X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=60040d83117783a28d23a1889c4e28260aa913d6;hb=65d6d09cd08743d481d39521bb0298ea683888f8;hp=2ff619bc37788f34251bf28202850b7f2e166148;hpb=06e3a52df5af8243cdb67c023c8ddd834711ad36;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 2ff619b..60040d8 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,8 @@
*/
package jalview.datamodel;
+import jalview.api.DBRefEntryI;
+
import java.util.List;
import java.util.Vector;
@@ -239,6 +241,7 @@ public interface SequenceI extends ASequenceI
/**
* DOCUMENT ME!
+ *
* @param position
* DOCUMENT ME!
* @param ch
@@ -247,17 +250,20 @@ public interface SequenceI extends ASequenceI
public void insertCharAt(int position, int count, char ch);
/**
- * DOCUMENT ME!
+ * Gets array holding sequence features associated with this sequence. The
+ * array may be held by the sequence's dataset sequence if that is defined.
*
- * @return DOCUMENT ME!
+ * @return hard reference to array
*/
public SequenceFeature[] getSequenceFeatures();
/**
- * DOCUMENT ME!
+ * Replaces the array of sequence features associated with this sequence with
+ * a new array reference. If this sequence has a dataset sequence, then this
+ * method will update the dataset sequence's feature array
*
- * @param v
- * DOCUMENT ME!
+ * @param features
+ * New array of sequence features
*/
public void setSequenceFeatures(SequenceFeature[] features);
@@ -295,9 +301,9 @@ public interface SequenceI extends ASequenceI
public void setVamsasId(String id);
- public void setDBRef(DBRefEntry[] dbs);
+ public void setDBRefs(DBRefEntry[] dbs);
- public DBRefEntry[] getDBRef();
+ public DBRefEntry[] getDBRefs();
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
@@ -382,8 +388,8 @@ public interface SequenceI extends ASequenceI
/**
* Transfer any database references or annotation from entry under a sequence
* mapping.
- * Note: DOES NOT transfer sequence associated alignment
- * annotation
+ * Note: DOES NOT transfer sequence associated alignment annotation
+ *
*
* @param entry
* @param mp
@@ -428,4 +434,8 @@ public interface SequenceI extends ASequenceI
* @return
*/
public PDBEntry getPDBEntry(String pdbId);
+
+ public void setSourceDBRef(DBRefEntryI dbRef);
+
+ public DBRefEntryI getSourceDBRef();
}