X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FMultiAnnotatedSequence.java;h=1a889e38d3de77155b8844473950fed056a1a9b8;hb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;hp=580a22e8614aab0afbf930747a230295e420d812;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java b/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java
index 580a22e..1a889e3 100644
--- a/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java
+++ b/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java
@@ -2,6 +2,9 @@ package compbio.data.sequence;
 
 import java.util.EnumMap;
 import java.util.List;
+import java.util.Map;
+
+import compbio.util.annotation.NotThreadSafe;
 
 /**
  * TODO complete
@@ -11,23 +14,67 @@ import java.util.List;
  * @param <T>
  *            enum type
  */
+@NotThreadSafe
 public class MultiAnnotatedSequence<T extends Enum<T>> {
 
-    private final EnumMap<T, List<Float>> annotation;
+	private final Map<T, List<Float>> annotations;
+
+	public MultiAnnotatedSequence(Class<T> enumeration) {
+		this.annotations = new EnumMap<T, List<Float>>(enumeration);
+	}
+
+	public void addAnnotation(T type, List<Float> annotation) {
+		assert type != null : "Type is expected";
+		assert annotation != null : "Not empty value is expected!";
+		if (!annotations.isEmpty()) {
+			assert annotations.values().iterator().next().size() == annotation
+					.size() : "Annotations must contain the same number of elements!";
+		}
+		this.annotations.put(type, annotation);
+	}
+
+	public Map<T, List<Float>> getAnnotations() {
+		return new EnumMap<T, List<Float>>(this.annotations);
+	}
 
-    private MultiAnnotatedSequence(Class<T> type) {
-	this.annotation = new EnumMap<T, List<Float>>(type);
-    }
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result
+				+ ((annotations == null) ? 0 : annotations.hashCode());
+		return result;
+	}
 
-    //    public MultiAnnotatedSequence getFloatInstance(FastaSequence fsequence) {
-    //	return null;
-    //}
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		MultiAnnotatedSequence other = (MultiAnnotatedSequence) obj;
+		if (annotations == null) {
+			if (other.annotations != null)
+				return false;
+		} else if (!annotations.equals(other.annotations))
+			return false;
+		return true;
+	}
 
-    public EnumMap<T, List<Integer>> getIntegerInstance(Class<T> enumeration) {
-	return new EnumMap<T, List<Integer>>(enumeration);
-    }
+	@Override
+	public String toString() {
+		String value = "";
+		for (Map.Entry<T, List<Float>> annt : annotations.entrySet()) {
+			value += annt.getKey() + " ";
+			value += annt.getValue() + "\n";
+		}
+		return value;
+	}
 
-    public EnumMap<T, List<Float>> getFloatInstance(Class<T> enumeration) {
-	return new EnumMap<T, List<Float>>(enumeration);
-    }
+	public JalviewAnnotation toJalviewAnnotation() {
+		// TODO Auto-generated method stub
+		return null;
+	}
 }