JAL-1926 JAL-2106 remove startRes/endRes fields - not used

[jalview.git] / src / jalview / api / DBRefEntryI.java

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index b927fa5..32245b3 100644 (file)
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,5 +1,8 @@
 package jalview.api;
 
+import jalview.datamodel.Mapping;
+
+//JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI)
 
 public interface DBRefEntryI
 {
@@ -45,28 +48,26 @@ public interface DBRefEntryI
   public void setVersion(String version);
 
   /**
+   * access a mapping, if present that can be used to map positions from the
+   * associated dataset sequence to the DBRef's sequence frame.
    * 
-   * @param startRes
-   *          index of start residue in the source DB
-   */
-  public void setStartRes(int startRes);
-
-  /**
-   * 
-   * @return index of start residue in the source DB
-   */
-  public int getStartRes();
-
-  /**
-   * 
-   * @param endRes
-   *          index of end residue in the source DB
+   * @return null or a valid mapping.
    */
-  public void setEndRes(int endRes);
+  public Mapping getMap();
 
   /**
+   * Answers true if this object is either equivalent to, or can be 'improved'
+   * by, the given entry. Specifically, answers true if
+   * <ul>
+   * <li>source and accession are identical</li>
+   * <li>version is identical, or this version is of the format "someSource:0",
+   * in which case the version for the other entry replaces it</li>
+   * <li>mappings are not compared but if this entry has no mapping, replace
+   * with that for the other entry</li>
+   * </ul>
    * 
-   * @return index of end residue in the source DB
+   * @param otherEntry
+   * @return
    */
-  public int getEndRes();
+  public boolean updateFrom(DBRefEntryI otherEntry);
 }