From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Tue, 21 Dec 2010 18:28:57 +0000 (+0000)
Subject: Write javadoc for new datamodel classes , remove some incomplete staff
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1f6064c0e1d3a64b9faabf9a2be4850ec9b06645;p=jabaws.git

Write javadoc for new datamodel classes , remove some incomplete staff

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3555 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/datamodel/compbio/data/sequence/JalviewAnnotation.java b/datamodel/compbio/data/sequence/JalviewAnnotation.java
deleted file mode 100644
index cf19937..0000000
--- a/datamodel/compbio/data/sequence/JalviewAnnotation.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package compbio.data.sequence;
-
-public class JalviewAnnotation {
-
-	String annotation;
-
-}
diff --git a/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java b/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java
index 92d475d..1212a7d 100644
--- a/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java
+++ b/datamodel/compbio/data/sequence/MultiAnnotatedSequence.java
@@ -79,8 +79,4 @@ public class MultiAnnotatedSequence<T extends Enum<T>> {
 		return value;
 	}
 
-	public JalviewAnnotation toJalviewAnnotation() {
-		// TODO Auto-generated method stub
-		return null;
-	}
 }
diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index 127df64..d401aa8 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -5,6 +5,7 @@ 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;
@@ -15,11 +16,17 @@ import javax.xml.bind.annotation.XmlAccessorType;
 
 import compbio.util.annotation.Immutable;
 
+/**
+ * A value class for AACon annotation results storage
+ * 
+ * @author pvtroshin
+ * 
+ */
 @XmlAccessorType(XmlAccessType.FIELD)
 @Immutable
 public class Score {
 
-	public static final NumberFormat NUMBER_FORMAT = NumberFormat
+	static final NumberFormat NUMBER_FORMAT = NumberFormat
 			.getNumberInstance(Locale.UK);
 	static {
 		NUMBER_FORMAT.setGroupingUsed(false);
@@ -34,15 +41,35 @@ public class Score {
 		// JaXB default constructor
 	}
 
+	/**
+	 * 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);
 	}
 
+	/**
+	 * 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;
 	}
@@ -88,8 +115,35 @@ public class Score {
 		return true;
 	}
 
+	/**
+	 * Outputs the List of Score objects into the Output stream. The output
+	 * format is as follows:
+	 * 
+	 * <pre>
+	 * 	  #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) {
diff --git a/website/AAConWSClientExample.pdf b/website/AAConWSClientExample.pdf
deleted file mode 100644
index 82a315e..0000000
Binary files a/website/AAConWSClientExample.pdf and /dev/null differ