jalviewX
File Rfam.java
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47% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Rfam | 33 | 7 | 7 | 10 |
Contributing tests
This file is covered by 6 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.bin.Cache; | |
| 24 | import jalview.datamodel.DBRefSource; | |
| 25 | ||
| 26 | import com.stevesoft.pat.Regex; | |
| 27 | ||
| 28 | /** | |
| 29 | * Contains methods for fetching sequences from Rfam database | |
| 30 | * | |
| 31 | * @author Lauren Michelle Lui | |
| 32 | */ | |
| 33 | abstract public class Rfam extends Xfam | |
| 34 | { | |
| 35 | static final String RFAM_BASEURL_KEY = "RFAM_BASEURL"; | |
| 36 | ||
| 37 | private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org"; | |
| 38 | ||
| 39 | 4 |  @Override |
| 40 | protected String getURLPrefix() | |
| 41 | { | |
| 42 | 4 | return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL); |
| 43 | } | |
| 44 | ||
| 45 | 10 | public Rfam() |
| 46 | { | |
| 47 | 10 | super(); |
| 48 | } | |
| 49 | ||
| 50 | /* | |
| 51 | * (non-Javadoc) | |
| 52 | * | |
| 53 | * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for | |
| 54 | * consistency with Pfam class | |
| 55 | */ | |
| 56 | 0 | @Override |
| 57 | public String getAccessionSeparator() | |
| 58 | { | |
| 59 | 0 | return null; |
| 60 | } | |
| 61 | ||
| 62 | /* | |
| 63 | * (non-Javadoc) | |
| 64 | * | |
| 65 | * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for | |
| 66 | */ | |
| 67 | 0 | @Override |
| 68 | public Regex getAccessionValidator() | |
| 69 | { | |
| 70 | 0 | return null; |
| 71 | } | |
| 72 | ||
| 73 | /* | |
| 74 | * (non-Javadoc) | |
| 75 | * | |
| 76 | * Left here for consistency with Pfam class | |
| 77 | * | |
| 78 | * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { * | |
| 79 | * this doesn't work - DbSource is key for the hash of DbSourceProxy instances | |
| 80 | * - 1:many mapping for DbSource to proxy will be lost. * suggest : RFAM is an | |
| 81 | * 'alignment' source - means proxy is higher level than a sequence source. | |
| 82 | * return jalview.datamodel.DBRefSource.RFAM; } | |
| 83 | */ | |
| 84 | ||
| 85 | /* | |
| 86 | * (non-Javadoc) | |
| 87 | * | |
| 88 | * @see jalview.ws.DbSourceProxy#getDbVersion() | |
| 89 | */ | |
| 90 | 0 | @Override |
| 91 | public String getDbVersion() | |
| 92 | { | |
| 93 | 0 | return null; |
| 94 | } | |
| 95 | ||
| 96 | /* | |
| 97 | * (non-Javadoc) | |
| 98 | * | |
| 99 | * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) | |
| 100 | */ | |
| 101 | 0 | @Override |
| 102 | public boolean isValidReference(String accession) | |
| 103 | { | |
| 104 | 0 | return accession.indexOf("RF") == 0; |
| 105 | } | |
| 106 | ||
| 107 | /* | |
| 108 | * (non-Javadoc) | |
| 109 | * | |
| 110 | * @see jalview.ws.dbsources.Xfam#getXfamSource() | |
| 111 | */ | |
| 112 | 0 | @Override |
| 113 | public String getXfamSource() | |
| 114 | { | |
| 115 | 0 | return DBRefSource.RFAM; |
| 116 | } | |
| 117 | ||
| 118 | } |