X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=55c59db27ec69e5ec73202893e5e3b153e4ce9e1;hb=c06a9af4331b34a8537b28b5e749c442e1bc1682;hp=355e27102970e4ae7f9e174d477b5bdc70d48d30;hpb=63c08febd1f76249b308628611857b9698baaf8d;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 355e271..55c59db 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.api.DBRefEntryI;
-
 import java.util.List;
 import java.util.Vector;
 
@@ -239,19 +237,21 @@ public interface SequenceI extends ASequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *          DOCUMENT ME!
+   *          alignment column number
    * @param c
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
+   * insert given character at alignment column position
    * 
    * @param position
-   *          DOCUMENT ME!
+   *          alignment column number
+   * @param count
+   *          length of insert
    * @param ch
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int position, int count, char ch);
 
@@ -289,7 +289,12 @@ public interface SequenceI extends ASequenceI
   public Vector<PDBEntry> getAllPDBEntries();
 
   /**
-   * add entry to the vector of PDBIds, if it isn't in the list already
+   * add entry to the *normalised* vector of PDBIds.
+   * 
+   * If a PDBEntry is passed with an entry.getID() string, as one already in the
+   * list, or one is added that appears to be the same but has a chain ID
+   * appended, then the existing PDBEntry will be updated with the new
+   * attributes.
    * 
    * @param entry
    */
@@ -441,21 +446,14 @@ public interface SequenceI extends ASequenceI
    */
   public PDBEntry getPDBEntry(String pdbId);
 
-  /**
-   * Set the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from. This is very important
-   * for SIFTS mappings and must be set prior to performing SIFTS mapping.
-   * 
-   * @param dbRef
-   *          the source dbRef for the sequence
-   */
-  public void setSourceDBRef(DBRefEntryI dbRef);
 
   /**
-   * Get the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from.
+   * Get all primary database/accessions for this sequence's data. These
+   * DBRefEntry are expected to resolve to a valid record in the associated
+   * external database, either directly or via a provided 1:1 Mapping.
    * 
-   * @return
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
    */
-  public DBRefEntryI getSourceDBRef();
+  public List<DBRefEntry> getPrimaryDBRefs();
 }