/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010-2018, The GROMACS development team.
+ * Copyright (c) 2019, 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.
{
//! Enum values for plot formats.
-const char *const g_plotFormats[] = {
- "none", "xmgrace", "xmgr"
-};
+const char* const g_plotFormats[] = { "none", "xmgrace", "xmgr" };
} // namespace
* AnalysisDataPlotSettings
*/
-AnalysisDataPlotSettings::AnalysisDataPlotSettings()
- : selections_(nullptr), timeUnit_(TimeUnit_Default), plotFormat_(1)
+AnalysisDataPlotSettings::AnalysisDataPlotSettings() :
+ selections_(nullptr),
+ timeUnit_(TimeUnit_Default),
+ plotFormat_(1)
{
}
-void
-AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection *selections)
+void AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection* selections)
{
selections_ = selections;
}
-void
-AnalysisDataPlotSettings::initOptions(IOptionsContainer *options)
+void AnalysisDataPlotSettings::initOptions(IOptionsContainer* options)
{
- options->addOption(EnumIntOption("xvg").enumValue(g_plotFormats)
- .store(&plotFormat_)
- .description("Plot formatting"));
+ options->addOption(
+ EnumIntOption("xvg").enumValue(g_plotFormats).store(&plotFormat_).description("Plot formatting"));
}
class AbstractPlotModule::Impl
{
- public:
- explicit Impl(const AnalysisDataPlotSettings &settings);
- ~Impl();
-
- void closeFile();
-
- AnalysisDataPlotSettings settings_;
- std::string filename_;
- FILE *fp_;
-
- bool bPlain_;
- bool bOmitX_;
- bool bErrorsAsSeparateColumn_;
- std::string title_;
- std::string subtitle_;
- std::string xlabel_;
- std::string ylabel_;
- std::vector<std::string> legend_;
- std::string xformat_;
- std::string yformat_;
- real xscale_;
+public:
+ explicit Impl(const AnalysisDataPlotSettings& settings);
+ ~Impl();
+
+ void closeFile();
+
+ AnalysisDataPlotSettings settings_;
+ std::string filename_;
+ FILE* fp_;
+
+ bool bPlain_;
+ bool bOmitX_;
+ bool bErrorsAsSeparateColumn_;
+ std::string title_;
+ std::string subtitle_;
+ std::string xlabel_;
+ std::string ylabel_;
+ std::vector<std::string> legend_;
+ std::string xformat_;
+ std::string yformat_;
+ real xscale_;
};
-AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
- : settings_(settings), fp_(nullptr), bPlain_(false), bOmitX_(false),
- bErrorsAsSeparateColumn_(false),
- xformat_("%11.3f"), yformat_(" %8.3f"), xscale_(1.0)
+AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings& settings) :
+ settings_(settings),
+ fp_(nullptr),
+ bPlain_(false),
+ bOmitX_(false),
+ bErrorsAsSeparateColumn_(false),
+ xformat_("%11.3f"),
+ yformat_(" %8.3f"),
+ xscale_(1.0)
{
}
}
-void
-AbstractPlotModule::Impl::closeFile()
+void AbstractPlotModule::Impl::closeFile()
{
if (fp_ != nullptr)
{
* AbstractPlotModule
*/
/*! \cond libapi */
-AbstractPlotModule::AbstractPlotModule()
- : impl_(new Impl(AnalysisDataPlotSettings()))
-{
-}
+AbstractPlotModule::AbstractPlotModule() : impl_(new Impl(AnalysisDataPlotSettings())) {}
-AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings &settings)
- : impl_(new Impl(settings))
+AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings& settings) :
+ impl_(new Impl(settings))
{
}
//! \endcond
-AbstractPlotModule::~AbstractPlotModule()
-{
-}
+AbstractPlotModule::~AbstractPlotModule() {}
-void
-AbstractPlotModule::setSettings(const AnalysisDataPlotSettings &settings)
+void AbstractPlotModule::setSettings(const AnalysisDataPlotSettings& settings)
{
impl_->settings_ = settings;
}
-void
-AbstractPlotModule::setFileName(const std::string &filename)
+void AbstractPlotModule::setFileName(const std::string& filename)
{
impl_->filename_ = filename;
}
-void
-AbstractPlotModule::setPlainOutput(bool bPlain)
+void AbstractPlotModule::setPlainOutput(bool bPlain)
{
impl_->bPlain_ = bPlain;
}
-void
-AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
+void AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
{
impl_->bErrorsAsSeparateColumn_ = bSeparate;
}
-void
-AbstractPlotModule::setOmitX(bool bOmitX)
+void AbstractPlotModule::setOmitX(bool bOmitX)
{
impl_->bOmitX_ = bOmitX;
}
-void
-AbstractPlotModule::setTitle(const char *title)
+void AbstractPlotModule::setTitle(const char* title)
{
impl_->title_ = title;
}
-void
-AbstractPlotModule::setTitle(const std::string &title)
+void AbstractPlotModule::setTitle(const std::string& title)
{
impl_->title_ = title;
}
-void
-AbstractPlotModule::setSubtitle(const char *subtitle)
+void AbstractPlotModule::setSubtitle(const char* subtitle)
{
impl_->subtitle_ = subtitle;
}
-void
-AbstractPlotModule::setSubtitle(const std::string &subtitle)
+void AbstractPlotModule::setSubtitle(const std::string& subtitle)
{
impl_->subtitle_ = subtitle;
}
-void
-AbstractPlotModule::setXLabel(const char *label)
+void AbstractPlotModule::setXLabel(const char* label)
{
impl_->xlabel_ = label;
}
-void
-AbstractPlotModule::setXAxisIsTime()
+void AbstractPlotModule::setXAxisIsTime()
{
TimeUnitManager manager(impl_->settings_.timeUnit());
impl_->xlabel_ = formatString("Time (%s)", manager.timeUnitAsString());
}
-void
-AbstractPlotModule::setYLabel(const char *label)
+void AbstractPlotModule::setYLabel(const char* label)
{
impl_->ylabel_ = label;
}
-void
-AbstractPlotModule::setLegend(int nsets, const char * const *setname)
+void AbstractPlotModule::setLegend(int nsets, const char* const* setname)
{
impl_->legend_.reserve(impl_->legend_.size() + nsets);
for (int i = 0; i < nsets; ++i)
}
-void
-AbstractPlotModule::appendLegend(const char *setname)
+void AbstractPlotModule::appendLegend(const char* setname)
{
impl_->legend_.emplace_back(setname);
}
-void
-AbstractPlotModule::appendLegend(const std::string &setname)
+void AbstractPlotModule::appendLegend(const std::string& setname)
{
impl_->legend_.push_back(setname);
}
-void
-AbstractPlotModule::setXFormat(int width, int precision, char format)
+void AbstractPlotModule::setXFormat(int width, int precision, char format)
{
- GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
- && width <= 99 && precision <= 99,
+ GMX_RELEASE_ASSERT(width >= 0 && precision >= 0 && width <= 99 && precision <= 99,
"Invalid width or precision");
- GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr,
- "Invalid format specifier");
+ GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr, "Invalid format specifier");
impl_->xformat_ = formatString("%%%d.%d%c", width, precision, format);
}
-void
-AbstractPlotModule::setYFormat(int width, int precision, char format)
+void AbstractPlotModule::setYFormat(int width, int precision, char format)
{
- GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
- && width <= 99 && precision <= 99,
+ GMX_RELEASE_ASSERT(width >= 0 && precision >= 0 && width <= 99 && precision <= 99,
"Invalid width or precision");
- GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr,
- "Invalid format specifier");
+ GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr, "Invalid format specifier");
impl_->yformat_ = formatString(" %%%d.%d%c", width, precision, format);
}
-int
-AbstractPlotModule::flags() const
+int AbstractPlotModule::flags() const
{
- return efAllowMissing | efAllowMulticolumn | efAllowMultipoint
- | efAllowMultipleDataSets;
+ return efAllowMissing | efAllowMulticolumn | efAllowMultipoint | efAllowMultipleDataSets;
}
-void
-AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
+void AbstractPlotModule::dataStarted(AbstractAnalysisData* /* data */)
{
if (!impl_->filename_.empty())
{
}
else
{
- time_unit_t time_unit
- = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1); // NOLINT(bugprone-misplaced-widening-cast)
- xvg_format_t xvg_format
- = (impl_->settings_.plotFormat() > 0
- ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
- : exvgNONE);
- gmx_output_env_t *oenv;
+ time_unit_t time_unit = static_cast<time_unit_t>(
+ impl_->settings_.timeUnit() + 1); // NOLINT(bugprone-misplaced-widening-cast)
+ xvg_format_t xvg_format = (impl_->settings_.plotFormat() > 0
+ ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
+ : exvgNONE);
+ gmx_output_env_t* oenv;
output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
const unique_cptr<gmx_output_env_t, output_env_done> oenvGuard(oenv);
- impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
- impl_->xlabel_, impl_->ylabel_,
- oenv);
- const SelectionCollection *selections
- = impl_->settings_.selectionCollection();
+ impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(), impl_->xlabel_,
+ impl_->ylabel_, oenv);
+ const SelectionCollection* selections = impl_->settings_.selectionCollection();
if (selections != nullptr && output_env_get_xvg_format(oenv) != exvgNONE)
{
selections->printXvgrInfo(impl_->fp_);
{
xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
}
- if (output_env_get_print_xvgr_codes(oenv)
- && !impl_->legend_.empty())
+ if (output_env_get_print_xvgr_codes(oenv) && !impl_->legend_.empty())
{
- std::vector<const char *> legend;
+ std::vector<const char*> legend;
legend.reserve(impl_->legend_.size());
for (size_t i = 0; i < impl_->legend_.size(); ++i)
{
}
-void
-AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader &header)
+void AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader& header)
{
if (!isFileOpen())
{
}
-void
-AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
+void AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader& /*header*/)
{
if (!isFileOpen())
{
}
-void
-AbstractPlotModule::dataFinished()
+void AbstractPlotModule::dataFinished()
{
impl_->closeFile();
}
/*! \cond libapi */
-bool
-AbstractPlotModule::isFileOpen() const
+bool AbstractPlotModule::isFileOpen() const
{
return impl_->fp_ != nullptr;
}
-void
-AbstractPlotModule::writeValue(const AnalysisDataValue &value) const
+void AbstractPlotModule::writeValue(const AnalysisDataValue& value) const
{
GMX_ASSERT(isFileOpen(), "File not opened, but write attempted");
const real y = value.isSet() ? value.value() : 0.0;
* DataPlotModule
*/
-AnalysisDataPlotModule::AnalysisDataPlotModule()
-{
-}
+AnalysisDataPlotModule::AnalysisDataPlotModule() {}
-AnalysisDataPlotModule::AnalysisDataPlotModule(
- const AnalysisDataPlotSettings &settings)
- : AbstractPlotModule(settings)
+AnalysisDataPlotModule::AnalysisDataPlotModule(const AnalysisDataPlotSettings& settings) :
+ AbstractPlotModule(settings)
{
}
-void
-AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
+void AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef& points)
{
if (!isFileOpen())
{
* DataVectorPlotModule
*/
-AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule()
- : bWrite_ {true, true, true, false}
-{
-}
+AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule() : bWrite_{ true, true, true, false } {}
-AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(
- const AnalysisDataPlotSettings &settings)
- : AbstractPlotModule(settings),
- bWrite_ {true, true, true, false}
+AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(const AnalysisDataPlotSettings& settings) :
+ AbstractPlotModule(settings),
+ bWrite_{ true, true, true, false }
{
}
-void
-AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
+void AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
{
bWrite_[XX] = bWrite;
}
-void
-AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
+void AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
{
bWrite_[YY] = bWrite;
}
-void
-AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
+void AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
{
bWrite_[ZZ] = bWrite;
}
-void
-AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
+void AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
{
bWrite_[DIM] = bWrite;
}
-void
-AnalysisDataVectorPlotModule::setWriteMask(const bool bWrite[DIM + 1])
+void AnalysisDataVectorPlotModule::setWriteMask(const bool bWrite[DIM + 1])
{
for (int i = 0; i < DIM + 1; ++i)
{
}
-void
-AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
+void AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef& points)
{
if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff