/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.xdb.embl.EmblEntry;
+import jalview.datamodel.xdb.embl.EmblFile;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import java.io.File;
-import java.util.Iterator;
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
/**
* Last properly parsed embl file.
*/
- public jalview.datamodel.xdb.embl.EmblFile efile = null;
+ public EmblFile efile = null;
public EmblXmlSource()
{
} catch (Exception e)
{
stopQuery();
- throw new Exception(MessageManager.formatMessage("exception.ebiembl_retrieval_failed_on", new String[]{emprefx.toLowerCase(),query.trim()}), e);
+ throw new Exception(MessageManager.formatMessage(
+ "exception.ebiembl_retrieval_failed_on", new String[] {
+ emprefx.toLowerCase(), query.trim() }), e);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
file = reply.getAbsolutePath();
if (reply.length() > 25)
{
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+ efile = EmblFile.getEmblFile(reply);
}
else
{
- result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
+ result.append(MessageManager.formatMessage(
+ "label.no_embl_record_found",
+ new String[] { emprefx.toLowerCase(), query.trim() }));
}
}
if (efile != null)
{
- for (Iterator i = efile.getEntries().iterator(); i.hasNext();)
+ for (EmblEntry entry : efile.getEntries())
{
- EmblEntry entry = (EmblEntry) i.next();
- SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
- // use
- // !fetchNa,!fetchPeptide
- // here
- // instead
- // -
- // see
- // todo
- // in
- // emblEntry
+ SequenceI[] seqparts = entry.getSequences(false, true, emprefx);
+ // TODO: use !fetchNa,!fetchPeptide here instead - see todo in EmblEntry
if (seqparts != null)
{
SequenceI[] newseqs = null;
}
for (int j = 0; j < seqparts.length; si++, j++)
{
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
- // dataset and refer
+ newseqs[si] = seqparts[j].deriveSequence();
+ // place DBReferences on dataset and refer
}
seqs = newseqs;
if (seqs != null && seqs.length > 0)
{
al = new Alignment(seqs);
- result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
+ result.append(MessageManager.formatMessage(
+ "label.embl_successfully_parsed", new String[] { emprefx }));
results = result;
}
stopQuery();