Coverage Report
File UrlProviderImpl.java
Coverage histogram
12% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| UrlProviderImpl | 39 | 26 | 12 |
Contributing tests
This file is covered by 19 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.urls; | |
| 22 | ||
| 23 | import jalview.urls.api.UrlProviderI; | |
| 24 | import jalview.util.UrlLink; | |
| 25 | ||
| 26 | import java.util.ArrayList; | |
| 27 | import java.util.HashMap; | |
| 28 | import java.util.List; | |
| 29 | import java.util.Map.Entry; | |
| 30 | import java.util.regex.Pattern; | |
| 31 | ||
| 32 | /** | |
| 33 | * Leaf node of UrlProvider composite | |
| 34 | * | |
| 35 | * @author $author$ | |
| 36 | * @version $Revision$ | |
| 37 | */ | |
| 38 | ||
| 39 | public abstract class UrlProviderImpl implements UrlProviderI | |
| 40 | { | |
| 41 | // minimum length of substitution in url link string | |
| 42 | protected static final int MIN_SUBST_LENGTH = 4; | |
| 43 | ||
| 44 | private static final Pattern MIRIAM_PATTERN = Pattern | |
| 45 | .compile("^MIR:\\d{8}$"); | |
| 46 | ||
| 47 | protected String primaryUrl; | |
| 48 | ||
| 49 | 21 |  protected String getPrimaryUrl(String seqid, |
| 50 | HashMap<String, UrlLink> urls) | |
| 51 | { | |
| 52 | 21 | if (seqid.length() < MIN_SUBST_LENGTH) |
| 53 | { | |
| 54 | 3 | return null; |
| 55 | } | |
| 56 | 18 | else if (primaryUrl == null) |
| 57 | { | |
| 58 | 7 | return null; |
| 59 | } | |
| 60 | 11 | else if (!urls.containsKey(primaryUrl)) |
| 61 | { | |
| 62 | 0 | return null; |
| 63 | } | |
| 64 | else | |
| 65 | { | |
| 66 | 11 | String url = null; |
| 67 | 11 | UrlLink urlLink = urls.get(primaryUrl); |
| 68 | 11 | String[] primaryUrls = urlLink.makeUrls(seqid, true); |
| 69 | 11 | if (primaryUrls == null || primaryUrls[0] == null |
| 70 | || primaryUrls[0].length() < MIN_SUBST_LENGTH) | |
| 71 | { | |
| 72 | 0 | url = null; |
| 73 | } | |
| 74 | else | |
| 75 | { | |
| 76 | // just take first URL made from regex | |
| 77 | 11 | url = primaryUrls[1]; |
| 78 | } | |
| 79 | 11 | return url; |
| 80 | } | |
| 81 | } | |
| 82 | ||
| 83 | 0 | @Override |
| 84 | public List<UrlLinkDisplay> getLinksForTable() | |
| 85 | { | |
| 86 | 0 | return null; |
| 87 | } | |
| 88 | ||
| 89 | 65 | protected ArrayList<UrlLinkDisplay> getLinksForTable( |
| 90 | HashMap<String, UrlLink> urls, ArrayList<String> selectedUrls, | |
| 91 | boolean selected) | |
| 92 | { | |
| 93 | 65 | ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>(); |
| 94 | 65 | for (Entry<String, UrlLink> entry : urls.entrySet()) |
| 95 | { | |
| 96 | 6349 | String key = entry.getKey(); |
| 97 | 6349 | boolean isPrimary = (key.equals(primaryUrl)); |
| 98 | 6349 | boolean isSelected; |
| 99 | 6349 | if (selectedUrls != null) |
| 100 | { | |
| 101 | 6274 | isSelected = selectedUrls.contains(key); |
| 102 | } | |
| 103 | else | |
| 104 | { | |
| 105 | 75 | isSelected = selected; |
| 106 | } | |
| 107 | 6349 | displayLinks.add(new UrlLinkDisplay(key, entry.getValue(), isSelected, |
| 108 | isPrimary)); | |
| 109 | } | |
| 110 | 65 | return displayLinks; |
| 111 | } | |
| 112 | ||
| 113 | 662 | protected boolean isMiriamId(String id) |
| 114 | { | |
| 115 | 662 | return MIRIAM_PATTERN.matcher(id).matches(); |
| 116 | } | |
| 117 | ||
| 118 | 20 | @Override |
| 119 | public boolean isUserEntry(String id) | |
| 120 | { | |
| 121 | 20 | return !isMiriamId(id); |
| 122 | } | |
| 123 | } |