/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
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.ArrayList;
import java.util.List;
public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
/*
* JAL-1856 Embl returns this text for query not found
*/
private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
public EmblXmlSource()
{
super();
}
/**
* retrieve and parse an emblxml file
*
* @param emprefx
* either EMBL or EMBLCDS strings are allowed - anything else will
* not retrieve emblxml
* @param query
* @return
* @throws Exception
*/
public AlignmentI getEmblSequenceRecords(String emprefx, String query)
throws Exception
{
startQuery();
EBIFetchClient dbFetch = new EBIFetchClient();
File reply;
try
{
reply = dbFetch.fetchDataAsFile(
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);
}
return getEmblSequenceRecords(emprefx, query, reply);
}
/**
* parse an emblxml file stored locally
*
* @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
{
EmblFile efile = null;
List seqs = new ArrayList<>();
if (reply != null && reply.exists())
{
file = reply.getAbsolutePath();
if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
{
efile = EmblFile.getEmblFile(reply);
}
}
/*
* invalid accession gets a reply with no elements, text content of
* EmbFile reads something like (e.g.) this ungrammatical phrase
* Entry: display type is either not supported or entry is not found.
*/
List peptides = new ArrayList<>();
if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())
{
SequenceI seq = entry.getSequence(emprefx, peptides);
if (seq != null)
{
seqs.add(seq.deriveSequence());
// place DBReferences on dataset and refer
}
}
}
AlignmentI al = null;
if (!seqs.isEmpty())
{
al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
}
stopQuery();
return al;
}
@Override
public boolean isDnaCoding()
{
return true;
}
}