X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FDBRefEntryI.java;h=2ce7e4a3ed7980ee5a13e00de24edfd7f9093b6c;hb=f7c9911a43d7b85a3f0097eb99825b73f3a95713;hp=731c25895417568cabe3acb9b86a8b770d960920;hpb=1503bcb2b548b7f6bc11bcbf081455ab94839099;p=jalview.git

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 731c258..2ce7e4a 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,19 +1,99 @@
 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
 {
   public boolean equalRef(DBRefEntryI entry);
 
+  /**
+   * 
+   * @return Source DB name for this entry
+   */
   public String getSource();
 
-  public String getVersion();
-
+  /**
+   * 
+   * @return Accession Id for this entry
+   */
   public String getAccessionId();
 
+  /**
+   * 
+   * @param accessionId
+   *          Accession Id for this entry
+   */
   public void setAccessionId(String accessionId);
 
+  /**
+   * 
+   * @param source
+   *          Source DB name for this entry
+   */
   public void setSource(String source);
 
+  /**
+   * 
+   * @return Source DB version for this entry
+   */
+  public String getVersion();
+
+  /**
+   * 
+   * @param version
+   *          Source DB version for this entry
+   */
   public void setVersion(String version);
+
+  /**
+   * 
+   * @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
+   */
+  public void setEndRes(int endRes);
+
+  /**
+   * 
+   * @return index of end residue in the source DB
+   */
+  public int getEndRes();
+
+  /**
+   * access a mapping, if present that can be used to map positions from the
+   * associated dataset sequence to the DBRef's sequence frame.
+   * 
+   * @return null or a valid mapping.
+   */
+  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>
+   * 
+   * @param otherEntry
+   * @return
+   */
+  public boolean updateFrom(DBRefEntryI otherEntry);
 }