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JAL-2755 correct Javadoc and error handling
[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
d185d12
..
ca90d60
100644
(file)
--- a/
src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/
src/jalview/ws/dbsources/EmblXmlSource.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-64,13
+64,13
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
reply = dbFetch.fetchDataAsFile(
emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
{
reply = dbFetch.fetchDataAsFile(
emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
- ".xml");
+ "xml");
} catch (Exception e)
{
stopQuery();
throw new Exception(MessageManager.formatMessage(
} catch (Exception e)
{
stopQuery();
throw new Exception(MessageManager.formatMessage(
- "exception.ebiembl_retrieval_failed_on", new String[] {
- emprefx.toLowerCase(), query.trim() }), e);
+ "exception.ebiembl_retrieval_failed_on", new String[]
+ { emprefx.toLowerCase(), query.trim() }), e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
}
return getEmblSequenceRecords(emprefx, query, reply);
}
@@
-91,7
+91,7
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
File reply) throws Exception
{
EmblFile efile = null;
File reply) throws Exception
{
EmblFile efile = null;
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
if (reply != null && reply.exists())
{
if (reply != null && reply.exists())
{
@@
-107,7
+107,7
@@
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
* EmbFile reads something like (e.g.) this ungrammatical phrase
* Entry: <acc> display type is either not supported or entry is not found.
*/
* 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<>();
if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())
if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())