X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScore.java;h=f28bd0d6a34934551efb015baaa8290939a63e28;hb=aca9c5503b812c9c96aebb408748dc15728f9ad7;hp=8a58db3e78075ce8a64458c2bd50c49d29990636;hpb=212bbd43c19f645cccef34a608dc001fb694833c;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index 8a58db3..f28bd0d 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -1,58 +1,145 @@
 package compbio.data.sequence;
 
-import java.util.Arrays;
-import java.util.List;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.text.NumberFormat;
+import java.util.ArrayList;
+import java.util.Locale;
+import java.util.Set;
+import java.util.TreeSet;
 
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 
-import compbio.conservation.Method;
 import compbio.util.annotation.Immutable;
 
+/**
+ * A value class for AACon annotation results storage. The objects of this type
+ * are immutable
+ * 
+ * @author pvtroshin
+ * 
+ */
 @XmlAccessorType(XmlAccessType.FIELD)
 @Immutable
 public class Score {
 
-	private Method method;
+	static final NumberFormat NUMBER_FORMAT = NumberFormat
+			.getNumberInstance(Locale.UK);
+	static {
+		NUMBER_FORMAT.setGroupingUsed(false);
+		NUMBER_FORMAT.setMaximumFractionDigits(3);
+	}
+	// This should be Enum<?> but JAXB cannot serialize it.
+	private final String 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;
+	}
+
+	/**
+	 * Instantiate the Score
+	 * 
+	 * @param method
+	 *            the ConservationMethod with which {@code scores} were
+	 *            calculated
+	 * @param scores
+	 *            the actual conservation values for each column of the
+	 *            alignment
+	 */
+	public Score(Enum<?> method, ArrayList<Float> scores) {
+		this.method = method.toString();
+		this.scores = new ArrayList<Float>(scores);
 	}
 
-	public Score(Method method, List<Float> scores) {
-		this.method = method;
+	/**
+	 * @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 Method getMethod() {
+	public Score(Enum<?> method, TreeSet<Range> ranges) {
+		this.method = method.toString();
+		this.ranges = ranges;
+	}
+
+	public Score(Enum<?> method, float[] scores) {
+		this.method = method.toString();
+		this.scores = toList(scores);
+	}
+
+	private ArrayList<Float> toList(float[] values) {
+		ArrayList<Float> vlist = new ArrayList<Float>();
+		for (float v : values) {
+			vlist.add(new Float(v));
+		}
+		return vlist;
+	}
+	/**
+	 * Returns the ConservationMethod
+	 * 
+	 * @return the ConservationMethod
+	 */
+	public String getMethod() {
 		return method;
 	}
 
-	public List<Float> getScores() {
+	/**
+	 * The column scores for the alignment
+	 * 
+	 * @return the column scores for the alignment
+	 */
+	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)
@@ -62,16 +149,64 @@ 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;
 	}
+
+	/**
+	 * Outputs the List of Score objects into the Output stream. The output
+	 * format is as follows:
+	 * 
+	 * <pre>
+	 * {@code
+	 * #MethodName <space separated list of values>
+	 * 	  
+	 * For example:
+	 * 	 
+	 * #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
+	 * #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
+	 * }
+	 * </pre>
+	 * 
+	 * The maximum precision for values is 3 digits, but can be less.
+	 * 
+	 * @param scores
+	 *            the list of scores to output
+	 * @param output
+	 *            the stream to output the data to
+	 * @throws IOException
+	 *             if the OutputStream cannot be written into
+	 * @throws NullPointerException
+	 *             if the output stream is null
+	 */
+	public static void write(Set<Score> scores, OutputStream output)
+			throws IOException {
+		if (output == null) {
+			throw new NullPointerException("OutputStream must be provided!");
+		}
+		BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
+				output));
+		for (Score score : scores) {
+			writer.write("#" + score.method + " ");
+			for (Float scoreVal : score.getScores()) {
+				writer.write(NUMBER_FORMAT.format(scoreVal) + " ");
+			}
+			writer.write("\n");
+		}
+		writer.flush();
+	}
 }