jalviewX
File Pfam.java
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47% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Pfam | 36 | 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 | * TODO: later PFAM is a complex datasource - it could return a tree in addition | |
| 30 | * to an alignment TODO: create interface to pass alignment properties and tree | |
| 31 | * back to sequence fetcher | |
| 32 | * | |
| 33 | * @author JimP | |
| 34 | * | |
| 35 | */ | |
| 36 | abstract public class Pfam extends Xfam | |
| 37 | { | |
| 38 | static final String PFAM_BASEURL_KEY = "PFAM_BASEURL"; | |
| 39 | ||
| 40 | private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org"; | |
| 41 | ||
| 42 | 16 |  public Pfam() |
| 43 | { | |
| 44 | 16 | super(); |
| 45 | } | |
| 46 | ||
| 47 | /* | |
| 48 | * (non-Javadoc) | |
| 49 | * | |
| 50 | * @see jalview.ws.DbSourceProxy#getAccessionSeparator() | |
| 51 | */ | |
| 52 | 0 | @Override |
| 53 | public String getAccessionSeparator() | |
| 54 | { | |
| 55 | 0 | return null; |
| 56 | } | |
| 57 | ||
| 58 | /* | |
| 59 | * (non-Javadoc) | |
| 60 | * | |
| 61 | * @see jalview.ws.DbSourceProxy#getAccessionValidator() | |
| 62 | */ | |
| 63 | 0 | @Override |
| 64 | public Regex getAccessionValidator() | |
| 65 | { | |
| 66 | 0 | return null; |
| 67 | } | |
| 68 | ||
| 69 | /* | |
| 70 | * (non-Javadoc) | |
| 71 | * | |
| 72 | * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { * | |
| 73 | * this doesn't work - DbSource is key for the hash of DbSourceProxy instances | |
| 74 | * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an | |
| 75 | * 'alignment' source - means proxy is higher level than a sequence source. | |
| 76 | * return jalview.datamodel.DBRefSource.PFAM; } | |
| 77 | */ | |
| 78 | ||
| 79 | /* | |
| 80 | * (non-Javadoc) | |
| 81 | * | |
| 82 | * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable | |
| 83 | * getDbSourceProperties() { | |
| 84 | * | |
| 85 | * return null; } | |
| 86 | */ | |
| 87 | ||
| 88 | /* | |
| 89 | * (non-Javadoc) | |
| 90 | * | |
| 91 | * @see jalview.ws.DbSourceProxy#getDbVersion() | |
| 92 | */ | |
| 93 | 0 | @Override |
| 94 | public String getDbVersion() | |
| 95 | { | |
| 96 | 0 | return null; |
| 97 | } | |
| 98 | ||
| 99 | 4 | @Override |
| 100 | protected String getURLPrefix() | |
| 101 | { | |
| 102 | 4 | return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL); |
| 103 | } | |
| 104 | ||
| 105 | /* | |
| 106 | * (non-Javadoc) | |
| 107 | * | |
| 108 | * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String) | |
| 109 | */ | |
| 110 | 0 | @Override |
| 111 | public boolean isValidReference(String accession) | |
| 112 | { | |
| 113 | 0 | return accession.indexOf("PF") == 0; |
| 114 | } | |
| 115 | ||
| 116 | /* | |
| 117 | * public String getDbName() { return "PFAM"; // getDbSource(); } | |
| 118 | */ | |
| 119 | ||
| 120 | 0 | @Override |
| 121 | public String getXfamSource() | |
| 122 | { | |
| 123 | 0 | return DBRefSource.PFAM; |
| 124 | } | |
| 125 | ||
| 126 | } |