adding quality method to fastq variant

heuermh · heuermh · commit 56d458292593 · 2013-04-19T15:59:12.000-05:00
diff --git a/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqVariant.java b/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqVariant.java
@@ -51,6 +51,20 @@ public int qualityScore(final char c)
             return ((int) c) - 33;
         }
 
+        @Override
+        public char quality(final int qualityScore)
+        {
+            if (qualityScore < minimumQualityScore())
+            {
+                throw new IllegalArgumentException("qualityScore must be greater than or equal to minimumQualityScore()");
+            }
+            if (qualityScore > maximumQualityScore())
+            {
+                throw new IllegalArgumentException("qualityScore must be less than or equal to maximumQualityScore()");
+            }
+            return (char) (qualityScore + 33);
+        }
+
         @Override
         public double errorProbability(final int qualityScore)
         {
@@ -79,6 +93,20 @@ public int qualityScore(final char c)
             return ((int) c) - 64;
         }
 
+        @Override
+        public char quality(final int qualityScore)
+        {
+            if (qualityScore < minimumQualityScore())
+            {
+                throw new IllegalArgumentException("qualityScore must be greater than or equal to minimumQualityScore()");
+            }
+            if (qualityScore > maximumQualityScore())
+            {
+                throw new IllegalArgumentException("qualityScore must be less than or equal to maximumQualityScore()");
+            }
+            return (char) (qualityScore + 64);
+        }
+
         @Override
         public double errorProbability(final int qualityScore)
         {
@@ -108,6 +136,20 @@ public int qualityScore(final char c)
             return ((int) c) - 64;
         }
 
+        @Override
+        public char quality(final int qualityScore)
+        {
+            if (qualityScore < minimumQualityScore())
+            {
+                throw new IllegalArgumentException("qualityScore must be greater than or equal to minimumQualityScore()");
+            }
+            if (qualityScore > maximumQualityScore())
+            {
+                throw new IllegalArgumentException("qualityScore must be less than or equal to maximumQualityScore()");
+            }
+            return (char) (qualityScore + 64);
+        }
+
         @Override
         public double errorProbability(final int qualityScore)
         {
@@ -210,6 +252,16 @@ public boolean isIllumina()
      */
     public abstract int qualityScore(char c);
 
+    /**
+     * Convert the specified quality score to a quality in ASCII format.
+     *
+     * @since 3.0.6
+     * @param qualityScore quality score, must be <code>&gt;= minimumQualityScore()</code>
+     *    and <code>&lt;= maximumQualityScore()</code>
+     * @return the quality in ASCII format converted from the specified quality score
+     */
+    public abstract char quality(int qualityScore);
+
     /**
      * Convert the specified quality in ASCII format to an error probability.
      *
diff --git a/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqVariantTest.java b/biojava3-sequencing/src/test/java/org/biojava3/sequencing/io/fastq/FastqVariantTest.java
@@ -68,4 +68,47 @@ public void testParseFastqVariant()
         assertEquals(FASTQ_SANGER, parseFastqVariant("FASTQ_SANGER"));
         assertEquals(FASTQ_SANGER, parseFastqVariant("fastq-sanger"));
     }
+
+    public void testQualityLessThanMinimumQualityScore()
+    {
+        for (FastqVariant variant : values())
+        {
+            try
+            {
+                variant.quality(variant.minimumQualityScore() - 1);
+                fail("expected IllegalArgumentException");
+            }
+            catch (IllegalArgumentException e)
+            {
+                // expected
+            }
+        }
+    }
+
+    public void testQualityMoreThanMaximumQualityScore()
+    {
+        for (FastqVariant variant : values())
+        {
+            try
+            {
+                variant.quality(variant.maximumQualityScore() + 1);
+                fail("expected IllegalArgumentException");
+            }
+            catch (IllegalArgumentException e)
+            {
+                // expected
+            }
+        }
+    }
+
+    public void testQualityQualityScoreRoundTrip()
+    {
+        for (FastqVariant variant : values())
+        {
+            for (int i = variant.minimumQualityScore(); i < (variant.maximumQualityScore() + 1); i++)
+            {
+                assertEquals(i, variant.qualityScore(variant.quality(i)));
+            }
+        }
+    }
 }
