JAL-2144 TODO - new methods for canonicalisation and comparison of source strings...

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index a2243be..cf15ff8 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -23,7 +23,10 @@ package jalview.datamodel;
 /**
  * Defines internal constants for unambiguous annotation of DbRefEntry source
  * strings and describing the data retrieved from external database sources (see
- * jalview.ws.DbSourcProxy)
+ * jalview.ws.DbSourcProxy) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
  * 
  * @author JimP
  * 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 04cee93..891fdd6 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4825,6 +4825,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
              * align cdna to protein - currently only if 
              * fetching and aligning Ensembl transcripts!
              */
+            // TODO: generalise for other sources of locus/transcript/cds data
             if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
             {
               copyAlignment.alignAs(xrefsAlignment);