* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "cmdlinerunner.h"
-
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
+#include "gmxpre.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/rmpbc.h"
+#include "cmdlinerunner.h"
#include "gromacs/analysisdata/paralleloptions.h"
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/options/filenameoptionmanager.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionoptionmanager.h"
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
-#include "gromacs/trajectoryanalysis/runnercommon.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
+#include "runnercommon.h"
+
namespace gmx
{
SelectionCollection *selections,
int *argc, char *argv[])
{
- Options options(NULL, NULL);
- Options moduleOptions(module_->name(), module_->description());
- Options commonOptions("common", "Common analysis control");
- Options selectionOptions("selection", "Common selection control");
- module_->initOptions(&moduleOptions, settings);
- common->initOptions(&commonOptions);
- selections->initOptions(&selectionOptions);
+ FileNameOptionManager fileoptManager;
+ SelectionOptionManager seloptManager(selections);
+ Options options(NULL, NULL);
+ Options moduleOptions(module_->name(), module_->description());
+ Options commonOptions("common", "Common analysis control");
+ Options selectionOptions("selection", "Common selection control");
+ options.addManager(&fileoptManager);
+ options.addManager(&seloptManager);
options.addSubSection(&commonOptions);
options.addSubSection(&selectionOptions);
options.addSubSection(&moduleOptions);
- SelectionOptionManager seloptManager(selections);
- setManagerForSelectionOptions(&options, &seloptManager);
+ module_->initOptions(&moduleOptions, settings);
+ common->initOptions(&commonOptions);
+ selections->initOptions(&selectionOptions);
{
CommandLineParser parser(&options);
// Load first frame.
common.initFirstFrame();
- module->initAfterFirstFrame(common.frame());
+ module->initAfterFirstFrame(settings, common.frame());
t_pbc pbc;
t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
TrajectoryAnalysisSettings settings;
TrajectoryAnalysisRunnerCommon common(&settings);
- Options options(NULL, NULL);
- Options moduleOptions(impl_->module_->name(), impl_->module_->description());
- Options commonOptions("common", "Common analysis control");
- Options selectionOptions("selection", "Common selection control");
-
- impl_->module_->initOptions(&moduleOptions, &settings);
- common.initOptions(&commonOptions);
- selections.initOptions(&selectionOptions);
+ SelectionOptionManager seloptManager(&selections);
+ Options options(NULL, NULL);
+ Options moduleOptions(impl_->module_->name(), impl_->module_->description());
+ Options commonOptions("common", "Common analysis control");
+ Options selectionOptions("selection", "Common selection control");
+ options.addManager(&seloptManager);
options.addSubSection(&commonOptions);
options.addSubSection(&selectionOptions);
options.addSubSection(&moduleOptions);
- SelectionOptionManager seloptManager(&selections);
- setManagerForSelectionOptions(&options, &seloptManager);
+ impl_->module_->initOptions(&moduleOptions, &settings);
+ common.initOptions(&commonOptions);
+ selections.initOptions(&selectionOptions);
CommandLineHelpWriter(options)
.setShowDescriptions(true)
virtual const char *name() const { return name_; }
virtual const char *shortDescription() const { return description_; };
+ virtual void init(CommandLineModuleSettings *settings);
virtual int run(int argc, char *argv[]);
virtual void writeHelp(const CommandLineHelpContext &context) const;
GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
};
+void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
+ CommandLineModuleSettings * /*settings*/)
+{
+}
+
int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
int argc, char *argv[])
{