/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, 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.
GMX_RELEASE_ASSERT(rowCount > 0, "Invalid number of rows");
GMX_RELEASE_ASSERT(!isAllocated(),
"Cannot change row count after data has been allocated");
- GMX_RELEASE_ASSERT(bUniformX_ || rowCount_ == 0
+ GMX_RELEASE_ASSERT(bUniformX_ || xvalue_.empty()
|| rowCount == static_cast<int>(xvalue_.size()),
"X axis set with setXAxisValue() does not match the row count");
xvalue_.resize(rowCount);
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}
{
AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
- int prevResind = -1;
- int row = 0;
+ int nextRow = 0;
for (int i = 0; i < surfaceSel_.posCount(); ++i)
{
- const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
- const int residueIndex = atoms.atom[atomIndex].resind;
- if (residueIndex != prevResind)
+ const int residueGroup = surfaceSel_.position(i).mappedId();
+ if (residueGroup >= nextRow)
{
- avem->setXAxisValue(row, atoms.resinfo[residueIndex].nr);
- prevResind = residueIndex;
- ++row;
+ GMX_ASSERT(residueGroup == nextRow,
+ "Inconsistent (non-uniformly increasing) residue grouping");
+ const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
+ const int residueIndex = atoms.atom[atomIndex].resind;
+ avem->setXAxisValue(nextRow, atoms.resinfo[residueIndex].nr);
+ ++nextRow;
}
}
residueArea_.addModule(avem);
</AnalysisData>
</OutputData>
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+s1 legend "Standard deviation (nm\S2\N)"
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+ <File Name="-oa">
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</pre>
</xsl:template>
+<xsl:template match="OutputFiles/File/XvgLegend/String[@Name='XvgLegend']">
+ <pre>
+ <xsl:value-of select="substring(.,2)"/>
+ </pre>
+</xsl:template>
+
+<xsl:template match="OutputFiles/File/XvgData">
+ <xsl:choose>
+ <xsl:when test="*">
+ <table>
+ <xsl:apply-templates />
+ </table>
+ </xsl:when>
+ <xsl:otherwise>Data omitted</xsl:otherwise>
+ </xsl:choose>
+</xsl:template>
+
+<xsl:template match="OutputFiles/File/XvgData/Sequence">
+ <tr>
+ <xsl:apply-templates select="Real"/>
+ </tr>
+</xsl:template>
+
+<xsl:template match="OutputFiles/File/XvgData/Sequence/Real">
+ <td><xsl:value-of select="."/></td>
+</xsl:template>
+
<xsl:template match="InteractiveSession">
<pre>
<xsl:for-each select="*">
* Tests for functionality of the "sasa" trajectory analysis module.
*
* These tests test the basic functionality of the tool itself, but currently
- * the following are missing:
- * - Tests related to -odg output. This would require a full tpr file, and
- * some investigation on what kind of tpr it should be to produce reasonable
- * output.
- * - Tests for the X axes in the area per atom/residue plots. These could be
- * added once better X axes are implemented.
- * - Tests for XVG labels. This is a limitation of the current testing
- * framework.
+ * the tests related to -odg output are missing. This would require a full tpr
+ * file, and some investigation on what kind of tpr it should be to produce
+ * reasonable output.
*
* The actual surface area algorithm is tested separately in surfacearea.cpp.
*
#include "testutils/cmdlinetest.h"
#include "testutils/testasserts.h"
#include "testutils/textblockmatchers.h"
+#include "testutils/xvgtest.h"
#include "moduletest.h"
using gmx::test::CommandLine;
using gmx::test::ExactTextMatch;
using gmx::test::NoTextMatch;
+using gmx::test::XvgMatch;
/********************************************************************
* Tests for gmx::analysismodules::Sasa.
"-output", "name N CA C O H"
};
setTopology("lysozyme.gro");
- setOutputFile("-o", ".xvg", NoTextMatch());
- setOutputFile("-or", ".xvg", NoTextMatch());
- setOutputFile("-oa", ".xvg", NoTextMatch());
- setOutputFile("-tv", ".xvg", NoTextMatch());
+ setOutputFile("-o", ".xvg", XvgMatch().testData(false));
+ setOutputFile("-or", ".xvg", XvgMatch());
+ setOutputFile("-oa", ".xvg", XvgMatch());
+ setOutputFile("-tv", ".xvg", XvgMatch().testData(false));
excludeDataset("dgsolv");
setDatasetTolerance("area", gmx::test::ulpTolerance(8));
setDatasetTolerance("volume", gmx::test::ulpTolerance(8));
runTest(CommandLine(cmdline));
}
+TEST_F(SasaModuleTest, HandlesSelectedResidues)
+{
+ const char *const cmdline[] = {
+ "sasa",
+ "-surface", "resnr 2 4 to 5 8"
+ };
+ setTopology("lysozyme.gro");
+ setOutputFile("-o", ".xvg", XvgMatch().testData(false));
+ setOutputFile("-or", ".xvg", XvgMatch());
+ setOutputFile("-oa", ".xvg", XvgMatch());
+ excludeDataset("dgsolv");
+ excludeDataset("volume");
+ setDatasetTolerance("area", gmx::test::ulpTolerance(8));
+ runTest(CommandLine(cmdline));
+}
+
TEST_F(SasaModuleTest, WritesConnollySurfaceWithSolute)
{
const char *const cmdline[] = {
return endsWith(str.c_str(), suffix);
}
+/*! \brief
+ * Tests whether a string contains another as a substring.
+ *
+ * \param[in] str String to process.
+ * \param[in] substr Substring to find.
+ * \returns true if \p str contains \p substr.
+ *
+ * Does not throw.
+ */
+static inline bool contains(const std::string &str, const char *substr)
+{
+ return str.find(substr) != std::string::npos;
+}
+
/*!\brief Returns number of space-separated words in zero-terminated char ptr
*
* \param s Character pointer to zero-terminated, which will not be changed.
</pre>
</xsl:template>
+<xsl:template match="OutputFiles/File/XvgLegend/String[@Name='XvgLegend']">
+ <pre>
+ <xsl:value-of select="substring(.,2)"/>
+ </pre>
+</xsl:template>
+
+<xsl:template match="OutputFiles/File/XvgData">
+ <xsl:choose>
+ <xsl:when test="*">
+ <table>
+ <xsl:apply-templates />
+ </table>
+ </xsl:when>
+ <xsl:otherwise>Data omitted</xsl:otherwise>
+ </xsl:choose>
+</xsl:template>
+
+<xsl:template match="OutputFiles/File/XvgData/Sequence">
+ <tr>
+ <xsl:apply-templates select="Real"/>
+ </tr>
+</xsl:template>
+
+<xsl:template match="OutputFiles/File/XvgData/Sequence/Real">
+ <td><xsl:value-of select="."/></td>
+</xsl:template>
+
<xsl:template match="InteractiveSession">
<pre>
<xsl:for-each select="*">
#include <gtest/gtest.h>
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/refdata-impl.h"
std::string value_;
};
+//! Helper function to parse a floating-point value.
+// TODO: Move this into src/gromacs/utility/, and consolidate with similar code
+// elsewhere.
+double convertDouble(const std::string &value)
+{
+ char *endptr;
+ double convertedValue = std::strtod(value.c_str(), &endptr);
+ // TODO: Check for overflow
+ if (*endptr != '\0')
+ {
+ GMX_THROW(InvalidInputError("Invalid floating-point value: " + value));
+ }
+ return convertedValue;
+}
+
+//! Helper function to parse a floating-point reference data value.
+double convertDoubleReferenceValue(const std::string &value)
+{
+ try
+ {
+ return convertDouble(value);
+ }
+ catch (const InvalidInputError &ex)
+ {
+ GMX_THROW_WRAPPER_TESTEXCEPTION(ex);
+ }
+}
+
template <typename FloatType>
class FloatingPointChecker : public IReferenceDataEntryChecker
{
virtual ::testing::AssertionResult
checkEntry(const ReferenceDataEntry &entry, const std::string &fullId) const
{
- char *endptr;
- FloatType refValue = static_cast<FloatType>(std::strtod(entry.value().c_str(), &endptr));
- if (*endptr != '\0')
- {
- GMX_THROW(TestException("Invalid floating-point reference value: " + entry.value()));
- }
+ FloatType refValue = static_cast<FloatType>(convertDoubleReferenceValue(entry.value()));
FloatingPointDifference diff(refValue, value_);
if (tolerance_.isWithin(diff))
{
FloatingPointTolerance tolerance_;
};
+template <typename FloatType>
+class FloatingPointFromStringChecker : public IReferenceDataEntryChecker
+{
+ public:
+ FloatingPointFromStringChecker(
+ const std::string &value, const FloatingPointTolerance &tolerance)
+ : value_(value), tolerance_(tolerance)
+ {
+ }
+
+ virtual void fillEntry(ReferenceDataEntry *entry) const
+ {
+ entry->setValue(value_);
+ }
+ virtual ::testing::AssertionResult
+ checkEntry(const ReferenceDataEntry &entry, const std::string &fullId) const
+ {
+ FloatType value = static_cast<FloatType>(convertDouble(value_));
+ FloatType refValue = static_cast<FloatType>(convertDoubleReferenceValue(entry.value()));
+ FloatingPointDifference diff(refValue, value);
+ if (tolerance_.isWithin(diff))
+ {
+ return ::testing::AssertionSuccess();
+ }
+ return ::testing::AssertionFailure()
+ << " In item: " << fullId << std::endl
+ << " Actual: " << value << std::endl
+ << " Reference: " << entry.value() << std::endl
+ << "Difference: " << diff.toString() << std::endl
+ << " Tolerance: " << tolerance_.toString(diff);
+ }
+
+ private:
+ std::string value_;
+ FloatingPointTolerance tolerance_;
+};
+
} // namespace test
} // namespace gmx
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/path.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/refdata-checkers.h"
}
+void TestReferenceChecker::checkRealFromString(const std::string &value, const char *id)
+{
+ FloatingPointFromStringChecker<real> checker(value, impl_->defaultTolerance_);
+ EXPECT_PLAIN(impl_->processItem(Impl::cRealNodeName, id, checker));
+}
+
+
void TestReferenceChecker::checkVector(const int value[3], const char *id)
{
TestReferenceChecker compound(checkCompound(Impl::cVectorType, id));
void checkVector(const float value[3], const char *id);
//! Check a vector of three double-precision floating point values.
void checkVector(const double value[3], const char *id);
+ //! Check a single floating-point value from a string.
+ void checkRealFromString(const std::string &value, const char *id);
/*! \name Overloaded versions of simple checker methods
*
XvgMatchSettings settings_;
};
+//! Helper function to identify which @ lines in xvg files should be tested.
+bool isRelevantXvgCommand(const std::string &line)
+{
+ return contains(line, " title ")
+ || contains(line, " subtitle ")
+ || contains(line, " label ")
+ || contains(line, "@TYPE ")
+ || contains(line, " legend \"");
+}
+
+//! Helper function to check a single xvg value in a sequence.
+void checkXvgDataPoint(TestReferenceChecker *checker, const std::string &value)
+{
+ checker->checkRealFromString(value, NULL);
+}
+
} // namespace
void checkXvgFile(TextInputStream *input,
TestReferenceChecker *checker,
const XvgMatchSettings &settings)
{
+ TestReferenceChecker legendChecker(checker->checkCompound("XvgLegend", "Legend"));
TestReferenceChecker dataChecker(checker->checkCompound("XvgData", "Data"));
dataChecker.setDefaultTolerance(settings.tolerance);
+ std::string legendText;
+ int dataRowCount = 0;
std::string line;
- int nrow = 0;
-
while (input->readLine(&line))
{
- if (!((line.find("#") != line.npos) ||
- (line.find("@") != line.npos)))
+ // Ignore comments, as they contain dynamic content, and very little of
+ // that would be useful to test (and in particular, not with every
+ // output file).
+ if (startsWith(line, "#"))
{
- std::vector<std::string> split = splitString(line);
- std::vector<real> row;
-
- for (std::vector<std::string>::iterator si = split.begin();
- (si < split.end()); ++si)
+ continue;
+ }
+ if (startsWith(line, "@"))
+ {
+ if (isRelevantXvgCommand(line))
{
- const char *ptr = si->c_str();
- char *endptr;
- errno = 0;
- double dval = std::strtod(ptr, &endptr);
- if (errno == ERANGE)
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + *si
- + "'; it causes an overflow/underflow"));
- }
- if (*ptr == '\0' || *endptr != '\0')
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + *si
- + "'; expected a number"));
- }
- row.push_back(dval);
+ legendText.append(stripString(line.substr(1)));
+ legendText.append("\n");
}
- std::string buf = formatString("Row%d", nrow++);
- dataChecker.checkSequence(row.begin(), row.end(), buf.c_str());
+ continue;
}
+ if (!settings.testData)
+ {
+ break;
+ }
+ const std::vector<std::string> columns = splitString(line);
+ const std::string id = formatString("Row%d", dataRowCount);
+ dataChecker.checkSequence(columns.begin(), columns.end(), id.c_str(),
+ &checkXvgDataPoint);
+ ++dataRowCount;
+ }
+ if (settings.testData)
+ {
+ dataChecker.checkPresent(false, formatString("Row%d", dataRowCount).c_str());
}
- std::string buf = formatString("Row%d", nrow++);
- dataChecker.checkPresent(false, buf.c_str());
+ legendChecker.checkTextBlock(legendText, "XvgLegend");
}
TextBlockMatcherPointer XvgMatch::createMatcher() const
struct XvgMatchSettings
{
- XvgMatchSettings() : tolerance(defaultRealTolerance()) {}
+ XvgMatchSettings() : tolerance(defaultRealTolerance()), testData(true)
+ {
+ }
FloatingPointTolerance tolerance;
+ bool testData;
};
/*! \brief
* Adds content of xvg file to TestReferenceChecker object.
*
- * A stream of strings is parsed. The columns
- * are analyzed with a relative tolerance provided by the input.
- * Xmgrace formatting is ignored and only multi-column data is
- * understood.
- *
- * \param[in] input Object returning the lines of the file/data
- * one by one.
- * \param[in,out] checker The checker object.
+ * \param[in] input Stream that provides the xvg content.
+ * \param[in,out] checker Checker to use.
* \param[in] settings Settings to use for matching.
+ *
+ * Parses an xvg file from the input stream, and checks the contents against
+ * reference data. \p settings can be used to customize the matching.
+ * Only a single data set is supported (but multiple columns work).
+ * A subset of xmgrace formatting is also checked; static content that is
+ * nearly always the same is skipped.
+ *
+ * \see XvgMatch
*/
void checkXvgFile(TextInputStream *input,
TestReferenceChecker *checker,
settings_.tolerance = tolerance;
return *this;
}
+ /*! \brief
+ * Sets whether the actual data is checked.
+ *
+ * If set to `false`, only the legends are checked. Use this if the
+ * data is already tested using different means.
+ */
+ XvgMatch &testData(bool test)
+ {
+ settings_.testData = test;
+ return *this;
+ }
virtual TextBlockMatcherPointer createMatcher() const;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff