/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, 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
* \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 "gromacs/legacyheaders/statutil.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/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/programinfo.h"
namespace gmx
{
Impl(TrajectoryAnalysisModule *module);
~Impl();
- bool parseOptions(TrajectoryAnalysisSettings *settings,
+ void parseOptions(TrajectoryAnalysisSettings *settings,
TrajectoryAnalysisRunnerCommon *common,
SelectionCollection *selections,
int *argc, char *argv[]);
TrajectoryAnalysisModule *module_;
+ bool bUseDefaultGroups_;
int debugLevel_;
};
TrajectoryAnalysisCommandLineRunner::Impl::Impl(
TrajectoryAnalysisModule *module)
- : module_(module), debugLevel_(0)
+ : module_(module), bUseDefaultGroups_(true), debugLevel_(0)
{
}
}
-bool
+void
TrajectoryAnalysisCommandLineRunner::Impl::parseOptions(
TrajectoryAnalysisSettings *settings,
TrajectoryAnalysisRunnerCommon *common,
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);
common->optionsFinished(&commonOptions);
module_->optionsFinished(&moduleOptions, settings);
- common->initIndexGroups(selections);
+ common->initIndexGroups(selections, bUseDefaultGroups_);
- // TODO: Check whether the input is a pipe.
- bool bInteractive = true;
+ const bool bInteractive = File::standardInput().isInteractive();
seloptManager.parseRequestedFromStdin(bInteractive);
common->doneIndexGroups(selections);
- return true;
+ common->initTopology(selections);
+ selections->compile();
}
}
+void
+TrajectoryAnalysisCommandLineRunner::setUseDefaultGroups(bool bUseDefaults)
+{
+ impl_->bUseDefaultGroups_ = bUseDefaults;
+}
+
+
void
TrajectoryAnalysisCommandLineRunner::setSelectionDebugLevel(int debuglevel)
{
- impl_->debugLevel_ = 1;
+ impl_->debugLevel_ = debuglevel;
}
TrajectoryAnalysisSettings settings;
TrajectoryAnalysisRunnerCommon common(&settings);
- if (!impl_->parseOptions(&settings, &common, &selections, &argc, argv))
- {
- return 0;
- }
-
- common.initTopology(&selections);
- selections.compile();
+ impl_->parseOptions(&settings, &common, &selections, &argc, argv);
const TopologyInformation &topology = common.topologyInformation();
module->initAnalysis(settings, topology);
// 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[])
{
void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::writeHelp(
const CommandLineHelpContext &context) const
{
- // TODO: Implement #969.
- if (context.writerContext().outputFormat() != eHelpOutputFormat_Console)
- {
- return;
- }
TrajectoryAnalysisModulePointer module(factory_());
TrajectoryAnalysisCommandLineRunner runner(module.get());
runner.writeHelp(context);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff