Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
Pfam | 39 | 13 | 10 |
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 com.stevesoft.pat.Regex; | |
26 | ||
27 | import jalview.bin.Cache; | |
28 | import jalview.datamodel.DBRefSource; | |
29 | import jalview.util.Platform; | |
30 | ||
31 | /** | |
32 | * TODO: later PFAM is a complex datasource - it could return a tree in addition | |
33 | * to an alignment TODO: create interface to pass alignment properties and tree | |
34 | * back to sequence fetcher | |
35 | * | |
36 | * @author JimP | |
37 | * | |
38 | */ | |
39 | abstract public class Pfam extends Xfam | |
40 | { | |
41 | public static final String FULL = "full", RP35 = "rp35", RP15 = "rp15", | |
42 | RP75 = "rp75", RP55 = "rp55", SEED = "seed", UNIPROT = "uniprot"; | |
43 | ||
44 | 4 | public String getPfamDownloadURL(String id, String alType) |
45 | { | |
46 | 4 | String url = Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL); |
47 | 4 | url = url.replace("$PFAMID$", id); |
48 | 4 | url = url.replace("$ALTYPE$", alType); |
49 | 4 | return url; |
50 | } | |
51 | ||
52 | static final String PFAM_BASEURL_KEY = "PFAM_INTERPRO_URL_TEMPLATE"; | |
53 | ||
54 | protected String alignmentType; | |
55 | ||
56 | /** | |
57 | * docs are http://www.ebi.ac.uk/interpro/api/ | |
58 | */ | |
59 | private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$"; | |
60 | ||
61 | 7 | static |
62 | { | |
63 | 7 | Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL); |
64 | } | |
65 | ||
66 | 36 | public Pfam() |
67 | { | |
68 | 36 | super(); |
69 | } | |
70 | ||
71 | 4 | @Override |
72 | String getURL(String queries) | |
73 | { | |
74 | 4 | return getPfamDownloadURL(queries.trim().toUpperCase(Locale.ROOT), |
75 | alignmentType); | |
76 | } | |
77 | ||
78 | /* | |
79 | * (non-Javadoc) | |
80 | * | |
81 | * @see jalview.ws.DbSourceProxy#getAccessionSeparator() | |
82 | */ | |
83 | 0 | @Override |
84 | public String getAccessionSeparator() | |
85 | { | |
86 | 0 | return null; |
87 | } | |
88 | ||
89 | /* | |
90 | * (non-Javadoc) | |
91 | * | |
92 | * @see jalview.ws.DbSourceProxy#getAccessionValidator() | |
93 | */ | |
94 | 0 | @Override |
95 | public Regex getAccessionValidator() | |
96 | { | |
97 | 0 | return null; |
98 | } | |
99 | ||
100 | /* | |
101 | * (non-Javadoc) | |
102 | * | |
103 | * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { * | |
104 | * this doesn't work - DbSource is key for the hash of DbSourceProxy instances | |
105 | * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an | |
106 | * 'alignment' source - means proxy is higher level than a sequence source. | |
107 | * return jalview.datamodel.DBRefSource.PFAM; } | |
108 | */ | |
109 | ||
110 | /* | |
111 | * (non-Javadoc) | |
112 | * | |
113 | * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable | |
114 | * getDbSourceProperties() { | |
115 | * | |
116 | * return null; } | |
117 | */ | |
118 | ||
119 | /* | |
120 | * (non-Javadoc) | |
121 | * | |
122 | * @see jalview.ws.DbSourceProxy#getDbVersion() | |
123 | */ | |
124 | 0 | @Override |
125 | public String getDbVersion() | |
126 | { | |
127 | 0 | return null; |
128 | } | |
129 | ||
130 | 0 | @Override |
131 | protected String getURLPrefix() | |
132 | { | |
133 | 0 | return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL); |
134 | } | |
135 | ||
136 | /* | |
137 | * (non-Javadoc) | |
138 | * | |
139 | * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) | |
140 | */ | |
141 | 0 | @Override |
142 | public boolean isValidReference(String accession) | |
143 | { | |
144 | 0 | return accession.indexOf("PF") == 0; |
145 | } | |
146 | ||
147 | /* | |
148 | * public String getDbName() { return "PFAM"; // getDbSource(); } | |
149 | */ | |
150 | ||
151 | 0 | @Override |
152 | public String getXfamSource() | |
153 | { | |
154 | 0 | return DBRefSource.PFAM; |
155 | } | |
156 | } |