From bb9efbe53b2e92a1e3fcc78d7a6b6f5563e43e97 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 13 Dec 2021 17:49:19 +0000 Subject: [PATCH] =?utf8?q?JAL-3855=20JAL-3829=20don=E2=80=99t=20need=20to=20?= =?utf8?q?make=20up=20alphafold=20model=20retrieval=20URL=20when=20we=E2=80=99?= =?utf8?q?ve=20been=20given=20it?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/gui/StructureViewerBase.java | 2 +- src/jalview/ws/dbsources/EBIAlfaFold.java | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 30ecc80..ae2128b 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -1156,7 +1156,7 @@ public abstract class StructureViewerBase extends GStructureViewer { if (afclient.isValidReference(pdbid)) { - pdbseq = afclient.getSequenceRecords(pdbid); + pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl()); } else { if (processingEntry.hasRetrievalUrl()) { diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java index b77fc47..4449b0b 100644 --- a/src/jalview/ws/dbsources/EBIAlfaFold.java +++ b/src/jalview/ws/dbsources/EBIAlfaFold.java @@ -124,6 +124,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy @Override public AlignmentI getSequenceRecords(String queries) throws Exception { + return getSequenceRecords(queries, null); + } + public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception + { AlignmentI pdbAlignment = null; String chain = null; String id = null; @@ -145,6 +149,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy return null; } String alphaFoldCif = getAlphaFoldCifDownloadUrl(id); + if (retrievalUrl != null) + { + alphaFoldCif = retrievalUrl; + } try { @@ -327,4 +335,5 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy { return new PDBFeatureSettings(); } + } -- 1.7.10.2