Merge branch 'features/JAL-1705_ensembl' of http://source.jalview.org/git/jalview...

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index bd193fb..0e649c0 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -26,12 +26,13 @@ import java.util.Vector;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
  * 
  * @author $author$
  * @version $Revision$
  */
-public interface SequenceI
+public interface SequenceI extends ASequenceI
 {
   /**
    * Set the display name for the sequence
@@ -238,6 +239,7 @@ public interface SequenceI
 
   /**
    * DOCUMENT ME!
+   * 
    * @param position
    *          DOCUMENT ME!
    * @param ch
@@ -273,7 +275,7 @@ public interface SequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector<PDBEntry> getPDBId();
+  public Vector<PDBEntry> getAllPDBEntries();
 
   /**
    * add entry to the vector of PDBIds, if it isn't in the list already
@@ -381,8 +383,8 @@ public interface SequenceI
   /**
    * Transfer any database references or annotation from entry under a sequence
    * mapping. <br/>
-   * <strong>Note: DOES NOT transfer sequence associated alignment
-   * annotation </strong><br/>
+   * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+   * </strong><br/>
    * 
    * @param entry
    * @param mp
@@ -420,16 +422,11 @@ public interface SequenceI
   public List<int[]> getInsertions();
 
   /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
    * 
-   * @return returns true if the sequence is hidden
-   */
-  public boolean isHidden();
-
-  /**
-   * 
-   * @param hidden
-   *          visibility status of the sequence
+   * @param pdbId
+   * @return
    */
-  public void setHidden(Boolean hidden);
-
+  public PDBEntry getPDBEntry(String pdbId);
 }