From 0a7895a17bc2140c2e59ec04a8206102731ba5fd Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 24 Aug 2007 15:37:12 +0000 Subject: [PATCH] remove null pointer exception when embl file is not retrieved and comment about selecting for peptide or na sequences --- src/jalview/ws/dbsources/EmblXmlSource.java | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java index 1300c65..3179110 100644 --- a/src/jalview/ws/dbsources/EmblXmlSource.java +++ b/src/jalview/ws/dbsources/EmblXmlSource.java @@ -23,10 +23,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy super(); } /** - * set this to false to *not* add protein products to alignment dataset. - */ - public boolean getProteinProducts=false; - /** * retrieve and parse an emblxml file * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml * @param query @@ -53,13 +49,19 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy } if (reply != null && reply.exists()) { + efile=null; file = reply.getAbsolutePath(); - efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); + if (reply.length()>25) + { + efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); + } else { + result.append("# No EMBL record retrieved for "+emprefx.toLowerCase()+":"+query.trim()); + } } if (efile!=null) { for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry entry = (EmblEntry) i.next(); - SequenceI[] seqparts = entry.getSequences(false,!getProteinProducts, emprefx); + SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO: use !fetchNa,!fetchPeptide here instead - see todo in emblEntry if (seqparts!=null) { SequenceI[] newseqs = null; int si=0; -- 1.7.10.2