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  1. Project Clover database Wed Sep 17 2025 10:52:37 BST
  2. Package jalview.util

File UrlLink.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

88
150
26
1
687
404
85
0.57
5.77
26
3.27

Classes

Class Line # Actions
47 150 85
0.863636486.4%
 

Contributing tests

This file is covered by 92 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.util;
22   
23    import static jalview.util.UrlConstants.DB_ACCESSION;
24    import static jalview.util.UrlConstants.DELIM;
25    import static jalview.util.UrlConstants.SEP;
26    import static jalview.util.UrlConstants.SEQUENCE_ID;
27   
28    import jalview.datamodel.DBRefEntry;
29    import jalview.datamodel.SequenceI;
30   
31    import java.util.Arrays;
32    import java.util.Collections;
33    import java.util.Comparator;
34    import java.util.List;
35    import java.util.Map;
36    import java.util.Vector;
37   
38    /**
39    * A helper class to parse URL Link strings taken from applet parameters or
40    * jalview properties file using the com.stevesoft.pat.Regex implementation.
41    * Jalview 2.4 extension allows regular expressions to be used to parse ID
42    * strings and replace the result in the URL. Regex's operate on the whole ID
43    * string given to the matchURL method, if no regex is supplied, then only text
44    * following the first pipe symbol will be substituted. Usage documentation
45    * todo.
46    */
 
47    public class UrlLink
48    {
49    private static final String SEQUENCEID_PLACEHOLDER = DELIM + SEQUENCE_ID
50    + DELIM;
51   
52    private static final String ACCESSION_PLACEHOLDER = DELIM + DB_ACCESSION
53    + DELIM;
54   
55    /**
56    * A comparator that puts SEQUENCE_ID template links before DB_ACCESSION
57    * links, and otherwise orders by link name + url (not case sensitive). It
58    * expects to compare strings formatted as "Name|URLTemplate" where the
59    * template may include $SEQUENCE_ID$ or $DB_ACCESSION$ or neither.
60    */
61    public static final Comparator<String> LINK_COMPARATOR = new Comparator<String>()
62    {
 
63  118 toggle @Override
64    public int compare(String link1, String link2)
65    {
66  118 if (link1 == null || link2 == null)
67    {
68  3 return 0; // for failsafe only
69    }
70  115 if (link1.contains(SEQUENCEID_PLACEHOLDER)
71    && link2.contains(ACCESSION_PLACEHOLDER))
72    {
73  24 return -1;
74    }
75  91 if (link2.contains(SEQUENCEID_PLACEHOLDER)
76    && link1.contains(ACCESSION_PLACEHOLDER))
77    {
78  45 return 1;
79    }
80  46 return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
81    }
82    };
83   
84    private static final String EQUALS = "=";
85   
86    private static final String SPACE = " ";
87   
88    private String urlSuffix;
89   
90    private String urlPrefix;
91   
92    private String target;
93   
94    private String label;
95   
96    private String dbname;
97   
98    private String regexReplace;
99   
100    private boolean dynamic = false;
101   
102    private boolean usesDBaccession = false;
103   
104    private String invalidMessage = null;
105   
106    /**
107    * parse the given linkString of the form '<label>SEP<url>' into parts url may
108    * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
109    * must be of the form =/<perl style regex>/=$
110    *
111    * @param link
112    */
 
113  16623 toggle public UrlLink(String link)
114    {
115  16623 int sep = link.indexOf(SEP);
116  16623 int psqid = link.indexOf(DELIM + DB_ACCESSION);
117  16623 int nsqid = link.indexOf(DELIM + SEQUENCE_ID);
118  16623 if (psqid > -1)
119    {
120  16440 dynamic = true;
121  16440 usesDBaccession = true;
122   
123  16440 sep = parseLabel(sep, psqid, link);
124   
125  16440 int endOfRegex = parseUrl(link, DB_ACCESSION, psqid, sep);
126  16440 parseTarget(link, sep, endOfRegex);
127    }
128  183 else if (nsqid > -1)
129    {
130  172 dynamic = true;
131  172 sep = parseLabel(sep, nsqid, link);
132   
133  172 int endOfRegex = parseUrl(link, SEQUENCE_ID, nsqid, sep);
134   
135  172 parseTarget(link, sep, endOfRegex);
136    }
137    else
138    {
139  11 label = link.substring(0, sep).trim();
140   
141    // if there's a third element in the url link string
142    // it is the target name, otherwise target=label
143  11 int lastsep = link.lastIndexOf(SEP);
144  11 if (lastsep != sep)
145    {
146  8 urlPrefix = link.substring(sep + 1, lastsep).trim();
147  8 target = link.substring(lastsep + 1).trim();
148    }
149    else
150    {
151  3 urlPrefix = link.substring(sep + 1).trim();
152  3 target = label;
153    }
154   
155  11 regexReplace = null; // implies we trim any prefix if necessary //
156  11 urlSuffix = null;
157    }
158   
159  16623 label = label.trim();
160  16623 target = target.trim();
161    }
162   
163    /**
164    * Alternative constructor for separate name, link and description
165    *
166    * @param name
167    * The string used to match the link to a DB reference id
168    * @param url
169    * The url to link to
170    * @param desc
171    * The description of the associated target DB
172    */
 
173  16476 toggle public UrlLink(String name, String url, String desc)
174    {
175  16476 this(name + SEP + url + SEP + desc);
176    }
177   
178    /**
179    * @return the url_suffix
180    */
 
181  5 toggle public String getUrlSuffix()
182    {
183  5 return urlSuffix;
184    }
185   
186    /**
187    * @return the url_prefix
188    */
 
189  15 toggle public String getUrlPrefix()
190    {
191  15 return urlPrefix;
192    }
193   
194    /**
195    * @return the target
196    */
 
197  32 toggle public String getTarget()
198    {
199  32 return target;
200    }
201   
202    /**
203    * @return the label
204    */
 
205  135 toggle public String getLabel()
206    {
207  135 return label;
208    }
209   
 
210  374 toggle public String getUrlWithToken()
211    {
212  374 String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
213   
214  374 return urlPrefix
215  374 + (dynamic
216    ? (DELIM + var
217  363 + ((regexReplace != null)
218    ? EQUALS + regexReplace + EQUALS + DELIM
219    : DELIM))
220    : "")
221  374 + ((urlSuffix == null) ? "" : urlSuffix);
222    }
223   
224    /**
225    * @return the regexReplace
226    */
 
227  80 toggle public String getRegexReplace()
228    {
229  80 return regexReplace;
230    }
231   
232    /**
233    * @return the invalidMessage
234    */
 
235  13 toggle public String getInvalidMessage()
236    {
237  13 return invalidMessage;
238    }
239   
240    /**
241    * Check if URL string was parsed properly.
242    *
243    * @return boolean - if false then <code>getInvalidMessage</code> returns an
244    * error message
245    */
 
246  104 toggle public boolean isValid()
247    {
248  104 return invalidMessage == null;
249    }
250   
251    /**
252    *
253    * @return whether link is dynamic
254    */
 
255  6 toggle public boolean isDynamic()
256    {
257  6 return dynamic;
258    }
259   
260    /**
261    *
262    * @return whether link uses DB Accession id
263    */
 
264  136 toggle public boolean usesDBAccession()
265    {
266  136 return usesDBaccession;
267    }
268   
269    /**
270    * Set the label
271    *
272    * @param newlabel
273    */
 
274  44 toggle public void setLabel(String newlabel)
275    {
276  44 this.label = newlabel;
277    }
278   
279    /**
280    * Set the target
281    *
282    * @param desc
283    */
 
284  6 toggle public void setTarget(String desc)
285    {
286  6 target = desc;
287    }
288   
289    /**
290    * return one or more URL strings by applying regex to the given idstring
291    *
292    * @param idstring
293    * @param onlyIfMatches
294    * - when true url strings are only made if regex is defined and
295    * matches
296    * @return String[] { part of idstring substituted, full substituted url , ..
297    * next part, next url..}
298    */
 
299  55 toggle public String[] makeUrls(String idstring, boolean onlyIfMatches)
300    {
301  55 if (dynamic)
302    {
303  55 if (regexReplace != null)
304    {
305  8 com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
306    .perlCode("/" + regexReplace + "/");
307  8 if (rg.search(idstring))
308    {
309  6 int ns = rg.numSubs();
310  6 if (ns == 0)
311    {
312    // take whole regex
313  0 return new String[] { rg.stringMatched(),
314    urlPrefix + rg.stringMatched() + urlSuffix };
315    } /*
316    * else if (ns==1) { // take only subgroup match return new String[]
317    * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
318    * }; }
319    */
320    else
321    {
322    // debug
323  24 for (int s = 0; s <= rg.numSubs(); s++)
324    {
325  18 jalview.bin.Console.errPrintln("Sub " + s + " : "
326    + rg.matchedFrom(s) + " : " + rg.matchedTo(s) + " : '"
327    + rg.stringMatched(s) + "'");
328    }
329    // try to collate subgroup matches
330  6 Vector<String> subs = new Vector<>();
331    // have to loop through submatches, collating them at top level
332    // match
333  6 int s = 0; // 1;
334  24 while (s <= ns)
335    {
336  18 if (s + 1 <= ns && rg.matchedTo(s) > -1
337    && rg.matchedTo(s + 1) > -1
338    && rg.matchedTo(s + 1) < rg.matchedTo(s))
339    {
340    // s is top level submatch. search for submatches enclosed by
341    // this one
342  0 int r = s + 1;
343  0 String mtch = "";
344  0 while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
345    {
346  0 if (rg.matchedFrom(r) > -1)
347    {
348  0 mtch += rg.stringMatched(r);
349    }
350  0 r++;
351    }
352  0 if (mtch.length() > 0)
353    {
354  0 subs.addElement(mtch);
355  0 subs.addElement(urlPrefix + mtch + urlSuffix);
356    }
357  0 s = r;
358    }
359    else
360    {
361  18 if (rg.matchedFrom(s) > -1)
362    {
363  6 subs.addElement(rg.stringMatched(s));
364  6 subs.addElement(
365    urlPrefix + rg.stringMatched(s) + urlSuffix);
366    }
367  18 s++;
368    }
369    }
370   
371  6 String[] res = new String[subs.size()];
372  18 for (int r = 0, rs = subs.size(); r < rs; r++)
373    {
374  12 res[r] = subs.elementAt(r);
375    }
376  6 subs.removeAllElements();
377  6 return res;
378    }
379    }
380  2 if (onlyIfMatches)
381    {
382  1 return null;
383    }
384    }
385    /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
386  48 if (idstring.indexOf(SEP) > -1)
387    {
388  0 idstring = idstring.substring(idstring.lastIndexOf(SEP) + 1);
389    }
390   
391    // just return simple url substitution.
392  48 return new String[] { idstring, urlPrefix + idstring + urlSuffix };
393    }
394    else
395    {
396  0 return new String[] { "", urlPrefix };
397    }
398    }
399   
 
400  288 toggle @Override
401    public String toString()
402    {
403  288 return label + SEP + getUrlWithToken();
404    }
405   
406    /**
407    * @return delimited string containing label, url and target
408    */
 
409  17 toggle public String toStringWithTarget()
410    {
411  17 return label + SEP + getUrlWithToken() + SEP + target;
412    }
413   
414    /**
415    * Parse the label from the link string
416    *
417    * @param firstSep
418    * Location of first occurrence of separator in link string
419    * @param psqid
420    * Position of sequence id or name in link string
421    * @param link
422    * Link string containing database name and url
423    * @return Position of last separator symbol prior to any regex symbols
424    */
 
425  16612 toggle protected int parseLabel(int firstSep, int psqid, String link)
426    {
427  16612 int p = firstSep;
428  16612 int sep = firstSep;
429  16612 do
430    {
431  16612 sep = p;
432  16612 p = link.indexOf(SEP, sep + 1);
433  16612 } while (p > sep && p < psqid);
434    // Assuming that the URL itself does not contain any SEP symbols
435    // sep now contains last pipe symbol position prior to any regex symbols
436  16612 label = link.substring(0, sep);
437   
438  16612 return sep;
439    }
440   
441    /**
442    * Parse the target from the link string
443    *
444    * @param link
445    * Link string containing database name and url
446    * @param sep
447    * Location of first separator symbol
448    * @param endOfRegex
449    * Location of end of any regular expression in link string
450    */
 
451  16612 toggle protected void parseTarget(String link, int sep, int endOfRegex)
452    {
453  16612 int lastsep = link.lastIndexOf(SEP);
454   
455  16612 if ((lastsep != sep) && (lastsep > endOfRegex))
456    {
457    // final element in link string is the target
458  16469 target = link.substring(lastsep + 1).trim();
459    }
460    else
461    {
462  143 target = label;
463    }
464   
465  16612 if (target.indexOf(SEP) > -1)
466    {
467    // SEP terminated database name / www target at start of Label
468  0 target = target.substring(0, target.indexOf(SEP));
469    }
470  16612 else if (target.indexOf(SPACE) > 2)
471    {
472    // space separated label - first word matches database name
473  94 target = target.substring(0, target.indexOf(SPACE));
474    }
475    }
476   
477    /**
478    * Parse the URL part of the link string
479    *
480    * @param link
481    * Link string containing database name and url
482    * @param varName
483    * Name of variable in url string (e.g. SEQUENCE_ID, SEQUENCE_NAME)
484    * @param sqidPos
485    * Position of id or name in link string
486    * @param sep
487    * Position of separator in link string
488    * @return Location of end of any regex in link string
489    */
 
490  16612 toggle protected int parseUrl(String link, String varName, int sqidPos, int sep)
491    {
492  16612 urlPrefix = link.substring(sep + 1, sqidPos).trim();
493   
494    // delimiter at start of regex: e.g. $SEQUENCE_ID=/
495  16612 String startDelimiter = DELIM + varName + "=/";
496   
497    // delimiter at end of regex: /=$
498  16612 String endDelimiter = "/=" + DELIM;
499   
500  16612 int startLength = startDelimiter.length();
501   
502    // Parse URL : Whole URL string first
503  16612 int p = link.indexOf(endDelimiter, sqidPos + startLength);
504   
505  16612 if (link.indexOf(startDelimiter) == sqidPos
506    && (p > sqidPos + startLength))
507    {
508    // Extract Regex and suffix
509  4 urlSuffix = link.substring(p + endDelimiter.length());
510  4 regexReplace = link.substring(sqidPos + startLength, p);
511  4 try
512    {
513  4 com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
514    .perlCode("/" + regexReplace + "/");
515  4 if (rg == null)
516    {
517  1 invalidMessage = "Invalid Regular Expression : '" + regexReplace
518    + "'\n";
519    }
520    } catch (Exception e)
521    {
522  0 invalidMessage = "Invalid Regular Expression : '" + regexReplace
523    + "'\n";
524    }
525    }
526    else
527    {
528    // no regex
529  16608 regexReplace = null;
530    // verify format is really correct.
531  16608 if (link.indexOf(DELIM + varName + DELIM) == sqidPos)
532    {
533  16605 int lastsep = link.lastIndexOf(SEP);
534  16605 if (lastsep < sqidPos + startLength - 1)
535    {
536    // the last SEP character was before the regex, ignore
537  139 lastsep = link.length();
538    }
539  16605 urlSuffix = link.substring(sqidPos + startLength - 1, lastsep)
540    .trim();
541  16605 regexReplace = null;
542    }
543    else
544    {
545  3 invalidMessage = "Warning: invalid regex structure for URL link : "
546    + link;
547    }
548    }
549   
550  16612 return p;
551    }
552   
553    /**
554    * Create a set of URL links for a sequence
555    *
556    * @param seq
557    * The sequence to create links for
558    * @param linkset
559    * Map of links: key = id + SEP + link, value = [target, label, id,
560    * link]
561    */
 
562  97 toggle public void createLinksFromSeq(final SequenceI seq,
563    Map<String, List<String>> linkset)
564    {
565  97 if (seq != null && dynamic)
566    {
567  94 createDynamicLinks(seq, linkset);
568    }
569    else
570    {
571  3 createStaticLink(linkset);
572    }
573    }
574   
575    /**
576    * Create a static URL link
577    *
578    * @param linkset
579    * Map of links: key = id + SEP + link, value = [target, label, id,
580    * link]
581    */
 
582  3 toggle protected void createStaticLink(Map<String, List<String>> linkset)
583    {
584  3 if (!linkset.containsKey(label + SEP + getUrlPrefix()))
585    {
586    // Add a non-dynamic link
587  3 linkset.put(label + SEP + getUrlPrefix(),
588    Arrays.asList(target, label, null, getUrlPrefix()));
589    }
590    }
591   
592    /**
593    * Create dynamic URL links
594    *
595    * @param seq
596    * The sequence to create links for
597    * @param linkset
598    * Map of links: key = id + SEP + link, value = [target, label, id,
599    * link]
600    */
 
601  94 toggle protected void createDynamicLinks(final SequenceI seq,
602    Map<String, List<String>> linkset)
603    {
604    // collect id string too
605  94 String id = seq.getName();
606  94 String descr = seq.getDescription();
607  94 if (descr != null && descr.length() < 1)
608    {
609  0 descr = null;
610    }
611   
612  94 if (usesDBAccession()) // link is ID
613    {
614    // collect matching db-refs
615  70 List<DBRefEntry> dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
616    new String[]
617    { target });
618   
619    // if there are any dbrefs which match up with the link
620  70 if (dbr != null)
621    {
622  16 for (int r = 0, nd = dbr.size(); r < nd; r++)
623    {
624    // create Bare ID link for this URL
625  10 createBareURLLink(dbr.get(r).getAccessionId(), true, linkset);
626    }
627    }
628    }
629  24 else if (!usesDBAccession() && id != null) // link is name
630    {
631    // create Bare ID link for this URL
632  24 createBareURLLink(id, false, linkset);
633    }
634   
635    // Create urls from description but only for URL links which are regex
636    // links
637  94 if (descr != null && getRegexReplace() != null)
638    {
639    // create link for this URL from description where regex matches
640  0 createBareURLLink(descr, false, linkset);
641    }
642    }
643   
644    /*
645    * Create a bare URL Link
646    * Returns map where key = id + SEP + link, and value = [target, label, id, link]
647    */
 
648  34 toggle protected void createBareURLLink(String id, Boolean combineLabel,
649    Map<String, List<String>> linkset)
650    {
651  34 String[] urls = makeUrls(id, true);
652  34 if (urls != null)
653    {
654  68 for (int u = 0; u < urls.length; u += 2)
655    {
656  34 if (!linkset.containsKey(urls[u] + SEP + urls[u + 1]))
657    {
658  34 String thisLabel = label;
659  34 if (combineLabel)
660    {
661    // incorporate label with idstring
662  10 thisLabel = label + SEP + urls[u];
663    }
664   
665  34 linkset.put(urls[u] + SEP + urls[u + 1],
666    Arrays.asList(target, thisLabel, urls[u], urls[u + 1]));
667    }
668    }
669    }
670    }
671   
672    /**
673    * Sorts links (formatted as LinkName|LinkPattern) suitable for display in a
674    * menu
675    * <ul>
676    * <li>SEQUENCE_ID links precede DB_ACCESSION links (i.e. canonical lookup
677    * before cross-references)</li>
678    * <li>otherwise by Link name (case insensitive)</li>
679    * </ul>
680    *
681    * @param nlinks
682    */
 
683  23 toggle public static void sort(List<String> nlinks)
684    {
685  23 Collections.sort(nlinks, LINK_COMPARATOR);
686    }
687    }
  • Report generated by OpenClover v 4.4.1 on Wed Sep 17 2025 11:01:30 BST using coverage data from Wed Sep 17 2025 11:01:17 BST.
  • OpenClover is free and open-source software.