X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FScore.java;h=98ba06a5947da4fe3359bbc0b5b6048612ef5f8e;hb=14a41b0acd5d808ae1cdd8ecc82c85b4d3329b72;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..98ba06a 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -1,19 +1,40 @@
 package compbio.data.sequence;
 
+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.Arrays;
 import java.util.List;
+import java.util.Locale;
+import java.util.Set;
 
 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);
+	}
+
+	private ConservationMethod method;
 
 	private List<Float> scores;
 
@@ -21,15 +42,35 @@ public class Score {
 		// JaXB default constructor
 	}
 
-	public Score(Method method, List<Float> scores) {
+	/**
+	 * 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(ConservationMethod method, List<Float> scores) {
 		this.method = method;
-		this.scores = scores;
+		this.scores = new ArrayList<Float>(scores);
 	}
 
-	public Method getMethod() {
+	/**
+	 * Returns the ConservationMethod
+	 * 
+	 * @return the ConservationMethod
+	 */
+	public ConservationMethod getMethod() {
 		return method;
 	}
 
+	/**
+	 * The column scores for the alignment
+	 * 
+	 * @return the column scores for the alignment
+	 */
 	public List<Float> getScores() {
 		return scores;
 	}
@@ -74,4 +115,47 @@ public class Score {
 			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();
+	}
 }