From: Jim Procter Date: Wed, 9 Aug 2017 18:32:05 +0000 (+0100) Subject: JAL-2426 JAL-1270 report Xfam download URL used if debug enabled X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ef7ad1dc6a1b8c99a1a0ded71931c194b8530163;p=jalview.git JAL-2426 JAL-1270 report Xfam download URL used if debug enabled --- diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java index 3554f01..b0bea88 100644 --- a/src/jalview/ws/dbsources/Xfam.java +++ b/src/jalview/ws/dbsources/Xfam.java @@ -20,6 +20,7 @@ */ package jalview.ws.dbsources; +import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.io.DataSourceType; @@ -56,9 +57,17 @@ public abstract class Xfam extends DbSourceProxyImpl // retrieved. startQuery(); // TODO: trap HTTP 404 exceptions and return null - AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL() - + queries.trim().toUpperCase() + getXFAMURLSUFFIX(), + String xfamUrl = getXFAMURL() + + queries.trim().toUpperCase() + getXFAMURLSUFFIX(); + + if (Cache.log != null) + { + Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl); + } + + AlignmentI rcds = new FormatAdapter().readFile(xfamUrl , DataSourceType.URL, FileFormat.Stockholm); + for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++) { rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),