From: Jim Procter Date: Mon, 13 Dec 2021 17:49:19 +0000 (+0000) Subject: JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve... X-Git-Tag: Release_2_11_2_0~20^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bb9efbe53b2e92a1e3fcc78d7a6b6f5563e43e97;p=jalview.git JAL-3855 JAL-3829 don’t need to make up alphafold model retrieval URL when we’ve been given it --- 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(); } + }