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[jabaws.git] / datamodel / compbio / data / sequence / AnnotatedSequence.java

diff --git a/datamodel/compbio/data/sequence/AnnotatedSequence.java b/datamodel/compbio/data/sequence/AnnotatedSequence.java
index 5d09534..65dbce9 100644 (file)
--- a/datamodel/compbio/data/sequence/AnnotatedSequence.java
+++ b/datamodel/compbio/data/sequence/AnnotatedSequence.java
@@ -4,53 +4,58 @@ import java.util.Arrays;
 \r
 public class AnnotatedSequence extends FastaSequence {\r
 \r
-    private final float[] annotation;\r
-\r
-    public AnnotatedSequence(String id, String sequence, float[] annotation) {\r
-       super(id, sequence);\r
-       this.annotation = annotation;\r
-       if (annotation == null || annotation.length != sequence.length()) {\r
-           throw new IllegalArgumentException("The length of the annotation ("\r
-                   + ((annotation != null) ? annotation.length : "0")\r
-                   + ") does not match the length of the sequence ("\r
-                   + sequence.length() + ")!");\r
+       private float[] annotation;\r
+\r
+       private AnnotatedSequence() {\r
+               super();\r
+               // JAXB default constructor\r
+       }\r
+\r
+       public AnnotatedSequence(String id, String sequence, float[] annotation) {\r
+               super(id, sequence);\r
+               this.annotation = annotation;\r
+               if (annotation == null || annotation.length != sequence.length()) {\r
+                       throw new IllegalArgumentException("The length of the annotation ("\r
+                                       + ((annotation != null) ? annotation.length : "0")\r
+                                       + ") does not match the length of the sequence ("\r
+                                       + sequence.length() + ")!");\r
+               }\r
+       }\r
+\r
+       public AnnotatedSequence(FastaSequence fsequence, float[] annotation) {\r
+               this(fsequence.getId(), fsequence.getSequence(), annotation);\r
+       }\r
+\r
+       public float[] getAnnotation() {\r
+               return annotation;\r
+       }\r
+\r
+       @Override\r
+       public int hashCode() {\r
+               final int prime = 7;\r
+               int result = super.hashCode();\r
+               result = prime * result + Arrays.hashCode(annotation);\r
+               return result;\r
+       }\r
+\r
+       @Override\r
+       public boolean equals(Object obj) {\r
+               if (this == obj)\r
+                       return true;\r
+               if (!super.equals(obj))\r
+                       return false;\r
+               if (getClass() != obj.getClass())\r
+                       return false;\r
+               AnnotatedSequence other = (AnnotatedSequence) obj;\r
+               if (!Arrays.equals(annotation, other.annotation))\r
+                       return false;\r
+               return true;\r
+       }\r
+\r
+       @Override\r
+       public String toString() {\r
+               return super.toString() + "Annotation:\n "\r
+                               + Arrays.toString(annotation) + "\n";\r
        }\r
-    }\r
-\r
-    public AnnotatedSequence(FastaSequence fsequence, float[] annotation) {\r
-       this(fsequence.getId(), fsequence.getSequence(), annotation);\r
-    }\r
-\r
-    public float[] getAnnotation() {\r
-       return annotation;\r
-    }\r
-\r
-    @Override\r
-    public int hashCode() {\r
-       final int prime = 7;\r
-       int result = super.hashCode();\r
-       result = prime * result + Arrays.hashCode(annotation);\r
-       return result;\r
-    }\r
-\r
-    @Override\r
-    public boolean equals(Object obj) {\r
-       if (this == obj)\r
-           return true;\r
-       if (!super.equals(obj))\r
-           return false;\r
-       if (getClass() != obj.getClass())\r
-           return false;\r
-       AnnotatedSequence other = (AnnotatedSequence) obj;\r
-       if (!Arrays.equals(annotation, other.annotation))\r
-           return false;\r
-       return true;\r
-    }\r
-\r
-    @Override\r
-    public String toString() {\r
-       return super.toString() + "Annotation:\n "\r
-               + Arrays.toString(annotation) + "\n";\r
-    }\r
 \r
 }\r