jalviewX
File EmblXmlSource.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| EmblXmlSource | 35 | 27 | 12 | 39 |
Contributing tests
This file is covered by 4 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 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. | |
| 11 | * | |
| 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. | |
| 16 | * | |
| 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. | |
| 20 | */ | |
| 21 | package jalview.ws.dbsources; | |
| 22 | ||
| 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; | |
| 30 | ||
| 31 | import java.io.File; | |
| 32 | import java.util.ArrayList; | |
| 33 | import java.util.List; | |
| 34 | ||
| 35 | public abstract class EmblXmlSource extends EbiFileRetrievedProxy | |
| 36 | { | |
| 37 | /* | |
| 38 | * JAL-1856 Embl returns this text for query not found | |
| 39 | */ | |
| 40 | private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found."; | |
| 41 | ||
| 42 | 12 |  public EmblXmlSource() |
| 43 | { | |
| 44 | 12 | super(); |
| 45 | } | |
| 46 | ||
| 47 | /** | |
| 48 | * retrieve and parse an emblxml file | |
| 49 | * | |
| 50 | * @param emprefx | |
| 51 | * either EMBL or EMBLCDS strings are allowed - anything else will | |
| 52 | * not retrieve emblxml | |
| 53 | * @param query | |
| 54 | * @return | |
| 55 | * @throws Exception | |
| 56 | */ | |
| 57 | 0 | public AlignmentI getEmblSequenceRecords(String emprefx, String query) |
| 58 | throws Exception | |
| 59 | { | |
| 60 | 0 | startQuery(); |
| 61 | 0 | EBIFetchClient dbFetch = new EBIFetchClient(); |
| 62 | 0 | File reply; |
| 63 | 0 | try |
| 64 | { | |
| 65 | 0 | reply = dbFetch.fetchDataAsFile( |
| 66 | emprefx.toLowerCase() + ":" + query.trim(), "display=xml", | |
| 67 | "xml"); | |
| 68 | } catch (Exception e) | |
| 69 | { | |
| 70 | 0 | stopQuery(); |
| 71 | 0 | throw new Exception(MessageManager.formatMessage( |
| 72 | "exception.ebiembl_retrieval_failed_on", new String[] | |
| 73 | { emprefx.toLowerCase(), query.trim() }), e); | |
| 74 | } | |
| 75 | 0 | return getEmblSequenceRecords(emprefx, query, reply); |
| 76 | } | |
| 77 | ||
| 78 | /** | |
| 79 | * parse an emblxml file stored locally | |
| 80 | * | |
| 81 | * @param emprefx | |
| 82 | * either EMBL or EMBLCDS strings are allowed - anything else will | |
| 83 | * not retrieve emblxml | |
| 84 | * @param query | |
| 85 | * @param file | |
| 86 | * the EMBL XML file containing the results of a query | |
| 87 | * @return | |
| 88 | * @throws Exception | |
| 89 | */ | |
| 90 | 0 | public AlignmentI getEmblSequenceRecords(String emprefx, String query, |
| 91 | File reply) throws Exception | |
| 92 | { | |
| 93 | 0 | EmblFile efile = null; |
| 94 | 0 | List<SequenceI> seqs = new ArrayList<>(); |
| 95 | ||
| 96 | 0 | if (reply != null && reply.exists()) |
| 97 | { | |
| 98 | 0 | file = reply.getAbsolutePath(); |
| 99 | 0 | if (reply.length() > EMBL_NOT_FOUND_REPLY.length()) |
| 100 | { | |
| 101 | 0 | efile = EmblFile.getEmblFile(reply); |
| 102 | } | |
| 103 | } | |
| 104 | ||
| 105 | /* | |
| 106 | * invalid accession gets a reply with no <entry> elements, text content of | |
| 107 | * EmbFile reads something like (e.g.) this ungrammatical phrase | |
| 108 | * Entry: <acc> display type is either not supported or entry is not found. | |
| 109 | */ | |
| 110 | 0 | List<SequenceI> peptides = new ArrayList<>(); |
| 111 | 0 | if (efile != null && efile.getEntries() != null) |
| 112 | { | |
| 113 | 0 | for (EmblEntry entry : efile.getEntries()) |
| 114 | { | |
| 115 | 0 | SequenceI seq = entry.getSequence(emprefx, peptides); |
| 116 | 0 | if (seq != null) |
| 117 | { | |
| 118 | 0 | seqs.add(seq.deriveSequence()); |
| 119 | // place DBReferences on dataset and refer | |
| 120 | } | |
| 121 | } | |
| 122 | } | |
| 123 | ||
| 124 | 0 | AlignmentI al = null; |
| 125 | 0 | if (!seqs.isEmpty()) |
| 126 | { | |
| 127 | 0 | al = new Alignment(seqs.toArray(new SequenceI[seqs.size()])); |
| 128 | } | |
| 129 | 0 | stopQuery(); |
| 130 | 0 | return al; |
| 131 | } | |
| 132 | ||
| 133 | 0 | @Override |
| 134 | public boolean isDnaCoding() | |
| 135 | { | |
| 136 | 0 | return true; |
| 137 | } | |
| 138 | ||
| 139 | } |