adding implicit conversion in AbstractFastqWriter

heuermh · heuermh · commit 32060a87ae39 · 2015-09-23T13:52:08.000-05:00
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/AbstractFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/AbstractFastqWriter.java
@@ -20,7 +20,14 @@
  */
 package org.biojava.nbio.sequencing.io.fastq;
 
-import java.io.*;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+
 import java.util.Arrays;
 
 /**
@@ -33,12 +40,14 @@ abstract class AbstractFastqWriter
 {
 
     /**
-     * Validate the specified FASTQ formatted sequence for writing.
+     * Convert the specified FASTQ formatted sequence if necessary.
      *
-     * @param fastq FASTQ formatted sequence to validate, will not be null
-     * @throws IOException if the specified FASTQ formatted sequence is not valid for writing
+     * @since 4.2
+     * @param fastq FASTQ formatted sequence to convert, must not be null
+     * @return the specified FASTQ formatted sequence or a new FASTA formatted
+     *    sequence if conversion is necessary
      */
-    protected abstract void validate(final Fastq fastq) throws IOException;
+    protected abstract Fastq convert(final Fastq fastq);
 
     @Override
     public final <T extends Appendable> T append(final T appendable, final Fastq... fastq) throws IOException
@@ -59,16 +68,15 @@ public final <T extends Appendable> T append(final T appendable, final Iterable<
         }
         for (Fastq f : fastq)
         {
-            validate(f);
             if (f != null)
             {
+                Fastq converted = convert(f);
                 appendable.append("@");
-                appendable.append(f.getDescription());
-                appendable.append("\n");
-                appendable.append(f.getSequence());
+                appendable.append(converted.getDescription());
                 appendable.append("\n");
-                appendable.append("+\n");
-                appendable.append(f.getQuality());
+                appendable.append(converted.getSequence());
+                appendable.append("\n+\n");
+                appendable.append(converted.getQuality());
                 appendable.append("\n");
             }
         }
@@ -152,4 +160,4 @@ public final void write(final OutputStream outputStream, final Iterable<Fastq> f
             }
         }
     }
-}
+}
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriter.java
@@ -32,16 +32,8 @@ public final class IlluminaFastqWriter
 {
 
     @Override
-    protected void validate(final Fastq fastq) throws IOException
+    protected Fastq convert(final Fastq fastq)
     {
-        if (fastq == null)
-        {
-            return;
-        }
-        if (!fastq.getVariant().isIllumina())
-        {
-            throw new IOException("sequence " + fastq.getDescription()
-                                  + " not fastq-illumina format, was " + fastq.getVariant().lowercaseName());
-        }
+        return fastq.convertTo(FastqVariant.FASTQ_ILLUMINA);
     }
-}
+}
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriter.java
@@ -32,16 +32,8 @@ public final class SangerFastqWriter
 {
 
     @Override
-    protected void validate(final Fastq fastq) throws IOException
+    protected Fastq convert(final Fastq fastq)
     {
-        if (fastq == null)
-        {
-            return;
-        }
-        if (!fastq.getVariant().isSanger())
-        {
-            throw new IOException("sequence " + fastq.getDescription()
-                                  + " not fastq-sanger format, was " + fastq.getVariant().lowercaseName());
-        }
+        return fastq.convertTo(FastqVariant.FASTQ_SANGER);
     }
-}
+}
diff --git a/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriter.java b/biojava-sequencing/src/main/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriter.java
@@ -32,16 +32,8 @@ public final class SolexaFastqWriter
 {
 
     @Override
-    protected void validate(final Fastq fastq) throws IOException
+    protected Fastq convert(final Fastq fastq)
     {
-        if (fastq == null)
-        {
-            return;
-        }
-        if (!fastq.getVariant().isSolexa())
-        {
-            throw new IOException("sequence " + fastq.getDescription()
-                                  + " not fastq-solexa format, was " + fastq.getVariant().lowercaseName());
-        }
+        return fastq.convertTo(FastqVariant.FASTQ_SOLEXA);
     }
-}
+}
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/ConvertTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/ConvertTest.java
@@ -80,7 +80,7 @@ public void testConvert() throws Exception
                 FileWriter fileWriter = new FileWriter(tmp);
 
                 for (Fastq fastq : reader.read(getClass().getResource(inputFileName))) {
-                    writer.append(fileWriter, fastq.convertTo(variant2));
+                    writer.append(fileWriter, fastq);
                 }
 
                 try
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriterTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/IlluminaFastqWriterTest.java
@@ -46,7 +46,7 @@ public Fastq createFastq()
             .build();
     }
 
-    public void testValidateNotIlluminaVariant()
+    public void testConvertNotIlluminaVariant() throws Exception
     {
         IlluminaFastqWriter writer = new IlluminaFastqWriter();
         Appendable appendable = new StringBuilder();
@@ -56,14 +56,7 @@ public void testValidateNotIlluminaVariant()
             .withQuality("quality_")
             .withVariant(FastqVariant.FASTQ_SANGER)
             .build();
-        try
-        {
-            writer.append(appendable, invalid);
-            fail("validate not fastq-illumina variant expected IOException");
-        }
-        catch (IOException e)
-        {
-            // expected
-        }
+
+        writer.append(appendable, invalid);
     }
-}
+}
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriterTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SangerFastqWriterTest.java
@@ -46,7 +46,7 @@ public Fastq createFastq()
             .build();
     }
 
-    public void testValidateNotSangerVariant()
+    public void testConvertNotSangerVariant() throws Exception
     {
         SangerFastqWriter writer = new SangerFastqWriter();
         Appendable appendable = new StringBuilder();
@@ -56,14 +56,7 @@ public void testValidateNotSangerVariant()
             .withQuality("quality_")
             .withVariant(FastqVariant.FASTQ_SOLEXA)
             .build();
-        try
-        {
-            writer.append(appendable, invalid);
-            fail("validate not fastq-sanger variant expected IOException");
-        }
-        catch (IOException e)
-        {
-            // expected
-        }
+
+        writer.append(appendable, invalid);
     }
-}
+}
diff --git a/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriterTest.java b/biojava-sequencing/src/test/java/org/biojava/nbio/sequencing/io/fastq/SolexaFastqWriterTest.java
@@ -46,7 +46,7 @@ public Fastq createFastq()
             .build();
     }
 
-    public void testValidateNotSolexaVariant()
+    public void testConvertNotSolexaVariant() throws Exception
     {
         SolexaFastqWriter writer = new SolexaFastqWriter();
         Appendable appendable = new StringBuilder();
@@ -56,14 +56,7 @@ public void testValidateNotSolexaVariant()
             .withQuality("quality_")
             .withVariant(FastqVariant.FASTQ_ILLUMINA)
             .build();
-        try
-        {
-            writer.append(appendable, invalid);
-            fail("validate not fastq-solexa variant expected IOException");
-        }
-        catch (IOException e)
-        {
-            // expected
-        }
+
+        writer.append(appendable, invalid);
     }
-}
+}

Original file line number	Diff line number	Diff line change
`@@ -32,16 +32,8 @@ public final class IlluminaFastqWriter`
`32`	`32`	`{`
`33`	`33`
`34`	`34`	`@Override`
`35`		`- protected void validate(final Fastq fastq) throws IOException`
	`35`	`+ protected Fastq convert(final Fastq fastq)`
`36`	`36`	`{`
`37`		`- if (fastq == null)`
`38`		`- {`
`39`		`- return;`
`40`		`- }`
`41`		`- if (!fastq.getVariant().isIllumina())`
`42`		`- {`
`43`		`- throw new IOException("sequence " + fastq.getDescription()`
`44`		`- + " not fastq-illumina format, was " + fastq.getVariant().lowercaseName());`
`45`		`- }`
	`37`	`+ return fastq.convertTo(FastqVariant.FASTQ_ILLUMINA);`
`46`	`38`	`}`
`47`		`-}`
	`39`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -32,16 +32,8 @@ public final class SangerFastqWriter`
`32`	`32`	`{`
`33`	`33`
`34`	`34`	`@Override`
`35`		`- protected void validate(final Fastq fastq) throws IOException`
	`35`	`+ protected Fastq convert(final Fastq fastq)`
`36`	`36`	`{`
`37`		`- if (fastq == null)`
`38`		`- {`
`39`		`- return;`
`40`		`- }`
`41`		`- if (!fastq.getVariant().isSanger())`
`42`		`- {`
`43`		`- throw new IOException("sequence " + fastq.getDescription()`
`44`		`- + " not fastq-sanger format, was " + fastq.getVariant().lowercaseName());`
`45`		`- }`
	`37`	`+ return fastq.convertTo(FastqVariant.FASTQ_SANGER);`
`46`	`38`	`}`
`47`		`-}`
	`39`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -80,7 +80,7 @@ public void testConvert() throws Exception`
`80`	`80`	`FileWriter fileWriter = new FileWriter(tmp);`
`81`	`81`
`82`	`82`	`for (Fastq fastq : reader.read(getClass().getResource(inputFileName))) {`
`83`		`- writer.append(fileWriter, fastq.convertTo(variant2));`
	`83`	`+ writer.append(fileWriter, fastq);`
`84`	`84`	`}`
`85`	`85`
`86`	`86`	`try`