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;
+import java.util.ArrayList;
+import java.util.List;
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
-
- /**
- * Last properly parsed embl file.
+ /*
+ * JAL-1856 Embl returns this text for query not found
*/
- public jalview.datamodel.xdb.embl.EmblFile efile = null;
+ private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
public EmblXmlSource()
{
try
{
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
+ emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
+ ".xml");
} 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);
+ return getEmblSequenceRecords(emprefx, reply);
}
/**
* @param emprefx
* either EMBL or EMBLCDS strings are allowed - anything else will
* not retrieve emblxml
- * @param query
* @param file
* the EMBL XML file containing the results of a query
* @return
* @throws Exception
*/
- public AlignmentI getEmblSequenceRecords(String emprefx, String query,
- File reply) throws Exception
+ public AlignmentI getEmblSequenceRecords(String emprefx, File reply)
+ throws Exception
{
- SequenceI seqs[] = null;
- StringBuffer result = new StringBuffer();
+ EmblEntry entry = null;
+
if (reply != null && reply.exists())
{
- efile = null;
file = reply.getAbsolutePath();
- if (reply.length() > 25)
+ if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
- }
- else
- {
- result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
+ entry = EmblFile.getEmblEntry(reply);
}
}
- if (efile != null)
- {
- for (Iterator i = efile.getEntries().iterator(); i.hasNext();)
- {
- EmblEntry entry = (EmblEntry) i.next();
- SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
- // use
- // !fetchNa,!fetchPeptide
- // here
- // instead
- // -
- // see
- // todo
- // in
- // emblEntry
- if (seqparts != null)
- {
- SequenceI[] newseqs = null;
- int si = 0;
- if (seqs == null)
- {
- newseqs = new SequenceI[seqparts.length];
- }
- else
- {
- newseqs = new SequenceI[seqs.length + seqparts.length];
-
- for (; si < seqs.length; si++)
- {
- newseqs[si] = seqs[si];
- seqs[si] = null;
- }
- }
- for (int j = 0; j < seqparts.length; si++, j++)
- {
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
- // dataset and refer
- }
- seqs = newseqs;
- }
- }
- }
- else
- {
- result = null;
- }
+ // TODO don't need peptides any more?
+ List<SequenceI> peptides = new ArrayList<SequenceI>();
AlignmentI al = null;
- if (seqs != null && seqs.length > 0)
+ if (entry != null)
{
- al = new Alignment(seqs);
- result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
- results = result;
+ SequenceI seq = entry.getSequence(emprefx, peptides);
+ if (seq != null)
+ {
+ seq.deriveSequence();
+ // place DBReferences on dataset and refer
+ al = new Alignment(new SequenceI[] { seq });
+ }
}
stopQuery();
return al;
}
+ @Override
+ public boolean isDnaCoding()
+ {
+ return true;
+ }
+
}