typically, command-line options, including
input files and selections), \ref module_options module is used.
-The analysis tool code receives a pre-initialized gmx::Options object in one of
-its initialization methods, and fills it with its input options.
+The analysis tool code receives an instance of gmx::IOptionsContainer for one of
+its initialization methods, and uses it to provide its input options.
Basic options are declared in basicoptions.h, and also gmx::SelectionOption is
used in the same manner. For each option, the tool declares a local variable
that will receive the value for that option. After the options are parsed from
the command line (by the framework), the tool code can read the values from
-these variables. The option declarations, and other information filled into
-the gmx::Options object, are also used to provide help to the user (also
+these variables. The option declarations filled into the
+gmx::IOptionsContainer object are also used to provide help to the user (also
handled by the framework).
See the documentation for gmx::TrajectoryAnalysisModule and the
[options module documentation](\ref module_options) for more details.