*/
package jalview.ws.dbsources;
-import java.io.File;
-
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import java.io.File;
+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 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);
}
public AlignmentI getEmblSequenceRecords(String emprefx, String query,
File reply) throws Exception
{
- SequenceI seqs[] = null;
- StringBuffer result = new StringBuffer();
+ EmblFile efile = null;
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+
if (reply != null && reply.exists())
{
- efile = null;
file = reply.getAbsolutePath();
- if (reply.length() > 25)
+ if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
efile = EmblFile.getEmblFile(reply);
}
- else
- {
- result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
- }
}
- if (efile != null)
+
+ /*
+ * 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>();
+ if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())
{
- SequenceI[] seqparts = entry.getSequences(false, true, emprefx);
- // TODO: use !fetchNa,!fetchPeptide here instead - see todo in EmblEntry
- if (seqparts != null)
+ SequenceI seq = entry.getSequence(emprefx, peptides);
+ if (seq != 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;
-
+ seqs.add(seq.deriveSequence());
+ // place DBReferences on dataset and refer
}
}
}
- else
- {
- result = null;
- }
+
AlignmentI al = null;
- if (seqs != null && seqs.length > 0)
+ if (!seqs.isEmpty())
{
- al = new Alignment(seqs);
- result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));
- results = result;
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
}
stopQuery();
return al;
}
+ @Override
+ public boolean isDnaCoding()
+ {
+ return true;
+ }
+
}