2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.dbsources;
23 import jalview.datamodel.Alignment;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.SequenceI;
26 import jalview.datamodel.xdb.embl.EmblEntry;
27 import jalview.util.MessageManager;
28 import jalview.ws.ebi.EBIFetchClient;
31 import java.util.Iterator;
33 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
37 * Last properly parsed embl file.
39 public jalview.datamodel.xdb.embl.EmblFile efile = null;
41 public EmblXmlSource()
47 * retrieve and parse an emblxml file
50 * either EMBL or EMBLCDS strings are allowed - anything else will
51 * not retrieve emblxml
56 public AlignmentI getEmblSequenceRecords(String emprefx, String query)
60 EBIFetchClient dbFetch = new EBIFetchClient();
64 reply = dbFetch.fetchDataAsFile(
65 emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
69 throw new Exception(MessageManager.formatMessage("exception.ebiembl_retrieval_failed_on", new String[]{emprefx.toLowerCase(),query.trim()}), e);
71 return getEmblSequenceRecords(emprefx, query, reply);
75 * parse an emblxml file stored locally
78 * either EMBL or EMBLCDS strings are allowed - anything else will
79 * not retrieve emblxml
82 * the EMBL XML file containing the results of a query
86 public AlignmentI getEmblSequenceRecords(String emprefx, String query,
87 File reply) throws Exception
89 SequenceI seqs[] = null;
90 StringBuffer result = new StringBuffer();
91 if (reply != null && reply.exists())
94 file = reply.getAbsolutePath();
95 if (reply.length() > 25)
97 efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
101 result.append(MessageManager.formatMessage("label.no_embl_record_found", new String[]{emprefx.toLowerCase(),query.trim()}));
106 for (Iterator i = efile.getEntries().iterator(); i.hasNext();)
108 EmblEntry entry = (EmblEntry) i.next();
109 SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
111 // !fetchNa,!fetchPeptide
119 if (seqparts != null)
121 SequenceI[] newseqs = null;
125 newseqs = new SequenceI[seqparts.length];
129 newseqs = new SequenceI[seqs.length + seqparts.length];
131 for (; si < seqs.length; si++)
133 newseqs[si] = seqs[si];
137 for (int j = 0; j < seqparts.length; si++, j++)
139 newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
151 AlignmentI al = null;
152 if (seqs != null && seqs.length > 0)
154 al = new Alignment(seqs);
155 result.append(MessageManager.formatMessage("label.embl_successfully_parsed", new String[]{emprefx}));