X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FDBRefEntryI.java;h=52ee381454316a90ba1cd0b3d268c1c5bf688204;hb=fecb7871ff2ec644c4f3c9ea513df7c0fce30514;hp=2ce7e4a3ed7980ee5a13e00de24edfd7f9093b6c;hpb=4b4c98b3be626bff6d72048447ebbac6070c2ee4;p=jalview.git
diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 2ce7e4a..52ee381 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -48,32 +48,6 @@ public interface DBRefEntryI
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.
*
@@ -96,4 +70,25 @@ public interface DBRefEntryI
* @return
*/
public boolean updateFrom(DBRefEntryI otherEntry);
+
+ /**
+ * Answers true if the ref looks like a primary (direct) database reference.
+ * 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().
+ * 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.
+ * 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();
}