X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScore.java;h=f28bd0d6a34934551efb015baaa8290939a63e28;hb=aca9c5503b812c9c96aebb408748dc15728f9ad7;hp=8a110eea95f59e43f2732ffe6da58b44298a5f7b;hpb=8033a51860de2200a54e64add0809d6780f5b092;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index 8a110ee..f28bd0d 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -6,10 +6,9 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.text.NumberFormat;
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
 import java.util.Locale;
 import java.util.Set;
+import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
@@ -33,13 +32,16 @@ public class Score {
 		NUMBER_FORMAT.setGroupingUsed(false);
 		NUMBER_FORMAT.setMaximumFractionDigits(3);
 	}
+	// This should be Enum<?> but JAXB cannot serialize it.
+	private final String method;
 
-	private Enum<?> method;
+	private TreeSet<Range> ranges = new TreeSet<Range>();
 
-	private List<Float> scores;
+	private ArrayList<Float> scores = new ArrayList<Float>(0);
 
 	private Score() {
 		// JaXB default constructor
+		method = null;
 	}
 
 	/**
@@ -52,18 +54,40 @@ public class Score {
 	 *            the actual conservation values for each column of the
 	 *            alignment
 	 */
-	public Score(Enum<?> method, List<Float> scores) {
-		this.method = method;
+	public Score(Enum<?> method, ArrayList<Float> scores) {
+		this.method = method.toString();
 		this.scores = new ArrayList<Float>(scores);
 	}
 
+	/**
+	 * @param method
+	 *            the ConservationMethod with which {@code scores} were
+	 *            calculated
+	 * @param scores
+	 *            the actual conservation values for each column of the
+	 *            alignment
+	 * @param ranges
+	 *            The set of ranges i.e. parts of the sequence with specific
+	 *            function, usually can be calculated based on scores
+	 */
+	public Score(Enum<?> method, ArrayList<Float> scores, TreeSet<Range> ranges) {
+		this.method = method.toString();
+		this.ranges = ranges;
+		this.scores = scores;
+	}
+
+	public Score(Enum<?> method, TreeSet<Range> ranges) {
+		this.method = method.toString();
+		this.ranges = ranges;
+	}
+
 	public Score(Enum<?> method, float[] scores) {
-		this.method = method;
+		this.method = method.toString();
 		this.scores = toList(scores);
 	}
 
-	private List<Float> toList(float[] values) {
-		List<Float> vlist = new ArrayList<Float>();
+	private ArrayList<Float> toList(float[] values) {
+		ArrayList<Float> vlist = new ArrayList<Float>();
 		for (float v : values) {
 			vlist.add(new Float(v));
 		}
@@ -74,7 +98,7 @@ public class Score {
 	 * 
 	 * @return the ConservationMethod
 	 */
-	public Enum<?> getMethod() {
+	public String getMethod() {
 		return method;
 	}
 
@@ -83,29 +107,39 @@ public class Score {
 	 * 
 	 * @return the column scores for the alignment
 	 */
-	public List<Float> getScores() {
+	public ArrayList<Float> getScores() {
 		return scores;
 	}
 
+	/**
+	 * Return Ranges if any Collections.EMPTY_SET otherwise
+	 * 
+	 * @return
+	 */
+	public TreeSet<Range> getRanges() {
+		return ranges;
+	}
+
+	public void setRanges(TreeSet<Range> ranges) {
+		this.ranges = ranges;
+	}
+
 	@Override
 	public String toString() {
-		return "Score [method=" + method + ", scores=" + scores + "]";
+		return "Score [method=" + method + ", ranges=" + ranges + ", scores="
+				+ scores + "]";
 	}
 
 	@Override
 	public int hashCode() {
-		final int prime = 31;
+		final int prime = 7;
 		int result = 1;
 		result = prime * result + ((method == null) ? 0 : method.hashCode());
+		result = prime * result + ((ranges == null) ? 0 : ranges.hashCode());
 		result = prime * result + ((scores == null) ? 0 : scores.hashCode());
 		return result;
 	}
 
-	/*
-	 * TODO test ! (non-Javadoc)
-	 * 
-	 * @see java.lang.Object#equals(java.lang.Object)
-	 */
 	@Override
 	public boolean equals(Object obj) {
 		if (this == obj)
@@ -115,15 +149,20 @@ public class Score {
 		if (getClass() != obj.getClass())
 			return false;
 		Score other = (Score) obj;
-		if (method != other.method)
+		if (method == null) {
+			if (other.method != null)
+				return false;
+		} else if (!method.equals(other.method))
 			return false;
-		if (scores == other.scores) {
-			return true;
-		}
-		if (scores == null) {
+		if (ranges == null) {
+			if (other.ranges != null)
+				return false;
+		} else if (!ranges.equals(other.ranges))
 			return false;
-		}
-		if (!Arrays.deepEquals(scores.toArray(), other.scores.toArray()))
+		if (scores == null) {
+			if (other.scores != null)
+				return false;
+		} else if (!scores.equals(other.scores))
 			return false;
 		return true;
 	}