Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / trajectoryanalysis / modules.cpp

diff --git a/src/gromacs/trajectoryanalysis/modules.cpp b/src/gromacs/trajectoryanalysis/modules.cpp
index 428c88af072b6197fd4bea19252d2ff934144c1a..07a3a8c378bf63d7c7534d1f3d5f3f6b911f79fb 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules.cpp
+++ b/src/gromacs/trajectoryanalysis/modules.cpp
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2010,2011,2012,2013,2014, 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.
  *
  * GROMACS is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -39,14 +39,17 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_trajectoryanalysis
  */
-#include "gromacs/trajectoryanalysis/modules.h"
+#include "gmxpre.h"
+
+#include "modules.h"
 
-#include "gromacs/commandline/cmdlinemodule.h"
 #include "gromacs/commandline/cmdlinemodulemanager.h"
 #include "gromacs/trajectoryanalysis/cmdlinerunner.h"
 
 #include "modules/angle.h"
 #include "modules/distance.h"
+#include "modules/freevolume.h"
+#include "modules/sasa.h"
 #include "modules/select.h"
 
 namespace gmx
@@ -55,80 +58,41 @@ namespace gmx
 namespace
 {
 
-/*! \internal \brief
- * Base class for trajectory analysis module command-line wrappers.
- *
- * This class exists to avoid multiple identical copies of the \p run() method
- * to be generated for the TrajAnalysisCmdLineWrapper template classes.
- *
- * \ingroup module_trajectoryanalysis
- */
-class AbstractTrajAnalysisCmdLineWrapper : public CommandLineModuleInterface
-{
-    public:
-        virtual const char *name() const             = 0;
-        virtual const char *shortDescription() const = 0;
-
-        virtual int run(int argc, char *argv[]);
-        virtual void writeHelp(const HelpWriterContext &context) const;
-
-    protected:
-        //! Creates the analysis module for this wrapper.
-        virtual TrajectoryAnalysisModulePointer createModule() const = 0;
-};
-
-int AbstractTrajAnalysisCmdLineWrapper::run(int argc, char *argv[])
-{
-    TrajectoryAnalysisModulePointer     module(createModule());
-    TrajectoryAnalysisCommandLineRunner runner(module.get());
-    runner.setPrintCopyright(false);
-    return runner.run(argc, argv);
-}
-
-void AbstractTrajAnalysisCmdLineWrapper::writeHelp(const HelpWriterContext &context) const
-{
-    TrajectoryAnalysisModulePointer     module(createModule());
-    TrajectoryAnalysisCommandLineRunner runner(module.get());
-    runner.writeHelp(context);
-}
-
-/*! \internal \brief
- * Template for command-line wrapper of a trajectory analysis module.
+/*! \brief
+ * Convenience method for registering a command-line module for trajectory
+ * analysis.
  *
- * \tparam Module  Trajectory analysis module to wrap.
+ * \tparam ModuleInfo  Info about trajectory analysis module to wrap.
  *
- * \p Module should be default-constructible, derive from
- * TrajectoryAnalysisModule, and have a static public members
- * \c "const char name[]" and \c "const char shortDescription[]".
+ * \p ModuleInfo should have static public members
+ * `const char name[]`, `const char shortDescription[]`, and
+ * `gmx::TrajectoryAnalysisModulePointer create()`.
  *
  * \ingroup module_trajectoryanalysis
  */
-template <class Module>
-class TrajAnalysisCmdLineWrapper : public AbstractTrajAnalysisCmdLineWrapper
+template <class ModuleInfo>
+void registerModule(CommandLineModuleManager *manager,
+                    CommandLineModuleGroup    group)
 {
-    public:
-        virtual const char *name() const
-        {
-            return Module::name;
-        }
-        virtual const char *shortDescription() const
-        {
-            return Module::shortDescription;
-        }
-        virtual TrajectoryAnalysisModulePointer createModule() const
-        {
-            return TrajectoryAnalysisModulePointer(new Module);
-        }
-};
+    TrajectoryAnalysisCommandLineRunner::registerModule(
+            manager, ModuleInfo::name, ModuleInfo::shortDescription,
+            &ModuleInfo::create);
+    group.addModule(ModuleInfo::name);
+}
 
 }   // namespace
 
+//! \cond libapi
 void registerTrajectoryAnalysisModules(CommandLineModuleManager *manager)
 {
     using namespace gmx::analysismodules;
-    manager->registerModule<TrajAnalysisCmdLineWrapper<Angle> >();
-    manager->registerModule<TrajAnalysisCmdLineWrapper<Distance> >();
-    manager->registerModule<TrajAnalysisCmdLineWrapper<Select> >();
+    CommandLineModuleGroup group = manager->addModuleGroup("Trajectory analysis");
+    registerModule<AngleInfo>(manager, group);
+    registerModule<DistanceInfo>(manager, group);
+    registerModule<FreeVolumeInfo>(manager, group);
+    registerModule<SasaInfo>(manager, group);
+    registerModule<SelectInfo>(manager, group);
 }
+//! \endcond
 
 } // namespace gmx