Sort all includes in src/gromacs

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

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index 43f59ad33a0178449134b3d388c80cdb7835be83..60684c401919c1f7be6f5a8bd7820265acdba565 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * 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.
@@ -39,14 +39,9 @@
  * \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"
@@ -54,16 +49,19 @@
 #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 "gromacs/utility/programinfo.h"
+
+#include "runnercommon.h"
 
 namespace gmx
 {
@@ -110,20 +108,22 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
         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);
@@ -139,8 +139,7 @@ TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
 
     common->initIndexGroups(selections, bUseDefaultGroups_);
 
-    // TODO: Check whether the input is a pipe.
-    const bool bInteractive = true;
+    const bool bInteractive = File::standardInput().isInteractive();
     seloptManager.parseRequestedFromStdin(bInteractive);
     common->doneIndexGroups(selections);
 
@@ -197,7 +196,7 @@ TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
 
     // Load first frame.
     common.initFirstFrame();
-    module->initAfterFirstFrame(common.frame());
+    module->initAfterFirstFrame(settings, common.frame());
 
     t_pbc  pbc;
     t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
@@ -257,21 +256,20 @@ TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &con
     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)
@@ -308,6 +306,7 @@ class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
         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;
 
@@ -319,6 +318,11 @@ class TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule
         GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
 };
 
+void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
+        CommandLineModuleSettings * /*settings*/)
+{
+}
+
 int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
         int argc, char *argv[])
 {