Datasets:

ayeshgk

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java_iter_format_small_v1

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[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] if (inputEncoding != null) { if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { reader = ReaderFactory.newReader(inputFile, inputEncoding); } } else { [BUGGY] reader = ReaderFactory.newPlatformReader(inputFile); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newPlatformReader ( inputFile ) ;

[CONTEXT] private void parse(File inputFile, String inputEncoding, DoxiaFormat parserFormat, OutputFileWrapper output) throws ConverterException, UnsupportedFormatException { [BUGGY] parse(inputFile, inputEncoding, parserFormat, output, null); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output [VARIABLES] boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus String extension firstElement firstTag inputEncoding roleHint Logger LOGGER File inputFile OutputFileWrapper output

parse ( inputFile, inputEncoding, parserFormat, output, null ) ;

[CONTEXT] [BUGGY] private final String roleHint; [CLASS] DefaultConverter DoxiaFormat [VARIABLES]

private final String roleHint;

[CONTEXT] public static InputFileWrapper valueOf(String absolutePath, DefaultConverter.DoxiaFormat format, String charsetName) throws UnsupportedEncodingException, FileNotFoundException { [BUGGY] return new InputFileWrapper(absolutePath, format, charsetName); } [CLASS] InputFileWrapper [METHOD] valueOf [RETURN_TYPE] InputFileWrapper String absolutePath DoxiaFormat format String charsetName [VARIABLES] String absolutePath charsetName boolean DoxiaFormat format long serialVersionUID

return new InputFileWrapper ( absolutePath, format, charsetName ) ;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } if (o == null || getClass() != o.getClass()) { return false; } [BUGGY] if (!super.equals(o)) { [BUGGY] return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( !super.equals ( o ) ) { return false;

[CONTEXT] public static InputFileWrapper valueOf(String absolutePath, DefaultConverter.DoxiaFormat format, String charsetName) throws UnsupportedEncodingException, FileNotFoundException { [BUGGY] return new InputFileWrapper(absolutePath, format, charsetName); } [CLASS] InputFileWrapper [METHOD] valueOf [RETURN_TYPE] InputFileWrapper String absolutePath DoxiaFormat format String charsetName [VARIABLES] String absolutePath charsetName boolean DoxiaFormat format long serialVersionUID

return new InputFileWrapper ( absolutePath, format, charsetName ) ;

[CONTEXT] private OutputStreamWrapper(OutputStream out, String format, String encoding) { [BUGGY] this.format = DefaultConverter.DoxiaFormat.valueOf(format.toUpperCase()); this.out = out; this.encoding = encoding; } [CLASS] OutputStreamWrapper [METHOD] <init> [RETURN_TYPE] String) OutputStream out String format String encoding [VARIABLES] String encoding format boolean DoxiaFormat format long serialVersionUID OutputStream out

this.format = DefaultConverter.DoxiaFormat.valueOf ( format.toUpperCase ( ) ) ;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } [BUGGY] if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( o == null || getClass ( ) != o.getClass ( ) ) {

[CONTEXT] if (StringUtils.isEmpty(output.getEncoding()) || output.getEncoding().equals(OutputFileWrapper.AUTO_ENCODING)) { outputEncoding = inputEncoding; } else { [BUGGY] outputEncoding = output.getEncoding(); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

outputEncoding = output.getEncoding ( ) ;

[CONTEXT] public static OutputFileWrapper valueOf( String absolutePath, DefaultConverter.DoxiaFormat format, String charsetName) throws UnsupportedEncodingException { [BUGGY] return new OutputFileWrapper(absolutePath, format, charsetName); } [CLASS] OutputFileWrapper [METHOD] valueOf [RETURN_TYPE] OutputFileWrapper String absolutePath DoxiaFormat format String charsetName [VARIABLES] String absolutePath charsetName boolean DoxiaFormat format long serialVersionUID

return new OutputFileWrapper ( absolutePath, format, charsetName ) ;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; [BUGGY] this.extension = extension; [BUGGY] this.firstElement = firstElement; this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.extension = extension; this.firstElement = firstElement;

[CONTEXT] public DefaultConverter.DoxiaFormat getFormat() { [BUGGY] return format; [BUGGY] } [CLASS] InputFileWrapper [METHOD] getFormat [RETURN_TYPE] DoxiaFormat [VARIABLES] DoxiaFormat format long serialVersionUID boolean

return format; }

[CONTEXT] private void parse(File inputFile, String inputEncoding, DoxiaFormat parserFormat, OutputFileWrapper output) throws ConverterException, UnsupportedFormatException { [BUGGY] parse(inputFile, inputEncoding, parserFormat, output, null); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output [VARIABLES] boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus String extension firstElement firstTag inputEncoding roleHint Logger LOGGER File inputFile OutputFileWrapper output

parse ( inputFile, inputEncoding, parserFormat, output, null ) ;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; [BUGGY] this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.extension = extension;

[CONTEXT] public boolean equals(Object o) { [BUGGY] if (this == o) { return true; } if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( this == o ) {

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] private static final Options OPTIONS; [CLASS] CLIManager [VARIABLES]

private static final String EOL = System.lineSeparator ( ) ;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; [BUGGY] this.firstElement = firstElement; this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.firstElement = firstElement;

[CONTEXT] if (StringUtils.isEmpty(output.getEncoding()) || output.getEncoding().equals(OutputFileWrapper.AUTO_ENCODING)) { outputEncoding = inputEncoding; } else { [BUGGY] outputEncoding = output.getEncoding(); [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

outputEncoding = output.getEncoding ( ) ; }

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { [BUGGY] return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) { return format;

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } [BUGGY] if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( o == null || getClass ( ) != o.getClass ( ) ) {

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; [BUGGY] this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.hasSink = hasSink;

[CONTEXT] DoxiaFormat(String roleHint, String extension, boolean hasParser, boolean hasSink) { [BUGGY] this(roleHint, extension, null, hasParser, hasSink); } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this ( roleHint, extension, null, hasParser, hasSink ) ;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

[Delete]

[CONTEXT] private void parse(File inputFile, String inputEncoding, DoxiaFormat parserFormat, OutputFileWrapper output) throws ConverterException, UnsupportedFormatException { [BUGGY] parse(inputFile, inputEncoding, parserFormat, output, null); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output [VARIABLES] boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus String extension firstElement firstTag inputEncoding roleHint Logger LOGGER File inputFile OutputFileWrapper output

parse ( inputFile, inputEncoding, parserFormat, output, null ) ;

[CONTEXT] public boolean equals(Object o) { [BUGGY] if (this == o) { [BUGGY] return true; [BUGGY] } if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( this == o ) { return true; }

[CONTEXT] private void parse(File inputFile, String inputEncoding, DoxiaFormat parserFormat, OutputFileWrapper output) throws ConverterException, UnsupportedFormatException { [BUGGY] parse(inputFile, inputEncoding, parserFormat, output, null); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output [VARIABLES] boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus String extension firstElement firstTag inputEncoding roleHint Logger LOGGER File inputFile OutputFileWrapper output

parse ( inputFile, inputEncoding, parserFormat, output, null ) ;

[CONTEXT] private void stopPlexusContainer() { if (plexus == null) { return; } [BUGGY] plexus.dispose(); [BUGGY] plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

plexus.dispose ( ) ; plexus = null;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] [BUGGY] static final long serialVersionUID = 6510443036267371188L; [CLASS] InputFileWrapper [VARIABLES]

static final long serialVersionUID = 6510443036267371188L;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

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[CONTEXT] if (StringUtils.isEmpty(output.getEncoding()) || output.getEncoding().equals(OutputFileWrapper.AUTO_ENCODING)) { outputEncoding = inputEncoding; } else { [BUGGY] outputEncoding = output.getEncoding(); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

outputEncoding = output.getEncoding ( ) ;

[CONTEXT] [BUGGY] static final long serialVersionUID = 3260213754615748766L; [CLASS] InputReaderWrapper [VARIABLES]

static final long serialVersionUID = 3260213754615748766L;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] public boolean hasParser() { [BUGGY] return hasParser; } [CLASS] DefaultConverter DoxiaFormat [METHOD] hasParser [RETURN_TYPE] boolean [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

return hasParser;

[CONTEXT] void setFile(File file) { [BUGGY] this.file = file; } [CLASS] AbstractFileWrapper [METHOD] setFile [RETURN_TYPE] void File file [VARIABLES] File file filetoset String AUTO_ENCODING absolutePath encoding boolean

this.file = file;

[CONTEXT] private void stopPlexusContainer() { [BUGGY] if (plexus == null) { return; } plexus.dispose(); plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

if ( plexus == null ) {

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; [BUGGY] this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.extension = extension;

[CONTEXT] if (StringUtils.isEmpty(output.getEncoding()) || output.getEncoding().equals(OutputFileWrapper.AUTO_ENCODING)) { outputEncoding = inputEncoding; } else { [BUGGY] outputEncoding = output.getEncoding(); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

outputEncoding = output.getEncoding ( ) ;

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; [BUGGY] return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

return Objects.equals ( getFile ( ) , that.getFile ( ) ) ;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] private void stopPlexusContainer() { if (plexus == null) { return; } [BUGGY] plexus.dispose(); plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

plexus.dispose ( ) ;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] DoxiaFormat(String roleHint, String extension, boolean hasParser, boolean hasSink) { [BUGGY] this(roleHint, extension, null, hasParser, hasSink); } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this ( roleHint, extension, null, hasParser, hasSink ) ;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] private void stopPlexusContainer() { [BUGGY] if (plexus == null) { return; } plexus.dispose(); plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

if ( plexus == null ) {

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; [BUGGY] this.extension = extension; [BUGGY] this.firstElement = firstElement; [BUGGY] this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { [BUGGY] return format; [BUGGY] } [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

return format; } }

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } [BUGGY] if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( o == null || getClass ( ) != o.getClass ( ) ) {

[CONTEXT] private OutputStreamWrapper(OutputStream out, String format, String encoding) { this.format = DefaultConverter.DoxiaFormat.valueOf(format.toUpperCase()); [BUGGY] this.out = out; [BUGGY] this.encoding = encoding; } [CLASS] OutputStreamWrapper [METHOD] <init> [RETURN_TYPE] String) OutputStream out String format String encoding [VARIABLES] String encoding format boolean DoxiaFormat format long serialVersionUID OutputStream out

this.out = out; this.encoding = encoding;

[CONTEXT] public static OutputFileWrapper valueOf( String absolutePath, DefaultConverter.DoxiaFormat format, String charsetName) throws UnsupportedEncodingException { [BUGGY] return new OutputFileWrapper(absolutePath, format, charsetName); } [CLASS] OutputFileWrapper [METHOD] valueOf [RETURN_TYPE] OutputFileWrapper String absolutePath DoxiaFormat format String charsetName [VARIABLES] String absolutePath charsetName boolean DoxiaFormat format long serialVersionUID

return new OutputFileWrapper ( absolutePath, format, charsetName ) ;

[CONTEXT] [BUGGY] static final long serialVersionUID = 3329037527245430610L; [CLASS] OutputStreamWrapper [VARIABLES]

static final long serialVersionUID = 3329037527245430610L;

[CONTEXT] if (StringUtils.isEmpty(output.getEncoding()) || output.getEncoding().equals(OutputFileWrapper.AUTO_ENCODING)) { outputEncoding = inputEncoding; } else { [BUGGY] outputEncoding = output.getEncoding(); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

outputEncoding = output.getEncoding ( ) ;

[CONTEXT] public boolean equals(Object o) { [BUGGY] if (this == o) { return true; } if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

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[CONTEXT] private void stopPlexusContainer() { if (plexus == null) { return; } plexus.dispose(); [BUGGY] plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

plexus = null;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; [BUGGY] this.hasSink = hasSink; [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.hasSink = hasSink; }

[CONTEXT] if (inputEncoding != null) { if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { reader = ReaderFactory.newReader(inputFile, inputEncoding); } } else { [BUGGY] reader = ReaderFactory.newPlatformReader(inputFile); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newPlatformReader ( inputFile ) ;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; [BUGGY] this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.hasParser = hasParser;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { [BUGGY] this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.roleHint = roleHint;

[CONTEXT] public ConverterException(String message) { [BUGGY] super(message); } [CLASS] ConverterException [METHOD] <init> [RETURN_TYPE] String) String message [VARIABLES] long serialVersionUID String message boolean

super ( message ) ;

[CONTEXT] public boolean isXml() { [BUGGY] return firstElement != null; [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] isXml [RETURN_TYPE] boolean [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

return firstElement != null; }

[CONTEXT] public boolean equals(Object o) { if (this == o) { [BUGGY] return true; [BUGGY] } if (o == null || getClass() != o.getClass()) { return false; } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

return true; }

[CONTEXT] if (inputEncoding != null) { if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { reader = ReaderFactory.newReader(inputFile, inputEncoding); } } else { [BUGGY] reader = ReaderFactory.newPlatformReader(inputFile); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newPlatformReader ( inputFile ) ;

[CONTEXT] if (inputEncoding != null) { if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { reader = ReaderFactory.newReader(inputFile, inputEncoding); } } else { [BUGGY] reader = ReaderFactory.newPlatformReader(inputFile); [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newPlatformReader ( inputFile ) ; }

[CONTEXT] if (StringUtils.isEmpty(output.getEncoding()) || output.getEncoding().equals(OutputFileWrapper.AUTO_ENCODING)) { outputEncoding = inputEncoding; } else { [BUGGY] outputEncoding = output.getEncoding(); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

outputEncoding = output.getEncoding ( ) ;

[CONTEXT] private void stopPlexusContainer() { [BUGGY] if (plexus == null) { return; } plexus.dispose(); plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

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[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] private final String extension; [CLASS] DefaultConverter DoxiaFormat [VARIABLES]

private final String firstElement;

[CONTEXT] public static InputFileWrapper valueOf(String absolutePath, DefaultConverter.DoxiaFormat format) throws UnsupportedEncodingException, FileNotFoundException { [BUGGY] return valueOf(absolutePath, format, WriterFactory.UTF_8); } [CLASS] InputFileWrapper [METHOD] valueOf [RETURN_TYPE] InputFileWrapper String absolutePath DoxiaFormat format [VARIABLES] String absolutePath boolean DoxiaFormat format long serialVersionUID

return valueOf ( absolutePath, format, WriterFactory.UTF_8 ) ;

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; [BUGGY] this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.hasSink = hasSink;

[CONTEXT] if (inputEncoding != null) { if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { reader = ReaderFactory.newReader(inputFile, inputEncoding); } } else { [BUGGY] reader = ReaderFactory.newPlatformReader(inputFile); [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newPlatformReader ( inputFile ) ; } } catch ( IOException e ) {

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { [BUGGY] return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

return format;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] DoxiaFormat(String roleHint, String extension, boolean hasParser, boolean hasSink) { [BUGGY] this(roleHint, extension, null, hasParser, hasSink); } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this ( roleHint, extension, null, hasParser, hasSink ) ;

[CONTEXT] [BUGGY] static final long serialVersionUID = 6510443036267371188L; [CLASS] InputFileWrapper [VARIABLES]

static final long serialVersionUID = 6510443036267371188L;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; this.hasParser = hasParser; [BUGGY] this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.hasSink = hasSink;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ; } } else {

[CONTEXT] DoxiaFormat(String roleHint, String extension, boolean hasParser, boolean hasSink) { [BUGGY] this(roleHint, extension, null, hasParser, hasSink); } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this ( roleHint, extension, null, hasParser, hasSink ) ;

[CONTEXT] public ConverterException(String message, Throwable cause) { [BUGGY] super(message, cause); } [CLASS] ConverterException [METHOD] <init> [RETURN_TYPE] Throwable) String message Throwable cause [VARIABLES] Throwable cause String message boolean long serialVersionUID

super ( message, cause ) ;

[CONTEXT] private void stopPlexusContainer() { [BUGGY] if (plexus == null) { [BUGGY] return; [BUGGY] } plexus.dispose(); plexus = null; } [CLASS] DefaultConverter DoxiaFormat [METHOD] stopPlexusContainer [RETURN_TYPE] void [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag inputEncoding outputEncoding roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus Logger LOGGER

if ( plexus == null ) { return; }

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } [BUGGY] if (o == null || getClass() != o.getClass()) { [BUGGY] return false; [BUGGY] } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( o == null || getClass ( ) != o.getClass ( ) ) { return false; }

[CONTEXT] public static InputFileWrapper valueOf(String absolutePath, DefaultConverter.DoxiaFormat format) throws UnsupportedEncodingException, FileNotFoundException { [BUGGY] return valueOf(absolutePath, format, WriterFactory.UTF_8); [BUGGY] } [CLASS] InputFileWrapper [METHOD] valueOf [RETURN_TYPE] InputFileWrapper String absolutePath DoxiaFormat format [VARIABLES] String absolutePath boolean DoxiaFormat format long serialVersionUID

return valueOf ( absolutePath, format, WriterFactory.UTF_8 ) ; }

[CONTEXT] DoxiaFormat(String roleHint, String extension, String firstElement, boolean hasParser, boolean hasSink) { this.roleHint = roleHint; this.extension = extension; this.firstElement = firstElement; [BUGGY] this.hasParser = hasParser; this.hasSink = hasSink; } [CLASS] DefaultConverter DoxiaFormat [METHOD] <init> [RETURN_TYPE] String,boolean,boolean) String roleHint String extension String firstElement boolean hasParser boolean hasSink [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 PlexusContainer plexus Logger LOGGER

this.hasParser = hasParser;

[CONTEXT] private final String roleHint; [CLASS] DefaultConverter DoxiaFormat [VARIABLES]

private final String extension;

[CONTEXT] if (format.isXml()) { String firstTag = getFirstTag(f); if (firstTag == null) { continue; } if (firstTag.equals(format.firstElement)) { return format; } } else { [BUGGY] if (hasFileExtensionIgnoreCase(f.getName(), format.getExtension())) { return format; } } [CLASS] DefaultConverter DoxiaFormat [METHOD] autoDetectFormat [RETURN_TYPE] DefaultConverter$DoxiaFormat File f [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER File f

if ( hasFileExtensionIgnoreCase ( f.getName ( ) , format.getExtension ( ) ) ) {

[CONTEXT] private void parse(File inputFile, String inputEncoding, DoxiaFormat parserFormat, OutputFileWrapper output) throws ConverterException, UnsupportedFormatException { [BUGGY] parse(inputFile, inputEncoding, parserFormat, output, null); } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output [VARIABLES] boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat PlexusContainer plexus String extension firstElement firstTag inputEncoding roleHint Logger LOGGER File inputFile OutputFileWrapper output

parse ( inputFile, inputEncoding, parserFormat, output, null ) ;

[CONTEXT] public boolean equals(Object o) { if (this == o) { return true; } [BUGGY] if (o == null || getClass() != o.getClass()) { [BUGGY] return false; [BUGGY] } if (!super.equals(o)) { return false; } AbstractFileWrapper that = (AbstractFileWrapper) o; return Objects.equals(getFile(), that.getFile()); } [CLASS] AbstractFileWrapper [METHOD] equals [RETURN_TYPE] boolean Object o [VARIABLES] Object o String AUTO_ENCODING absolutePath encoding boolean File file filetoset AbstractFileWrapper that

if ( o == null || getClass ( ) != o.getClass ( ) ) { return false; }

[CONTEXT] public void setFormatOutput(boolean formatOutput) { [BUGGY] this.formatOutput = formatOutput; } [CLASS] DefaultConverter DoxiaFormat [METHOD] setFormatOutput [RETURN_TYPE] void boolean formatOutput [VARIABLES] boolean formatOutput hasParser hasSink String extension firstElement firstTag roleHint DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format PlexusContainer plexus Logger LOGGER

this.formatOutput = formatOutput;

[CONTEXT] if (parser.getType() == Parser.XML_TYPE) { reader = ReaderFactory.newXmlReader(inputFile); } else { [BUGGY] reader = ReaderFactory.newReader(inputFile, inputEncoding); [BUGGY] } [CLASS] DefaultConverter DoxiaFormat [METHOD] parse [RETURN_TYPE] void File inputFile String inputEncoding DoxiaFormat parserFormat OutputFileWrapper output File relativeOutputDirectory [VARIABLES] PlexusContainer plexus OutputStream out Reader r reader ComponentLookupException e String extension firstElement firstTag inputEncoding outputEncoding roleHint IOException e Logger LOGGER OutputFileWrapper output CharArrayWriter caw Parser parser boolean formatOutput hasParser hasSink DoxiaFormat APT FML MARKDOWN XDOC XHTML5 format parserFormat Sink sink SinkFactory sinkFactory File inputFile outputDirectoryOrFile outputFile relativeOutputDirectory Writer w

reader = ReaderFactory.newReader ( inputFile, inputEncoding ) ; }