From 72f71a390ca98525f99a5dcecc1202696b20e0d7 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 3 Oct 2016 09:21:10 +0100 Subject: [PATCH] =?utf8?q?JAL-2210=20need=20to=20add=20both=20transcript=20a?= =?utf8?q?nd=20product,=20and=20Ensembl=20needs=20to=20be=20marked=20as=20a=20?= =?utf8?q?primary=20ref=20on=20protein,=20otherwise=20the=20ensembl=20peptid?= =?utf8?q?e=20ids=20on=20uniprot=20don=E2=80=99t=20match=20up=20with=20the=20?= =?utf8?q?ones=20retrieved=20from=20ensembl?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/datamodel/DBRefSource.java | 2 +- src/jalview/ws/dbsources/Uniprot.java | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index aef18e9..0ac14e5 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -101,7 +101,7 @@ public class DBRefSource public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL }; public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB, - EMBLCDSProduct }; // , ENSEMBL }; // Ensembl ENSP* entries are protein + EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein public static String[] allSources() { diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index e26ccda..4c53ef9 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -236,7 +236,7 @@ public class Uniprot extends DbSourceProxyImpl dbRefs.add(dbr); } } - if (false) // "Ensembl".equals(pdb.getType())) + if ("Ensembl".equals(pdb.getType())) { /*UniprotXML * @@ -249,8 +249,6 @@ public class Uniprot extends DbSourceProxyImpl .get("protein sequence ID"); if (cdsId != null && cdsId.trim().length() > 0) { - // Only add the product ID - dbRefs.remove(dbr); dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim()); dbRefs.add(dbr); -- 1.7.10.2