Uncrustify files

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

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index 3dc042e97cbdc77dd178365afa9555a15eb399ae..0bc78ce8fad84fe6e0cb640461ad6505fce4b14c 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@ -81,7 +81,7 @@ class TrajectoryAnalysisCommandLineRunner::Impl
         void parseOptions(TrajectoryAnalysisSettings *settings,
                           TrajectoryAnalysisRunnerCommon *common,
                           SelectionCollection *selections,
-                          int *argc, char *argv[], bool full=true);
+                          int *argc, char *argv[], bool full = true);
 
         TrajectoryAnalysisModule *module_;
         bool                      bUseDefaultGroups_;
@@ -111,23 +111,18 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
     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");
+    IOptionsContainer     &commonOptions = options.addGroup();
+    IOptionsContainer     &moduleOptions = options.addGroup();
 
     options.addManager(&fileoptManager);
     options.addManager(&seloptManager);
-    if (full) {
-        options.addSubSection(&commonOptions);
-    }
-    options.addSubSection(&selectionOptions);
-    options.addSubSection(&moduleOptions);
 
     module_->initOptions(&moduleOptions, settings);
-    if (full) {
+    if (full)
+    {
         common->initOptions(&commonOptions);
     }
-    selections->initOptions(&selectionOptions);
+    selections->initOptions(&commonOptions);
 
     {
         CommandLineParser  parser(&options);
@@ -138,10 +133,11 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
         options.finish();
     }
 
-    if (full) {
-        common->optionsFinished(&commonOptions);
+    if (full)
+    {
+        common->optionsFinished();
     }
-    module_->optionsFinished(&moduleOptions, settings);
+    module_->optionsFinished(settings);
 
     common->initIndexGroups(selections, bUseDefaultGroups_);
 
@@ -201,15 +197,16 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
     const TopologyInformation &topology = common.topologyInformation();
     module->initAnalysis(settings, topology);
 
-    TrajectoryAnalysisModule::Batch batch = module->getBatch();
+    TrajectoryAnalysisModule::Batch   batch = module->getBatch();
     std::vector<SelectionCollection*> batchSelections;
-    std::vector<Impl*> impls;
-    for (size_t i = 0; i < batch.size(); i++) {
+    std::vector<Impl*>                impls;
+    for (size_t i = 0; i < batch.size(); i++)
+    {
         TrajectoryAnalysisModule *bmodule = batch[i];
         batchSelections.push_back(new SelectionCollection());
         impls.push_back(new Impl(bmodule));
         std::vector<char*> modArgv = module->getArgv(i);
-        int modArgc = modArgv.size();
+        int                modArgc = modArgv.size();
         impls.back()->parseOptions(&settings, &common, batchSelections.back(), &modArgc, modArgv.data(), false);
 
         batch[i]->initAnalysis(settings, topology);
@@ -227,14 +224,15 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
     TrajectoryAnalysisModuleDataPointer pdata(
             module->startFrames(dataOptions, selections));
 
-    std::vector<AnalysisDataParallelOptions> batchOptions;
+    std::vector<AnalysisDataParallelOptions>         batchOptions;
     std::vector<TrajectoryAnalysisModuleDataPointer> batchDataPointers;
-    for (size_t i = 0; i < batch.size(); i++) {
+    for (size_t i = 0; i < batch.size(); i++)
+    {
         batch[i]->initAfterFirstFrame(settings, common.frame());
 
         batchOptions.push_back(AnalysisDataParallelOptions());
         batchDataPointers.push_back(batch[i]->startFrames(
-            batchOptions.back(), *batchSelections[i]));
+                                            batchOptions.back(), *batchSelections[i]));
     }
 
     do
@@ -246,7 +244,8 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
             set_pbc(ppbc, topology.ePBC(), frame.box);
         }
 
-        for (size_t i = 0; i < batch.size(); i++) {
+        for (size_t i = 0; i < batch.size(); i++)
+        {
             batchSelections[i]->evaluate(&frame, ppbc);
             batch[i]->analyzeFrame(nframes, frame, ppbc, batchDataPointers[i].get());
             batch[i]->finishFrameSerial(nframes);
@@ -258,9 +257,11 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
         ++nframes;
     }
     while (common.readNextFrame());
-    for (size_t i = 0; i < batch.size(); i++) {
+    for (size_t i = 0; i < batch.size(); i++)
+    {
         batch[i]->finishFrames(batchDataPointers[i].get());
-        if (batchDataPointers[i].get() != NULL) {
+        if (batchDataPointers[i].get() != NULL)
+        {
             batchDataPointers[i]->finish();
         }
         batchDataPointers[i].reset();
@@ -284,7 +285,8 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
     }
 
     // Restore the maximal groups for dynamic selections.
-    for (size_t i = 0; i < batch.size(); i++) {
+    for (size_t i = 0; i < batch.size(); i++)
+    {
         batchSelections[i]->evaluateFinal(nframes);
         batch[i]->finishAnalysis(nframes);
         batch[i]->writeOutput();
@@ -313,21 +315,17 @@ TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &con
 
     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);
+    IOptionsContainer &commonOptions = options.addGroup();
+    IOptionsContainer &moduleOptions = options.addGroup();
 
     impl_->module_->initOptions(&moduleOptions, &settings);
     common.initOptions(&commonOptions);
-    selections.initOptions(&selectionOptions);
+    selections.initOptions(&commonOptions);
 
     CommandLineHelpWriter(options)
-        .setShowDescriptions(true)
+        .setHelpText(settings.helpText())
         .setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
         .writeHelp(context);
 }
@@ -339,7 +337,7 @@ TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &con
  * \ingroup module_trajectoryanalysis
  */
 class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
-    : public CommandLineModuleInterface
+    : public ICommandLineModule
 {
     public:
         /*! \brief
@@ -375,10 +373,10 @@ class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
         virtual void writeHelp(const CommandLineHelpContext &context) const;
 
     private:
-        const char            *name_;
-        const char            *description_;
-        bool                   hasFunction_;
-        ModuleFactoryMethod    factory_;
+        const char             *name_;
+        const char             *description_;
+        bool                    hasFunction_;
+        ModuleFactoryMethod     factory_;
         ModuleFactoryFunctor   *functor_;
 
         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
@@ -392,7 +390,7 @@ void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
         int argc, char *argv[])
 {
-    TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
+    TrajectoryAnalysisModulePointer     module(hasFunction_ ? factory_() : (*functor_)());
     TrajectoryAnalysisCommandLineRunner runner(module.get());
     return runner.run(argc, argv);
 }
@@ -400,7 +398,7 @@ int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
 void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
         const CommandLineHelpContext &context) const
 {
-    TrajectoryAnalysisModulePointer     module(hasFunction_? factory_() : (*functor_)());
+    TrajectoryAnalysisModulePointer     module(hasFunction_ ? factory_() : (*functor_)());
     TrajectoryAnalysisCommandLineRunner runner(module.get());
     runner.writeHelp(context);
 }