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.datamodel.xdb.embl.EmblFile;
28 import jalview.util.MessageManager;
29 import jalview.ws.ebi.EBIFetchClient;
33 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
37 * Last properly parsed embl file.
39 public 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(
70 "exception.ebiembl_retrieval_failed_on", new String[] {
71 emprefx.toLowerCase(), query.trim() }), e);
73 return getEmblSequenceRecords(emprefx, query, reply);
77 * parse an emblxml file stored locally
80 * either EMBL or EMBLCDS strings are allowed - anything else will
81 * not retrieve emblxml
84 * the EMBL XML file containing the results of a query
88 public AlignmentI getEmblSequenceRecords(String emprefx, String query,
89 File reply) throws Exception
91 SequenceI seqs[] = null;
92 StringBuffer result = new StringBuffer();
93 if (reply != null && reply.exists())
96 file = reply.getAbsolutePath();
97 if (reply.length() > 25)
99 efile = EmblFile.getEmblFile(reply);
103 result.append(MessageManager.formatMessage(
104 "label.no_embl_record_found",
105 new String[] { emprefx.toLowerCase(), query.trim() }));
110 for (EmblEntry entry : efile.getEntries())
112 SequenceI[] seqparts = entry.getSequences(false, true, emprefx);
113 // TODO: use !fetchNa,!fetchPeptide here instead - see todo in EmblEntry
114 if (seqparts != null)
116 SequenceI[] newseqs = null;
120 newseqs = new SequenceI[seqparts.length];
124 newseqs = new SequenceI[seqs.length + seqparts.length];
126 for (; si < seqs.length; si++)
128 newseqs[si] = seqs[si];
132 for (int j = 0; j < seqparts.length; si++, j++)
134 newseqs[si] = seqparts[j].deriveSequence();
135 // place DBReferences on dataset and refer
146 AlignmentI al = null;
147 if (seqs != null && seqs.length > 0)
149 al = new Alignment(seqs);
150 result.append(MessageManager.formatMessage(
151 "label.embl_successfully_parsed", new String[] { emprefx }));