Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
EmblFlatfileSource | 45 | 29 | 16 |
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 java.util.Locale; | |
24 | ||
25 | import java.io.File; | |
26 | import java.io.IOException; | |
27 | ||
28 | import com.stevesoft.pat.Regex; | |
29 | ||
30 | import jalview.bin.Console; | |
31 | import jalview.datamodel.Alignment; | |
32 | import jalview.datamodel.AlignmentI; | |
33 | import jalview.datamodel.SequenceI; | |
34 | import jalview.io.DataSourceType; | |
35 | import jalview.io.EmblFlatFile; | |
36 | import jalview.io.FileParse; | |
37 | import jalview.ws.ebi.EBIFetchClient; | |
38 | ||
39 | /** | |
40 | * A class that does partial parsing of an EMBL flatfile. | |
41 | * | |
42 | * @author gmcarstairs | |
43 | * | |
44 | */ | |
45 | public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy | |
46 | { | |
47 | private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+"); | |
48 | ||
49 | 0 | @Override |
50 | public String getDbVersion() | |
51 | { | |
52 | 0 | return "0"; |
53 | } | |
54 | ||
55 | 0 | @Override |
56 | public String getAccessionSeparator() | |
57 | { | |
58 | 0 | return null; |
59 | } | |
60 | ||
61 | 0 | @Override |
62 | public Regex getAccessionValidator() | |
63 | { | |
64 | 0 | return ACCESSION_REGEX; |
65 | } | |
66 | ||
67 | 0 | @Override |
68 | public boolean isValidReference(String accession) | |
69 | { | |
70 | 0 | if (accession == null || accession.length() < 2) |
71 | { | |
72 | 0 | return false; |
73 | } | |
74 | 0 | return getAccessionValidator().search(accession); |
75 | } | |
76 | ||
77 | 0 | @Override |
78 | public AlignmentI getSequenceRecords(String queries) throws Exception | |
79 | { | |
80 | 0 | return null; |
81 | } | |
82 | ||
83 | 0 | @Override |
84 | public int getTier() | |
85 | { | |
86 | 0 | return 0; |
87 | } | |
88 | ||
89 | 0 | protected AlignmentI getEmblSequenceRecords(String dbName, String query) |
90 | throws Exception | |
91 | { | |
92 | 0 | startQuery(); |
93 | 0 | EBIFetchClient dbFetch = new EBIFetchClient(); |
94 | 0 | File reply; |
95 | 0 | try |
96 | { | |
97 | 0 | reply = dbFetch.fetchDataAsFile( |
98 | dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, | |
99 | "gz"); | |
100 | } catch (Exception e) | |
101 | { | |
102 | 0 | stopQuery(); |
103 | 0 | throw new Exception( |
104 | String.format("EBI EMBL retrieval failed for %s:%s", | |
105 | dbName.toLowerCase(Locale.ROOT), query.trim()), | |
106 | e); | |
107 | } | |
108 | 0 | return getEmblSequenceRecords(dbName, query, reply); |
109 | } | |
110 | ||
111 | 0 | private AlignmentI getEmblSequenceRecords(String dbName, String query, |
112 | File reply) throws IOException | |
113 | { | |
114 | 0 | AlignmentI al = null; |
115 | ||
116 | 0 | if (reply != null && reply.exists()) |
117 | { | |
118 | 0 | file = reply.getAbsolutePath(); |
119 | 0 | FileParse fp = new FileParse(file, DataSourceType.FILE); |
120 | 0 | EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource()); |
121 | 0 | SequenceI[] seqs = emblParser.getSeqsAsArray(); |
122 | 0 | if (seqs.length > 0) |
123 | { | |
124 | 0 | al = new Alignment(seqs); |
125 | } | |
126 | ||
127 | 0 | if (al == null) |
128 | { | |
129 | 0 | Console.error("No record found for '" + dbName + ":" + query + "'"); |
130 | } | |
131 | } | |
132 | ||
133 | 0 | stopQuery(); |
134 | 0 | return al; |
135 | } | |
136 | ||
137 | 0 | @Override |
138 | public boolean isDnaCoding() | |
139 | { | |
140 | 0 | return true; |
141 | } | |
142 | } |