JAL-1712 fixes/tests for Castor binding and 'show flanking regions'

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index fc57b27..3f890ba 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -20,6 +20,11 @@
  */
 package jalview.datamodel.xdb.embl;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
@@ -28,11 +33,14 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
+/**
+ * Data model for one entry returned from an EMBL query, as marshalled by a
+ * Castor binding file
+ * 
+ * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ * 
+ * @see embl_mapping.xml
+ */
 public class EmblEntry
 {
   String accession;
@@ -49,13 +57,11 @@ public class EmblEntry
 
   String lastUpdated;
 
-  Vector keywords;
-
-  Vector refs;
+  Vector<String> keywords;
 
-  Vector dbRefs;
+  Vector<DBRefEntry> dbRefs;
 
-  Vector features;
+  Vector<EmblFeature> features;
 
   EmblSequence sequence;
 
@@ -79,7 +85,7 @@ public class EmblEntry
   /**
    * @return the dbRefs
    */
-  public Vector getDbRefs()
+  public Vector<DBRefEntry> getDbRefs()
   {
     return dbRefs;
   }
@@ -88,7 +94,7 @@ public class EmblEntry
    * @param dbRefs
    *          the dbRefs to set
    */
-  public void setDbRefs(Vector dbRefs)
+  public void setDbRefs(Vector<DBRefEntry> dbRefs)
   {
     this.dbRefs = dbRefs;
   }
@@ -113,7 +119,7 @@ public class EmblEntry
   /**
    * @return the features
    */
-  public Vector getFeatures()
+  public Vector<EmblFeature> getFeatures()
   {
     return features;
   }
@@ -122,7 +128,7 @@ public class EmblEntry
    * @param features
    *          the features to set
    */
-  public void setFeatures(Vector features)
+  public void setFeatures(Vector<EmblFeature> features)
   {
     this.features = features;
   }
@@ -130,7 +136,7 @@ public class EmblEntry
   /**
    * @return the keywords
    */
-  public Vector getKeywords()
+  public Vector<String> getKeywords()
   {
     return keywords;
   }
@@ -139,7 +145,7 @@ public class EmblEntry
    * @param keywords
    *          the keywords to set
    */
-  public void setKeywords(Vector keywords)
+  public void setKeywords(Vector<String> keywords)
   {
     this.keywords = keywords;
   }
@@ -162,23 +168,6 @@ public class EmblEntry
   }
 
   /**
-   * @return the refs
-   */
-  public Vector getRefs()
-  {
-    return refs;
-  }
-
-  /**
-   * @param refs
-   *          the refs to set
-   */
-  public void setRefs(Vector refs)
-  {
-    this.refs = refs;
-  }
-
-  /**
    * @return the releaseCreated
    */
   public String getRCreated()
@@ -190,7 +179,7 @@ public class EmblEntry
    * @param releaseCreated
    *          the releaseCreated to set
    */
-  public void setRcreated(String releaseCreated)
+  public void setRCreated(String releaseCreated)
   {
     this.rCreated = releaseCreated;
   }