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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;
*/
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;
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 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;
public class EmblEntry
{
String accession;
@@
-49,13
+57,11
@@
public class EmblEntry
String lastUpdated;
String lastUpdated;
- Vector keywords;
-
- Vector refs;
+ Vector<String> keywords;
- Vector dbRefs;
+ Vector<DBRefEntry> dbRefs;
- Vector features;
+ Vector<EmblFeature> features;
EmblSequence sequence;
EmblSequence sequence;
@@
-79,7
+85,7
@@
public class EmblEntry
/**
* @return the dbRefs
*/
/**
* @return the dbRefs
*/
- public Vector getDbRefs()
+ public Vector<DBRefEntry> getDbRefs()
{
return dbRefs;
}
{
return dbRefs;
}
@@
-88,7
+94,7
@@
public class EmblEntry
* @param dbRefs
* the dbRefs to set
*/
* @param dbRefs
* the dbRefs to set
*/
- public void setDbRefs(Vector dbRefs)
+ public void setDbRefs(Vector<DBRefEntry> dbRefs)
{
this.dbRefs = dbRefs;
}
{
this.dbRefs = dbRefs;
}
@@
-113,7
+119,7
@@
public class EmblEntry
/**
* @return the features
*/
/**
* @return the features
*/
- public Vector getFeatures()
+ public Vector<EmblFeature> getFeatures()
{
return features;
}
{
return features;
}
@@
-122,7
+128,7
@@
public class EmblEntry
* @param features
* the features to set
*/
* @param features
* the features to set
*/
- public void setFeatures(Vector features)
+ public void setFeatures(Vector<EmblFeature> features)
{
this.features = features;
}
{
this.features = features;
}
@@
-130,7
+136,7
@@
public class EmblEntry
/**
* @return the keywords
*/
/**
* @return the keywords
*/
- public Vector getKeywords()
+ public Vector<String> getKeywords()
{
return keywords;
}
{
return keywords;
}
@@
-139,7
+145,7
@@
public class EmblEntry
* @param keywords
* the keywords to set
*/
* @param keywords
* the keywords to set
*/
- public void setKeywords(Vector keywords)
+ public void setKeywords(Vector<String> keywords)
{
this.keywords = 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()
* @return the releaseCreated
*/
public String getRCreated()
@@
-190,7
+179,7
@@
public class EmblEntry
* @param releaseCreated
* the releaseCreated to set
*/
* @param releaseCreated
* the releaseCreated to set
*/
- public void setRcreated(String releaseCreated)
+ public void setRCreated(String releaseCreated)
{
this.rCreated = releaseCreated;
}
{
this.rCreated = releaseCreated;
}