X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FDBRefEntryI.java;h=ed6358eec9823c3d4edd6dd45e68e45e6b05fb6d;hb=427b5193ff4e96cf2a28cf72c1857a1ab5250201;hp=701acb663ce60ad3b3e5fe30fa5d437f5b40a210;hpb=168ef5a045478ef56a5d9f8c71fbddb53a6b8a58;p=jalview.git
diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 701acb6..ed6358e 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 .
+ * 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.
+ *
+ * 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.
- *
+ * 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
- *
- * 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();
}