From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 12 Jul 2016 16:41:50 +0000 (+0100)
Subject: JAL-2144 TODO - new methods for canonicalisation and comparison of source strings... 
X-Git-Tag: Release_2_10_0~140^2~5^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b2afeb815dcec916179fdec147523aba4dd4c9c1;p=jalview.git

JAL-2144 TODO - new methods for canonicalisation and comparison of source strings, regularisation of properties from SequenceDbSource implementations, recognition of coding databases in a more generic way.
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index a2243be..cf15ff8 100755
--- 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
--- 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);