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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.urls

File CustomUrlProvider.java

 

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42
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1
354
255
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0.43
6.19
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2.69

Classes

Class Line # Actions
CustomUrlProvider 49 99 43 12
0.923566992.4%
 

Contributing tests

This file is covered by 19 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   
22    package jalview.urls;
23   
24    import static jalview.util.UrlConstants.DB_ACCESSION;
25    import static jalview.util.UrlConstants.DELIM;
26    import static jalview.util.UrlConstants.SEP;
27    import static jalview.util.UrlConstants.SEQUENCE_ID;
28   
29    import jalview.util.MessageManager;
30    import jalview.util.UrlConstants;
31    import jalview.util.UrlLink;
32   
33    import java.util.ArrayList;
34    import java.util.HashMap;
35    import java.util.Iterator;
36    import java.util.List;
37    import java.util.Map;
38    import java.util.Map.Entry;
39    import java.util.StringTokenizer;
40   
41    /**
42    *
43    * Implements the UrlProviderI interface for a UrlProvider object which serves
44    * custom URLs defined by the user
45    *
46    * @author $author$
47    * @version $Revision$
48    */
 
49    public class CustomUrlProvider extends UrlProviderImpl
50    {
51    // Default sequence URL link label for SRS
52    private static final String SRS_LABEL = "SRS";
53   
54    // map of string ids to urlLinks (selected)
55    private HashMap<String, UrlLink> selectedUrls;
56   
57    // map of string ids to urlLinks (not selected)
58    private HashMap<String, UrlLink> nonselectedUrls;
59   
60    /**
61    * Construct UrlProvider for custom (user-entered) URLs
62    *
63    * @param inMenuUrlList
64    * list of URLs set to be displayed in menu, in form stored in Cache.
65    * i.e. SEP delimited string
66    * @param storedUrlList
67    * list of custom URLs entered by user but not currently displayed in
68    * menu, in form stored in Cache
69    */
 
70  31 toggle public CustomUrlProvider(String inMenuUrlList, String storedUrlList)
71    {
72  31 try
73    {
74  31 selectedUrls = parseUrlStrings(inMenuUrlList);
75  31 nonselectedUrls = parseUrlStrings(storedUrlList);
76    } catch (Exception ex)
77    {
78  0 System.out
79    .println(ex.getMessage() + "\nError parsing sequence links");
80    }
81    }
82   
83    /**
84    * Construct UrlProvider for custom (user-entered) URLs
85    *
86    * @param urlList
87    * list of URLs to be displayed in menu, as (label,url) pairs
88    * @param storedUrlList
89    * list of custom URLs entered by user but not currently displayed in
90    * menu, as (label,url) pairs
91    */
 
92  2 toggle public CustomUrlProvider(Map<String, String> inMenuUrlList,
93    Map<String, String> storedUrlList)
94    {
95  2 try
96    {
97  2 selectedUrls = parseUrlList(inMenuUrlList);
98  2 nonselectedUrls = parseUrlList(storedUrlList);
99    } catch (Exception ex)
100    {
101  0 System.out
102    .println(ex.getMessage() + "\nError parsing sequence links");
103    }
104    }
105   
 
106  62 toggle private HashMap<String, UrlLink> parseUrlStrings(String urlStrings)
107    {
108    // cachedUrlList is in form <label>|<url>|<label>|<url>...
109    // parse cachedUrlList into labels (used as id) and url links
110  62 HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
111   
112  62 StringTokenizer st = new StringTokenizer(urlStrings, SEP);
113  240 while (st.hasMoreElements())
114    {
115  178 String name = st.nextToken();
116   
117  178 if (!isMiriamId(name))
118    {
119    // this one of our custom urls
120  139 String url = st.nextToken();
121    // check for '|' within a regex
122  139 int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
123  139 if (rxstart == -1)
124    {
125  65 rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
126    }
127  139 while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
128    && st.hasMoreTokens())
129    {
130  0 url = url + SEP + st.nextToken();
131    }
132  139 urls.put(name, new UrlLink(name, url, name));
133    }
134    }
135  62 upgradeOldLinks(urls);
136  62 return urls;
137    }
138   
 
139  4 toggle private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
140    {
141  4 HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
142  4 if (urlList == null)
143    {
144  1 return urls;
145    }
146   
147  3 Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator();
148  11 while (it.hasNext())
149    {
150  8 Map.Entry<String, String> pair = it.next();
151  8 urls.put(pair.getKey(),
152    new UrlLink(pair.getKey(), pair.getValue(), pair.getKey()));
153    }
154  3 upgradeOldLinks(urls);
155  3 return urls;
156    }
157   
158    /*
159    * Upgrade any legacy links which may have been left lying around
160    */
 
161  65 toggle private void upgradeOldLinks(HashMap<String, UrlLink> urls)
162    {
163  65 boolean upgrade = false;
164    // upgrade old SRS link
165  65 if (urls.containsKey(SRS_LABEL))
166    {
167  12 urls.remove(SRS_LABEL);
168  12 upgrade = true;
169    }
170    // upgrade old EBI link - easier just to remove and re-add than faffing
171    // around checking exact url
172  65 if (urls.containsKey(UrlConstants.DEFAULT_LABEL))
173    {
174    // note because this is called separately for selected and nonselected
175    // urls, the default url will not always be present
176  3 urls.remove(UrlConstants.DEFAULT_LABEL);
177  3 upgrade = true;
178    }
179  65 if (upgrade)
180    {
181  15 UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
182  15 link.setLabel(UrlConstants.DEFAULT_LABEL);
183  15 urls.put(UrlConstants.DEFAULT_LABEL, link);
184    }
185    }
186   
 
187  19 toggle @Override
188    public List<String> getLinksForMenu()
189    {
190  19 List<String> links = new ArrayList<String>();
191  19 Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
192    .iterator();
193  80 while (it.hasNext())
194    {
195  61 Map.Entry<String, UrlLink> pair = it.next();
196  61 links.add(pair.getValue().toString());
197    }
198  19 return links;
199    }
200   
 
201  13 toggle @Override
202    public List<UrlLinkDisplay> getLinksForTable()
203    {
204  13 ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
205  13 displayLinks = getLinksForTable(selectedUrls, true);
206  13 displayLinks.addAll(getLinksForTable(nonselectedUrls, false));
207  13 return displayLinks;
208    }
209   
 
210  26 toggle private ArrayList<UrlLinkDisplay> getLinksForTable(
211    HashMap<String, UrlLink> urlList, boolean selected)
212    {
213  26 return super.getLinksForTable(urlList, null, selected);
214    }
215   
 
216  25 toggle @Override
217    public boolean setPrimaryUrl(String id)
218    {
219  25 if (selectedUrls.containsKey(id))
220    {
221  22 primaryUrl = id;
222    }
223  3 else if (nonselectedUrls.containsKey(id))
224    {
225  0 primaryUrl = id;
226    }
227    else
228    {
229  3 primaryUrl = null;
230    }
231   
232  25 return (primaryUrl != null);
233    }
234   
 
235  7 toggle @Override
236    public String writeUrlsAsString(boolean selected)
237    {
238  7 StringBuffer links = new StringBuffer();
239  7 HashMap<String, UrlLink> urls;
240  7 if (selected)
241    {
242  4 urls = selectedUrls;
243    }
244    else
245    {
246  3 urls = nonselectedUrls;
247    }
248  7 if (urls.size() > 0)
249    {
250  7 for (Entry<String, UrlLink> entry : urls.entrySet())
251    {
252  22 links.append(entry.getValue().toString());
253  22 links.append(SEP);
254    }
255   
256    // remove last SEP
257  7 links.setLength(links.length() - 1);
258    }
259    else
260    {
261  0 urls.clear();
262    }
263  7 return links.toString();
264    }
265   
 
266  12 toggle @Override
267    public String getPrimaryUrl(String seqid)
268    {
269  12 String result = super.getPrimaryUrl(seqid, selectedUrls);
270  12 if (result == null)
271    {
272  2 result = super.getPrimaryUrl(seqid, nonselectedUrls);
273    }
274  12 return result;
275    }
276   
 
277  8 toggle @Override
278    public String getPrimaryUrlId()
279    {
280  8 return primaryUrl;
281    }
282   
 
283  0 toggle @Override
284    public String getPrimaryTarget(String seqid)
285    {
286  0 return selectedUrls.get(primaryUrl).getTarget();
287    }
288   
 
289  9 toggle @Override
290    public void setUrlData(List<UrlLinkDisplay> links)
291    {
292  9 HashMap<String, UrlLink> unselurls = new HashMap<String, UrlLink>();
293  9 HashMap<String, UrlLink> selurls = new HashMap<String, UrlLink>();
294   
295  9 Iterator<UrlLinkDisplay> it = links.iterator();
296  99 while (it.hasNext())
297    {
298  90 UrlLinkDisplay link = it.next();
299   
300    // MIRIAM ids will be handled by a different UrlProvider class
301  90 if (!isMiriamId(link.getId()))
302    {
303    // don't allow duplicate key names as entries will be overwritten
304  55 if (unselurls.containsKey(link.getId())
305    || selurls.containsKey(link.getId()))
306    {
307  0 throw new IllegalArgumentException(MessageManager.formatMessage(
308    "exception.url_cannot_have_duplicate_id", link.getId()));
309    }
310  55 if (link.getIsSelected())
311    {
312  37 selurls.put(link.getId(), new UrlLink(link.getDescription(),
313    link.getUrl(), link.getDescription()));
314    }
315    else
316    {
317  18 unselurls.put(link.getId(), new UrlLink(link.getDescription(),
318    link.getUrl(), link.getDescription()));
319    }
320    // sort out primary and selected ids
321  55 if (link.getIsPrimary())
322    {
323  8 setPrimaryUrl(link.getId());
324    }
325    }
326   
327    }
328  9 nonselectedUrls = unselurls;
329  9 selectedUrls = selurls;
330    }
331   
 
332  15 toggle @Override
333    public String choosePrimaryUrl()
334    {
335    // unilaterally set the primary id to the EMBL_EBI link
336  15 if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
337    && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
338    {
339  14 UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
340  14 link.setLabel(UrlConstants.DEFAULT_LABEL);
341  14 selectedUrls.put(UrlConstants.DEFAULT_LABEL, link);
342    }
343  15 primaryUrl = UrlConstants.DEFAULT_LABEL;
344  15 return UrlConstants.DEFAULT_LABEL;
345    }
346   
 
347  26 toggle @Override
348    public boolean contains(String id)
349    {
350  26 return (selectedUrls.containsKey(id)
351    || nonselectedUrls.containsKey(id));
352    }
353   
354    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.