JWS-113 Commented Jpred entries in the datamodel, runner and webservices java source...

[jabaws.git] / datamodel / compbio / data / sequence / Alignment.java

diff --git a/datamodel/compbio/data/sequence/Alignment.java b/datamodel/compbio/data/sequence/Alignment.java
index 8fddd0b..35c4df0 100644 (file)
--- a/datamodel/compbio/data/sequence/Alignment.java
+++ b/datamodel/compbio/data/sequence/Alignment.java
@@ -22,6 +22,7 @@ import java.util.List;
 \r
 import javax.xml.bind.annotation.XmlAccessType;\r
 import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlSeeAlso;\r
 \r
 import compbio.util.annotation.Immutable;\r
 \r
@@ -40,14 +41,14 @@ import compbio.util.annotation.Immutable;
  * @version 1.0 September 2009\r
  * \r
  */\r
+//@XmlSeeAlso({JpredAlignment.class})\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@Immutable\r
-public final class Alignment {\r
+public class Alignment {\r
 \r
-       private AlignmentMetadata metadata;\r
-       private List<FastaSequence> sequences;\r
+       protected AlignmentMetadata metadata;\r
+       protected List<FastaSequence> sequences;\r
 \r
-       private Alignment() {\r
+       protected Alignment() {\r
                // This has to has a default constructor for JaxB\r
        }\r
 \r
@@ -59,7 +60,7 @@ public final class Alignment {
        public Alignment(List<FastaSequence> sequences, Program program,\r
                        char gapchar) {\r
                this.sequences = sequences;\r
-               this.metadata = new AlignmentMetadata(Program.CLUSTAL, gapchar);\r
+               this.metadata = new AlignmentMetadata(program, gapchar);\r
        }\r
 \r
        /**\r