JAL-3863 passing test to verify a uniprot accession with canonical flag set is transf...

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

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 701acb6..ed6358e 100644 (file)
--- 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;
@@ -72,26 +92,26 @@ public interface DBRefEntryI
   public boolean updateFrom(DBRefEntryI otherEntry);
 
   /**
-   * Method to distinguish between direct and indirect database references
-   * 
-   * primary references indicate the local sequence data directly corresponds
-   * with the database record. All other references are secondary. direct
+   * 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.
-   * 
+   * 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
-   * 
-   * 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();
+
+  public boolean isCanonical();
 }