use jdk 1.6 @OVERRIDES instead of /** {@inheritdoc} */ doc tags

heuermh · heuermh · commit 3686e7f1275e · 2013-04-25T10:49:57.000-05:00
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqReader.java
@@ -55,23 +55,23 @@ abstract class AbstractFastqReader
      */
     protected abstract FastqVariant getVariant();
 
-    /** {@inheritDoc} */
+    @Override
     public final <R extends Readable & Closeable> void parse(final InputSupplier<R> supplier,
                                                              final ParseListener listener)
         throws IOException
     {
         FastqParser.parse(supplier, listener);
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final <R extends Readable & Closeable> void stream(final InputSupplier<R> supplier,
                                                               final StreamListener listener)
         throws IOException
     {
         StreamingFastqParser.stream(supplier, getVariant(), listener);
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final Iterable<Fastq> read(final File file) throws IOException
     {
         if (file == null)
@@ -83,7 +83,7 @@ public final Iterable<Fastq> read(final File file) throws IOException
         return collect.getResult();
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final Iterable<Fastq> read(final URL url) throws IOException
     {
         if (url == null)
@@ -95,7 +95,7 @@ public final Iterable<Fastq> read(final URL url) throws IOException
         return collect.getResult();
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final Iterable<Fastq> read(final InputStream inputStream) throws IOException
     {
         if (inputStream == null)
@@ -105,7 +105,7 @@ public final Iterable<Fastq> read(final InputStream inputStream) throws IOExcept
         Collect collect = new Collect();
         stream(new InputSupplier<InputStreamReader>()
                {
-                   /** {@inheritDoc} */
+                   @Override
                    public InputStreamReader getInput() throws IOException
                    {
                        return new InputStreamReader(inputStream);
@@ -122,7 +122,7 @@ private static final class Collect implements StreamListener
         /** List of FASTQ formatted sequences. */
         private final List<Fastq> result = Lists.newLinkedList();
 
-        /** {@inheritDoc} */
+        @Override
         public void fastq(final Fastq fastq)
         {
             result.add(fastq);
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqWriter.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/AbstractFastqWriter.java
@@ -47,13 +47,13 @@ abstract class AbstractFastqWriter
      */
     protected abstract void validate(final Fastq fastq) throws IOException;
 
-    /** {@inheritDoc} */
+    @Override
     public final <T extends Appendable> T append(final T appendable, final Fastq... fastq) throws IOException
     {
         return append(appendable, Arrays.asList(fastq));
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final <T extends Appendable> T append(final T appendable, final Iterable<Fastq> fastq) throws IOException
     {
         if (appendable == null)
@@ -82,13 +82,13 @@ public final <T extends Appendable> T append(final T appendable, final Iterable<
         return appendable;
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final void write(final File file, final Fastq... fastq) throws IOException
     {
         write(file, Arrays.asList(fastq));
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final void write(final File file, final Iterable<Fastq> fastq) throws IOException
     {
         if (file == null)
@@ -121,13 +121,13 @@ public final void write(final File file, final Iterable<Fastq> fastq) throws IOE
         }
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final void write(final OutputStream outputStream, final Fastq... fastq) throws IOException
     {
         write(outputStream, Arrays.asList(fastq));
     }
 
-    /** {@inheritDoc} */
+    @Override
     public final void write(final OutputStream outputStream, final Iterable<Fastq> fastq) throws IOException
     {
         if (outputStream == null)
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqParser.java
@@ -115,13 +115,13 @@ private void setState(final State state)
             this.state = state;
         }
 
-        /** {@inheritDoc} */
+        @Override
         public Object getResult()
         {
             return null;
         }
 
-        /** {@inheritDoc} */
+        @Override
         public boolean processLine(final String line) throws IOException
         {
             String sequence = null;
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReader.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReader.java
@@ -29,7 +29,7 @@ public final class IlluminaFastqReader
     extends AbstractFastqReader
 {
 
-    /** {@inheritDoc} */
+    @Override
     protected FastqVariant getVariant()
     {
         return FastqVariant.FASTQ_ILLUMINA;
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqWriter.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqWriter.java
@@ -31,7 +31,7 @@ public final class IlluminaFastqWriter
     extends AbstractFastqWriter
 {
 
-    /** {@inheritDoc} */
+    @Override
     protected void validate(final Fastq fastq) throws IOException
     {
         if (fastq == null)
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqReader.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqReader.java
@@ -29,7 +29,7 @@ public final class SangerFastqReader
     extends AbstractFastqReader
 {
 
-    /** {@inheritDoc} */
+    @Override
     protected FastqVariant getVariant()
     {
         return FastqVariant.FASTQ_SANGER;
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqWriter.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqWriter.java
@@ -31,7 +31,7 @@ public final class SangerFastqWriter
     extends AbstractFastqWriter
 {
 
-    /** {@inheritDoc} */
+    @Override
     protected void validate(final Fastq fastq) throws IOException
     {
         if (fastq == null)
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqReader.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqReader.java
@@ -29,7 +29,7 @@ public final class SolexaFastqReader
     extends AbstractFastqReader
 {
 
-    /** {@inheritDoc} */
+    @Override
     protected FastqVariant getVariant()
     {
         return FastqVariant.FASTQ_SOLEXA;
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqWriter.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqWriter.java
@@ -31,7 +31,7 @@ public final class SolexaFastqWriter
     extends AbstractFastqWriter
 {
 
-    /** {@inheritDoc} */
+    @Override
     protected void validate(final Fastq fastq) throws IOException
     {
         if (fastq == null)
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/StreamingFastqParser.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/StreamingFastqParser.java
@@ -62,25 +62,25 @@ static <R extends Readable & Closeable> void stream(final InputSupplier<R> suppl
         final FastqBuilder builder = new FastqBuilder().withVariant(variant);
         FastqParser.parse(supplier, new ParseListener()
             {
-                /** {@inheritDoc} */
+                @Override
                 public void description(final String description) throws IOException
                 {
                     builder.withDescription(description);
                 }
 
-                /** {@inheritDoc} */
+                @Override
                 public void sequence(final String sequence) throws IOException
                 {
                     builder.withSequence(sequence);
                 }
 
-                /** {@inheritDoc} */
+                @Override
                 public void appendSequence(final String sequence) throws IOException
                 {
                     builder.appendSequence(sequence);
                 }
 
-                /** {@inheritDoc} */
+                @Override
                 public void repeatDescription(final String repeatDescription) throws IOException
                 {
                     String description = builder.getDescription();
@@ -114,21 +114,21 @@ private void validateQuality(final String quality) throws IOException
                     }
                 }
 
-                /** {@inheritDoc} */
+                @Override
                 public void quality(final String quality) throws IOException
                 {
                     validateQuality(quality);
                     builder.withQuality(quality);
                 }
 
-                /** {@inheritDoc} */
+                @Override
                 public void appendQuality(final String quality) throws IOException
                 {
                     validateQuality(quality);
                     builder.appendQuality(quality);
                 }
 
-                /** {@inheritDoc} */
+                @Override
                 public void complete() throws IOException
                 {
                     try
@@ -137,8 +137,7 @@ public void complete() throws IOException
                     }
                     catch (IllegalStateException e)
                     {
-                        throw new IOException("caught an IllegalStateException " + e.getMessage());
-                        //throw new IOException("caught an IllegalStateException", e);  jdk 1.6+
+                        throw new IOException("caught an IllegalStateException", e);
                     }
                 }
             });
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/AbstractFastqReaderTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/AbstractFastqReaderTest.java
@@ -338,43 +338,43 @@ public void testParse() throws Exception
         final String input = "";
         reader.parse(new InputSupplier<StringReader>()
                      {
-                         /** {@inheritDoc} */
+                         @Override
                          public StringReader getInput() throws IOException {
                              return new StringReader(input);
                          }
                      },
                      new ParseListener() {
-                         /** {@inheritDoc} */
+                         @Override
                          public void description(final String description) throws IOException {
                              // empty
                          }
  
-                         /** {@inheritDoc} */
+                         @Override
                          public void sequence(final String sequence) throws IOException {
                              // empty
                          }
  
-                         /** {@inheritDoc} */
+                         @Override
                          public void appendSequence(final String sequence) throws IOException {
                              // empty
                          }
  
-                         /** {@inheritDoc} */
+                         @Override
                          public void repeatDescription(final String repeatDescription) throws IOException {
                              // empty
                          }
  
-                         /** {@inheritDoc} */
+                         @Override
                          public void quality(final String quality) throws IOException {
                              // empty
                          }
  
-                         /** {@inheritDoc} */
+                         @Override
                          public void appendQuality(final String quality) throws IOException {
                              // empty
                          }
 
-                         /** {@inheritDoc} */
+                         @Override
                          public void complete() throws IOException {
                              // empty
                          }
@@ -388,37 +388,37 @@ public void testParseNullInputSupplier() throws Exception
         {
             reader.parse((InputSupplier<StringReader>) null,
                          new ParseListener() {
-                             /** {@inheritDoc} */
+                             @Override
                              public void description(final String description) throws IOException {
                                  // empty
                              }
  
-                             /** {@inheritDoc} */
+                             @Override
                              public void sequence(final String sequence) throws IOException {
                                  // empty
                              }
  
-                             /** {@inheritDoc} */
+                             @Override
                              public void appendSequence(final String sequence) throws IOException {
                                  // empty
                              }
  
-                             /** {@inheritDoc} */
+                             @Override
                              public void repeatDescription(final String repeatDescription) throws IOException {
                                  // empty
                              }
  
-                             /** {@inheritDoc} */
+                             @Override
                              public void quality(final String quality) throws IOException {
                                  // empty
                              }
  
-                             /** {@inheritDoc} */
+                             @Override
                              public void appendQuality(final String quality) throws IOException {
                                  // empty
                              }
 
-                             /** {@inheritDoc} */
+                             @Override
                              public void complete() throws IOException {
                                  // empty
                              }
@@ -439,7 +439,7 @@ public void testParseNullParseListener() throws Exception
         {
             reader.parse(new InputSupplier<StringReader>()
                          {
-                             /** {@inheritDoc} */
+                             @Override
                              public StringReader getInput() throws IOException {
                                  return new StringReader(input);
                              }
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReaderTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReaderTest.java
@@ -32,7 +32,7 @@ public final class IlluminaFastqReaderTest
     extends AbstractFastqReaderTest
 {
 
-    /** {@inheritDoc} */
+    @Override
     public Fastq createFastq()
     {
         return new FastqBuilder()
@@ -43,13 +43,13 @@ public Fastq createFastq()
             .build();
     }
 
-    /** {@inheritDoc} */
+    @Override
     public FastqReader createFastqReader()
     {
         return new IlluminaFastqReader();
     }
 
-    /** {@inheritDoc} */
+    @Override
     public FastqWriter createFastqWriter()
     {
         return new IlluminaFastqWriter();
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/IlluminaFastqWriterTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/IlluminaFastqWriterTest.java
@@ -29,13 +29,13 @@ public final class IlluminaFastqWriterTest
     extends AbstractFastqWriterTest
 {
 
-    /** {@inheritDoc} */
+    @Override
     public FastqWriter createFastqWriter()
     {
         return new IlluminaFastqWriter();
     }
 
-    /** {@inheritDoc} */
+    @Override
     public Fastq createFastq()
     {
         return new FastqBuilder()
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SangerFastqReaderTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SangerFastqReaderTest.java
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SangerFastqWriterTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SangerFastqWriterTest.java
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SolexaFastqReaderTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SolexaFastqReaderTest.java
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SolexaFastqWriterTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/SolexaFastqWriterTest.java
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/StreamingFastqParserTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/StreamingFastqParserTest.java

Original file line number	Diff line number	Diff line change
`@@ -55,23 +55,23 @@ abstract class AbstractFastqReader`
`55`	`55`	`*/`
`56`	`56`	`protected abstract FastqVariant getVariant();`
`57`	`57`
`58`		`- /** {@inheritDoc} */`
	`58`	`+ @Override`
`59`	`59`	`public final <R extends Readable & Closeable> void parse(final InputSupplier<R> supplier,`
`60`	`60`	`final ParseListener listener)`
`61`	`61`	`throws IOException`
`62`	`62`	`{`
`63`	`63`	`FastqParser.parse(supplier, listener);`
`64`	`64`	`}`
`65`	`65`
`66`		`- /** {@inheritDoc} */`
	`66`	`+ @Override`
`67`	`67`	`public final <R extends Readable & Closeable> void stream(final InputSupplier<R> supplier,`
`68`	`68`	`final StreamListener listener)`
`69`	`69`	`throws IOException`
`70`	`70`	`{`
`71`	`71`	`StreamingFastqParser.stream(supplier, getVariant(), listener);`
`72`	`72`	`}`
`73`	`73`
`74`		`- /** {@inheritDoc} */`
	`74`	`+ @Override`
`75`	`75`	`public final Iterable<Fastq> read(final File file) throws IOException`
`76`	`76`	`{`
`77`	`77`	`if (file == null)`
`@@ -83,7 +83,7 @@ public final Iterable<Fastq> read(final File file) throws IOException`
`83`	`83`	`return collect.getResult();`
`84`	`84`	`}`
`85`	`85`
`86`		`- /** {@inheritDoc} */`
	`86`	`+ @Override`
`87`	`87`	`public final Iterable<Fastq> read(final URL url) throws IOException`
`88`	`88`	`{`
`89`	`89`	`if (url == null)`
`@@ -95,7 +95,7 @@ public final Iterable<Fastq> read(final URL url) throws IOException`
`95`	`95`	`return collect.getResult();`
`96`	`96`	`}`
`97`	`97`
`98`		`- /** {@inheritDoc} */`
	`98`	`+ @Override`
`99`	`99`	`public final Iterable<Fastq> read(final InputStream inputStream) throws IOException`
`100`	`100`	`{`
`101`	`101`	`if (inputStream == null)`
`@@ -105,7 +105,7 @@ public final Iterable<Fastq> read(final InputStream inputStream) throws IOExcept`
`105`	`105`	`Collect collect = new Collect();`
`106`	`106`	`stream(new InputSupplier<InputStreamReader>()`
`107`	`107`	`{`
`108`		`- /** {@inheritDoc} */`
	`108`	`+ @Override`
`109`	`109`	`public InputStreamReader getInput() throws IOException`
`110`	`110`	`{`
`111`	`111`	`return new InputStreamReader(inputStream);`
`@@ -122,7 +122,7 @@ private static final class Collect implements StreamListener`
`122`	`122`	`/** List of FASTQ formatted sequences. */`
`123`	`123`	`private final List<Fastq> result = Lists.newLinkedList();`
`124`	`124`
`125`		`- /** {@inheritDoc} */`
	`125`	`+ @Override`
`126`	`126`	`public void fastq(final Fastq fastq)`
`127`	`127`	`{`
`128`	`128`	`result.add(fastq);`
Original file line number	Diff line number	Diff line change
`@@ -47,13 +47,13 @@ abstract class AbstractFastqWriter`
`47`	`47`	`*/`
`48`	`48`	`protected abstract void validate(final Fastq fastq) throws IOException;`
`49`	`49`
`50`		`- /** {@inheritDoc} */`
	`50`	`+ @Override`
`51`	`51`	`public final <T extends Appendable> T append(final T appendable, final Fastq... fastq) throws IOException`
`52`	`52`	`{`
`53`	`53`	`return append(appendable, Arrays.asList(fastq));`
`54`	`54`	`}`
`55`	`55`
`56`		`- /** {@inheritDoc} */`
	`56`	`+ @Override`
`57`	`57`	`public final <T extends Appendable> T append(final T appendable, final Iterable<Fastq> fastq) throws IOException`
`58`	`58`	`{`
`59`	`59`	`if (appendable == null)`
`@@ -82,13 +82,13 @@ public final <T extends Appendable> T append(final T appendable, final Iterable<`
`82`	`82`	`return appendable;`
`83`	`83`	`}`
`84`	`84`
`85`		`- /** {@inheritDoc} */`
	`85`	`+ @Override`
`86`	`86`	`public final void write(final File file, final Fastq... fastq) throws IOException`
`87`	`87`	`{`
`88`	`88`	`write(file, Arrays.asList(fastq));`
`89`	`89`	`}`
`90`	`90`
`91`		`- /** {@inheritDoc} */`
	`91`	`+ @Override`
`92`	`92`	`public final void write(final File file, final Iterable<Fastq> fastq) throws IOException`
`93`	`93`	`{`
`94`	`94`	`if (file == null)`
`@@ -121,13 +121,13 @@ public final void write(final File file, final Iterable<Fastq> fastq) throws IOE`
`121`	`121`	`}`
`122`	`122`	`}`
`123`	`123`
`124`		`- /** {@inheritDoc} */`
	`124`	`+ @Override`
`125`	`125`	`public final void write(final OutputStream outputStream, final Fastq... fastq) throws IOException`
`126`	`126`	`{`
`127`	`127`	`write(outputStream, Arrays.asList(fastq));`
`128`	`128`	`}`
`129`	`129`
`130`		`- /** {@inheritDoc} */`
	`130`	`+ @Override`
`131`	`131`	`public final void write(final OutputStream outputStream, final Iterable<Fastq> fastq) throws IOException`
`132`	`132`	`{`
`133`	`133`	`if (outputStream == null)`
Original file line number	Diff line number	Diff line change
`@@ -115,13 +115,13 @@ private void setState(final State state)`
`115`	`115`	`this.state = state;`
`116`	`116`	`}`
`117`	`117`
`118`		`- /** {@inheritDoc} */`
	`118`	`+ @Override`
`119`	`119`	`public Object getResult()`
`120`	`120`	`{`
`121`	`121`	`return null;`
`122`	`122`	`}`
`123`	`123`
`124`		`- /** {@inheritDoc} */`
	`124`	`+ @Override`
`125`	`125`	`public boolean processLine(final String line) throws IOException`
`126`	`126`	`{`
`127`	`127`	`String sequence = null;`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@ public final class IlluminaFastqReader`
`29`	`29`	`extends AbstractFastqReader`
`30`	`30`	`{`
`31`	`31`
`32`		`- /** {@inheritDoc} */`
	`32`	`+ @Override`
`33`	`33`	`protected FastqVariant getVariant()`
`34`	`34`	`{`
`35`	`35`	`return FastqVariant.FASTQ_ILLUMINA;`
Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@ public final class IlluminaFastqWriter`
`31`	`31`	`extends AbstractFastqWriter`
`32`	`32`	`{`
`33`	`33`
`34`		`- /** {@inheritDoc} */`
	`34`	`+ @Override`
`35`	`35`	`protected void validate(final Fastq fastq) throws IOException`
`36`	`36`	`{`
`37`	`37`	`if (fastq == null)`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@ public final class SangerFastqReader`
`29`	`29`	`extends AbstractFastqReader`
`30`	`30`	`{`
`31`	`31`
`32`		`- /** {@inheritDoc} */`
	`32`	`+ @Override`
`33`	`33`	`protected FastqVariant getVariant()`
`34`	`34`	`{`
`35`	`35`	`return FastqVariant.FASTQ_SANGER;`
Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@ public final class SangerFastqWriter`
`31`	`31`	`extends AbstractFastqWriter`
`32`	`32`	`{`
`33`	`33`
`34`		`- /** {@inheritDoc} */`
	`34`	`+ @Override`
`35`	`35`	`protected void validate(final Fastq fastq) throws IOException`
`36`	`36`	`{`
`37`	`37`	`if (fastq == null)`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@ public final class SolexaFastqReader`
`29`	`29`	`extends AbstractFastqReader`
`30`	`30`	`{`
`31`	`31`
`32`		`- /** {@inheritDoc} */`
	`32`	`+ @Override`
`33`	`33`	`protected FastqVariant getVariant()`
`34`	`34`	`{`
`35`	`35`	`return FastqVariant.FASTQ_SOLEXA;`
Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@ public final class SolexaFastqWriter`
`31`	`31`	`extends AbstractFastqWriter`
`32`	`32`	`{`
`33`	`33`
`34`		`- /** {@inheritDoc} */`
	`34`	`+ @Override`
`35`	`35`	`protected void validate(final Fastq fastq) throws IOException`
`36`	`36`	`{`
`37`	`37`	`if (fastq == null)`
Original file line number	Diff line number	Diff line change
`@@ -62,25 +62,25 @@ static <R extends Readable & Closeable> void stream(final InputSupplier<R> suppl`
`62`	`62`	`final FastqBuilder builder = new FastqBuilder().withVariant(variant);`
`63`	`63`	`FastqParser.parse(supplier, new ParseListener()`
`64`	`64`	`{`
`65`		`- /** {@inheritDoc} */`
	`65`	`+ @Override`
`66`	`66`	`public void description(final String description) throws IOException`
`67`	`67`	`{`
`68`	`68`	`builder.withDescription(description);`
`69`	`69`	`}`
`70`	`70`
`71`		`- /** {@inheritDoc} */`
	`71`	`+ @Override`
`72`	`72`	`public void sequence(final String sequence) throws IOException`
`73`	`73`	`{`
`74`	`74`	`builder.withSequence(sequence);`
`75`	`75`	`}`
`76`	`76`
`77`		`- /** {@inheritDoc} */`
	`77`	`+ @Override`
`78`	`78`	`public void appendSequence(final String sequence) throws IOException`
`79`	`79`	`{`
`80`	`80`	`builder.appendSequence(sequence);`
`81`	`81`	`}`
`82`	`82`
`83`		`- /** {@inheritDoc} */`
	`83`	`+ @Override`
`84`	`84`	`public void repeatDescription(final String repeatDescription) throws IOException`
`85`	`85`	`{`
`86`	`86`	`String description = builder.getDescription();`
`@@ -114,21 +114,21 @@ private void validateQuality(final String quality) throws IOException`
`114`	`114`	`}`
`115`	`115`	`}`
`116`	`116`
`117`		`- /** {@inheritDoc} */`
	`117`	`+ @Override`
`118`	`118`	`public void quality(final String quality) throws IOException`
`119`	`119`	`{`
`120`	`120`	`validateQuality(quality);`
`121`	`121`	`builder.withQuality(quality);`
`122`	`122`	`}`
`123`	`123`
`124`		`- /** {@inheritDoc} */`
	`124`	`+ @Override`
`125`	`125`	`public void appendQuality(final String quality) throws IOException`
`126`	`126`	`{`
`127`	`127`	`validateQuality(quality);`
`128`	`128`	`builder.appendQuality(quality);`
`129`	`129`	`}`
`130`	`130`
`131`		`- /** {@inheritDoc} */`
	`131`	`+ @Override`
`132`	`132`	`public void complete() throws IOException`
`133`	`133`	`{`
`134`	`134`	`try`
`@@ -137,8 +137,7 @@ public void complete() throws IOException`
`137`	`137`	`}`
`138`	`138`	`catch (IllegalStateException e)`
`139`	`139`	`{`
`140`		`- throw new IOException("caught an IllegalStateException " + e.getMessage());`
`141`		`- //throw new IOException("caught an IllegalStateException", e); jdk 1.6+`
	`140`	`+ throw new IOException("caught an IllegalStateException", e);`
`142`	`141`	`}`
`143`	`142`	`}`
`144`	`143`	`});`