Merge branch 'patch/JAL-2238_tcoffee_subgroups' into develop

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

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 49858cb..52ee381 100644 (file)
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,6 +1,5 @@
 package jalview.api;
 
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 
 //JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI)
@@ -49,31 +48,11 @@ 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
+   * @return null or a valid mapping.
    */
-  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();
-
   public Mapping getMap();
 
   /**
@@ -90,5 +69,26 @@ public interface DBRefEntryI
    * @param otherEntry
    * @return
    */
-  public boolean updateFrom(DBRefEntry otherEntry);
+  public boolean updateFrom(DBRefEntryI otherEntry);
+
+  /**
+   * Answers true if the ref looks like a primary (direct) database reference. <br>
+   * The only way a dbref's mappings can be fully verified is via the local
+   * sequence frame, so rather than use isPrimaryCandidate directly, please use
+   * SequenceI.getPrimaryDbRefs(). <br>
+   * Primary references indicate the local sequence data directly corresponds
+   * with the database record. All other references are secondary. Direct
+   * references indicate that part or all of the local sequence data can be
+   * mapped with another sequence, enabling annotation transfer.
+   * Cross-references indicate the local sequence data can be corresponded to
+   * some other linear coordinate system via a transformation. <br>
+   * This method is also sufficient to distinguish direct DBRefEntry mappings
+   * from other relationships - e.g. coding relationships (imply a 1:3/3:1
+   * mapping), but not transcript relationships, which imply a (possibly
+   * non-contiguous) 1:1 mapping.
+   *
+   * @return true if this reference provides a primary accession for the
+   *         associated sequence object
+   */
+  public boolean isPrimaryCandidate();
 }