Uncrustify files

Change-Id: I07a194d10afdbcf27755bcde1e291d869360725d
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>

diff --git a/admin/copyright.py b/admin/copyright.py
index 23c8a3b643a2ac170c80ac23c16aa5c50e3e514d..c5c60d37dcec171bd3d2dc4de6f727ea2d703857 100755 (executable)
--- a/admin/copyright.py
+++ b/admin/copyright.py
@@ -303,7 +303,7 @@ def select_comment_handler(override, filename):
             dummy, ext2 = os.path.splitext(root)
             if ext2:
                 ext = ext2
-        if ext in ('.c', '.cu', '.cpp', '.h', '.cuh', '.y', '.l', '.pre', '.bm'):
+        if ext in ('.c', '.cu', '.cpp', '.h', '.cuh', '.y', '.l', '.pre', '.bm', '.sip'):
             filetype = 'c'
         elif ext in ('.tex',):
             filetype = 'tex'

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index e70fafa138ae4b2c78dba26d9b992aa8c8e0ae64..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_;
@@ -111,14 +111,15 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
     FileNameOptionManager  fileoptManager;
     SelectionOptionManager seloptManager(selections);
     Options                options(NULL, NULL);
-    IOptionsContainer &commonOptions = options.addGroup();
-    IOptionsContainer &moduleOptions = options.addGroup();
+    IOptionsContainer     &commonOptions = options.addGroup();
+    IOptionsContainer     &moduleOptions = options.addGroup();
 
     options.addManager(&fileoptManager);
     options.addManager(&seloptManager);
 
     module_->initOptions(&moduleOptions, settings);
-    if (full) {
+    if (full)
+    {
         common->initOptions(&commonOptions);
     }
     selections->initOptions(&commonOptions);
@@ -132,7 +133,8 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
         options.finish();
     }
 
-    if (full) {
+    if (full)
+    {
         common->optionsFinished();
     }
     module_->optionsFinished(settings);
@@ -195,15 +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);
@@ -221,14 +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
@@ -240,7 +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);
@@ -252,9 +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();
@@ -278,7 +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();
@@ -365,10 +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);
@@ -382,7 +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);
 }
@@ -390,7 +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);
 }

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.h b/src/gromacs/trajectoryanalysis/cmdlinerunner.h
index 9bcc013418d1ee58b9f30c31d73e5820388bf2ab..0b703ea268485300ab0d70954064217634a8870d 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.h
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.h
@@ -87,7 +87,8 @@ class TrajectoryAnalysisCommandLineRunner
          * This abstract class should be subclassed to be used. The main usage is for
          * python bindings.
          */
-        class ModuleFactoryFunctor {
+        class ModuleFactoryFunctor
+        {
             public:
                 /*! \brief
                  * operator() that returns a pointer to valid TrajectoryAnalysisModule

diff --git a/src/python/include/numpy_conv.h b/src/python/include/numpy_conv.h
index b810832b051c99676de5f0c7308b31b538db651f..67d04da321dbc24a9416c03ef8c82a39fc9cf26c 100644 (file)
--- a/src/python/include/numpy_conv.h
+++ b/src/python/include/numpy_conv.h
@@ -39,25 +39,28 @@
 #include <Python.h>
 #include <numpy/ndarrayobject.h>
 
-PyObject* array2dToNumpy(int dim1, int dim2, const void *data) {
+PyObject* array2dToNumpy(int dim1, int dim2, const void *data)
+{
     npy_intp dims[] = {dim1, dim2};
     #ifdef GMX_DOUBLE
-        return PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (double*) data);
+    return PyArray_SimpleNewFromData(2, dims, NPY_DOUBLE, (double*) data);
     #else
-        return PyArray_SimpleNewFromData(2, dims, NPY_FLOAT, (float*) data);
+    return PyArray_SimpleNewFromData(2, dims, NPY_FLOAT, (float*) data);
     #endif
 }
 
-PyObject* array1dToNumpy(int dim, const void *data) {
+PyObject* array1dToNumpy(int dim, const void *data)
+{
     npy_intp n_dim = dim;
     #ifdef GMX_DOUBLE
-        return PyArray_SimpleNewFromData(1, &n_dim, NPY_DOUBLE, (double*) data);
+    return PyArray_SimpleNewFromData(1, &n_dim, NPY_DOUBLE, (double*) data);
     #else
-        return PyArray_SimpleNewFromData(1, &n_dim, NPY_FLOAT, (float*) data);
+    return PyArray_SimpleNewFromData(1, &n_dim, NPY_FLOAT, (float*) data);
     #endif
 }
 
-PyObject* iarray1dToNumpy(int dim, const int *data) {
+PyObject* iarray1dToNumpy(int dim, const int *data)
+{
     npy_intp n_dim = dim;
     return PyArray_SimpleNewFromData(1, &n_dim, NPY_INT, (int*) data);
 }