Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f69c8b6..0e649c0 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -239,6 +239,7 @@ public interface SequenceI extends ASequenceI
 
   /**
    * DOCUMENT ME!
+   * 
    * @param position
    *          DOCUMENT ME!
    * @param ch
@@ -274,7 +275,7 @@ public interface SequenceI extends ASequenceI
    * 
    * @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
@@ -382,8 +383,8 @@ public interface SequenceI extends ASequenceI
   /**
    * 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
@@ -420,4 +421,12 @@ public interface SequenceI extends ASequenceI
    */
   public List<int[]> getInsertions();
 
+  /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
+   * 
+   * @param pdbId
+   * @return
+   */
+  public PDBEntry getPDBEntry(String pdbId);
 }