Coverage Report
File Pfam.java
Coverage histogram
43% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| Pfam | 39 | 13 | 10 |
Contributing tests
This file is covered by 8 tests.
.
Source view
| 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 | } |