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Merge branch 'develop' into bug/JAL-98consensusMemory
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
EmblXmlSource.java
diff --git
a/src/jalview/ws/dbsources/EmblXmlSource.java
b/src/jalview/ws/dbsources/EmblXmlSource.java
index
b71f032
..
b139574
100644
(file)
--- a/
src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/
src/jalview/ws/dbsources/EmblXmlSource.java
@@
-64,7
+64,6
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
reply = dbFetch.fetchDataAsFile(
emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
{
reply = dbFetch.fetchDataAsFile(
emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
- null,
".xml");
} catch (Exception e)
{
".xml");
} catch (Exception e)
{
@@
-103,8
+102,13
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
}
}
}
}
+ /*
+ * invalid accession gets a reply with no <entry> elements, text content of
+ * EmbFile reads something like (e.g.) this ungrammatical phrase
+ * Entry: <acc> display type is either not supported or entry is not found.
+ */
List<SequenceI> peptides = new ArrayList<SequenceI>();
List<SequenceI> peptides = new ArrayList<SequenceI>();
- if (efile != null)
+ if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())
{
{
for (EmblEntry entry : efile.getEntries())
{