X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=66ebe1bedb298dedd9363b8e8ee36ca4369c7e62;hb=c6c67aaa8e2d236305a3495f4edfc8cc88e22b79;hp=89d9f0571c28daad59e1fd32d3b6e8f04e633f78;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 89d9f05..66ebe1b 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
@@ -22,10 +24,11 @@ import jalview.datamodel.Alignment;
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
{
@@ -33,7 +36,7 @@ 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()
{
@@ -63,8 +66,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
} catch (Exception e)
{
stopQuery();
- throw new Exception("EBI EMBL XML retrieval failed on "
- + 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);
}
@@ -92,29 +96,21 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
file = reply.getAbsolutePath();
if (reply.length() > 25)
{
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+ efile = EmblFile.getEmblFile(reply);
}
else
{
- result.append("# No EMBL record retrieved for "
- + 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;
@@ -135,8 +131,8 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
}
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;
@@ -151,12 +147,18 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
if (seqs != null && seqs.length > 0)
{
al = new Alignment(seqs);
- result.append("# Successfully parsed the " + emprefx
- + " queries into an Alignment");
+ result.append(MessageManager.formatMessage(
+ "label.embl_successfully_parsed", new String[] { emprefx }));
results = result;
}
stopQuery();
return al;
}
+ @Override
+ public boolean isDnaCoding()
+ {
+ return true;
+ }
+
}