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JAL-2136 JAL-2137 Modified STRUCTMODEL annotation format and added implementation...
[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
0085221
..
b2fb808
100644
(file)
--- a/
src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/
src/jalview/ws/dbsources/EmblXmlSource.java
@@
-63,8
+63,8
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
try
{
reply = dbFetch.fetchDataAsFile(
try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null,
- ".xml");
+ emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
+ "xml");
} catch (Exception e)
{
stopQuery();
} catch (Exception e)
{
stopQuery();
@@
-102,8
+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())
{