JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandidate()

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

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index a4ec575..52ee381 100644 (file)
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -72,7 +72,10 @@ public interface DBRefEntryI
   public boolean updateFrom(DBRefEntryI otherEntry);
 
   /**
-   * Method to distinguish between direct and indirect database references. <br>
+   * 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
@@ -82,13 +85,10 @@ public interface DBRefEntryI
    * 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().
+   * non-contiguous) 1:1 mapping.
    *
    * @return true if this reference provides a primary accession for the
    *         associated sequence object
    */
-  public boolean isPrimary();
+  public boolean isPrimaryCandidate();
 }