@VisibleForTesting
IBundleCoverage analyzeStructure() throws IOException {
  final CoverageBuilder coverageBuilder = new CoverageBuilder();
  final Analyzer analyzer = new Analyzer(execFileLoader.getExecutionDataStore(), coverageBuilder);
  Set<String> alreadyInstrumentedClasses = new HashSet<>();
  if (uninstrumentedClasses == null) {
    for (File classesJar : classesJars) {
      analyzeUninstrumentedClassesFromJar(analyzer, classesJar, alreadyInstrumentedClasses);
    }
  } else {
    for (Map.Entry<String, byte[]> entry : uninstrumentedClasses.entrySet()) {
      analyzer.analyzeClass(entry.getValue(), entry.getKey());
    }
  }

  // TODO(bazel-team): Find out where the name of the bundle can pop out in the report.
  return coverageBuilder.getBundle("isthisevenused");
}
 

public void processNBModule(String projectName, List<String> classDirectories, List<String> sourceDirectories) throws IOException {
	CoverageBuilder coverageBuilder = new CoverageBuilder();
	Analyzer analyzer = new Analyzer(execFileLoader.getExecutionDataStore(), coverageBuilder);

	for (String classDirectory : classDirectories) {
		analyzer.analyzeAll(new File(classDirectory));
	}

	IBundleCoverage bundleCoverage = coverageBuilder.getBundle(projectName);

	MultiSourceFileLocator sourceLocator = new MultiSourceFileLocator(4);
	for (String sourceDirectory : sourceDirectories) {
		sourceLocator.add(new DirectorySourceFileLocator(new File(sourceDirectory), DEF_ENCODING, 4));
	}

	groupVisitor.visitBundle(bundleCoverage, sourceLocator);
}
 

private IBundleCoverage analyzeStructure() throws IOException {
  CoverageBuilder coverageBuilder = new CoverageBuilder();
  Analyzer analyzer = new Analyzer(execFileLoader.getExecutionDataStore(), coverageBuilder);

  String[] classesDirs = classesPath.split(":");
  for (String classesDir : classesDirs) {
    File classesDirFile = new File(classesDir);
    if (classesDirFile.exists()) {
      for (File clazz : FileUtils.getFiles(classesDirFile, coverageIncludes, coverageExcludes)) {
        analyzer.analyzeAll(clazz);
      }
    }
  }

  return coverageBuilder.getBundle(title);
}
 

public void jacocoCheckpoint(File classFile, File csvDir) {
    int idx = nextFileIdx;
    csvDir.mkdirs();
    try {
        // Get exec data by dynamically calling RT.getAgent().getExecutionData()
        Class RT = Class.forName("org.jacoco.agent.rt.RT");
        Method getAgent = RT.getMethod("getAgent");
        Object agent = getAgent.invoke(null);
        Method dump = agent.getClass().getMethod("getExecutionData", boolean.class);
        byte[] execData = (byte[]) dump.invoke(agent, false);

        // Analyze exec data
        ExecFileLoader loader = new ExecFileLoader();
        loader.load(new ByteArrayInputStream(execData));
        final CoverageBuilder builder = new CoverageBuilder();
        Analyzer analyzer = new Analyzer(loader.getExecutionDataStore(), builder);
        analyzer.analyzeAll(classFile);

        // Generate CSV
        File csv = new File(csvDir, String.format("cov-%05d.csv", idx));
        try (FileOutputStream out = new FileOutputStream(csv)) {
            IReportVisitor coverageVisitor = new CSVFormatter().createVisitor(out);
            coverageVisitor.visitBundle(builder.getBundle("JQF"), null);
            coverageVisitor.visitEnd();
            out.flush();
        }


    } catch (Exception e) {
        System.err.println(e);
    }
}
 

/**
 * Analyzes all uninstrumented class files found in the given jar.
 *
 * <p>The uninstrumented classes are named using the .class.uninstrumented suffix.
 */
private void analyzeUninstrumentedClassesFromJar(
    Analyzer analyzer, File jar, Set<String> alreadyInstrumentedClasses) throws IOException {
  JarFile jarFile = new JarFile(jar);
  Enumeration<JarEntry> jarFileEntries = jarFile.entries();
  while (jarFileEntries.hasMoreElements()) {
    JarEntry jarEntry = jarFileEntries.nextElement();
    String jarEntryName = jarEntry.getName();
    if (jarEntryName.endsWith(".class.uninstrumented")
        && !alreadyInstrumentedClasses.contains(jarEntryName)) {
      analyzer.analyzeAll(jarFile.getInputStream(jarEntry), jarEntryName);
      alreadyInstrumentedClasses.add(jarEntryName);
    }
  }
}
 

/**
 * Load a JaCoCo binary report and convert it to HTML.
 * <br/>See <a href="http://www.eclemma.org/jacoco/trunk/doc/examples/java/ReportGenerator.java">report generator example code</a>.
 *
 * @param jacocoexec the JaCoCo binary report.
 * @param reportdir the folder to store HTML report.
 * @param prjClassesDir the directory containing project's compiled classes.
 * @param prjSourcesDir the directory containing project's Java source files.
 * @param projectName the project's name.
 * @return the absolute path of HTML report's {@code index.html} file.
 * @throws FileNotFoundException if the JaCoCo binary report, compiled classes or Java sources files directory can't be found.
 * @throws IOException if an I/O error occurs.
 */
public static String toHtmlReport(File jacocoexec, File reportdir, File prjClassesDir, File prjSourcesDir, String projectName)
        throws FileNotFoundException,
               IOException {
    // Load the JaCoCo binary report.
    FileInputStream fis = new FileInputStream(jacocoexec);
    ExecutionDataStore executionDataStore = new ExecutionDataStore();
    SessionInfoStore sessionInfoStore = new SessionInfoStore();
    try {
        ExecutionDataReader executionDataReader = new ExecutionDataReader(fis);
        executionDataReader.setExecutionDataVisitor(executionDataStore);
        executionDataReader.setSessionInfoVisitor(sessionInfoStore);
        while (executionDataReader.read()) {
        }
    } finally {
        fis.close();
    }

    // Convert the binary report to HTML.
    CoverageBuilder coverageBuilder = new CoverageBuilder();
    Analyzer analyzer = new Analyzer(executionDataStore, coverageBuilder);
    analyzer.analyzeAll(prjClassesDir);
    IBundleCoverage bundleCoverage = coverageBuilder.getBundle("JaCoCoverage analysis of project \"" + projectName
            + "\" (powered by JaCoCo from EclEmma)");
    HTMLFormatter htmlformatter = new HTMLFormatter();
    IReportVisitor visitor = htmlformatter.createVisitor(new FileMultiReportOutput(reportdir));
    visitor.visitInfo(sessionInfoStore.getInfos(), executionDataStore.getContents());
    visitor.visitBundle(bundleCoverage, new DirectorySourceFileLocator(prjSourcesDir, DEF_ENCODING, 4));
    visitor.visitEnd();
    return new File(reportdir, "index.html").getAbsolutePath();
}
 

/**
 * Load a JaCoCo binary report and convert it to XML.
 * <br/>See <a href="http://www.eclemma.org/jacoco/trunk/doc/examples/java/ReportGenerator.java">report generator example code</a>.
 *
 * @param jacocoexec the JaCoCo binary report.
 * @param xmlreport the XML file to generate.
 * @param prjClassesDir the directory containing project's compiled classes.
 * @param prjSourcesDir the directory containing project's Java source files.
 * @throws FileNotFoundException if the JaCoCo binary report, compiled classes or Java sources files directory can't be found.
 * @throws IOException if an I/O error occurs.
 */
public static void toXmlReport(File jacocoexec, File xmlreport, File prjClassesDir, File prjSourcesDir)
        throws FileNotFoundException,
               IOException {
    // Load the JaCoCo binary report.
    FileInputStream fis = new FileInputStream(jacocoexec);
    ExecutionDataStore executionDataStore = new ExecutionDataStore();
    SessionInfoStore sessionInfoStore = new SessionInfoStore();
    try {
        ExecutionDataReader executionDataReader = new ExecutionDataReader(fis);
        executionDataReader.setExecutionDataVisitor(executionDataStore);
        executionDataReader.setSessionInfoVisitor(sessionInfoStore);
        while (executionDataReader.read()) {
        }
    } finally {
        fis.close();
    }

    // Convert the binary report to XML.
    CoverageBuilder coverageBuilder = new CoverageBuilder();
    Analyzer analyzer = new Analyzer(executionDataStore, coverageBuilder);
    analyzer.analyzeAll(prjClassesDir);
    IBundleCoverage bundleCoverage = coverageBuilder.getBundle("JaCoCoverage analysis (powered by JaCoCo from EclEmma)");
    XMLFormatter xmlformatter = new XMLFormatter();
    xmlformatter.setOutputEncoding(DEF_ENCODING);
    IReportVisitor visitor = xmlformatter.createVisitor(new FileOutputStream(xmlreport));
    visitor.visitInfo(sessionInfoStore.getInfos(), executionDataStore.getContents());
    visitor.visitBundle(bundleCoverage, new DirectorySourceFileLocator(prjSourcesDir, DEF_ENCODING, 4));
    visitor.visitEnd();
}