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
*/
public boolean updateFrom(DBRefEntryI otherEntry);
+
+ /**
+ * Method to distinguish between direct and indirect database references. <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. <br>
+ * The only way a dbref's mappings can be fully verified is via the local
+ * sequence frame, so rather than use isPrimary directly, please use
+ * SequenceI.getPrimaryDbRefs().
+ *
+ * @return true if this reference provides a primary accession for the
+ * associated sequence object
+ */
+ public boolean isPrimary();
}