From b2afeb815dcec916179fdec147523aba4dd4c9c1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 12 Jul 2016 17:41:50 +0100 Subject: [PATCH] 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. --- src/jalview/datamodel/DBRefSource.java | 5 ++++- src/jalview/gui/AlignFrame.java | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) 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)
+ * 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); -- 1.7.10.2