X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FAnnotatedSequence.java;h=65dbce96f5f0f8bbb2245034c6a148967c8aaf82;hb=0c69f6b897b652489cdf0e740bb01cef51cc60c1;hp=5d09534a375a94315f4496227400a86072581c7a;hpb=48190e32e896a6f674284844a9ae75605aa40157;p=jabaws.git

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