X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FDBRefEntryI.java;h=672d6b4650e3f0794932a194d029ae8b316f5163;hb=0d1529f5a1f02b9cb959f0fe0d3e7f468723b83a;hp=a4ec575636e96161d3428b17ef581737a44efde2;hpb=d240900df4c81bd7b054afc0f569c7a75d4e1751;p=jalview.git

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index a4ec575..672d6b4 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
 import jalview.datamodel.Mapping;
@@ -72,7 +92,11 @@ 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 +106,10 @@ 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();
 }