2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import java.util.Vector;
28 * helper class to parse URL Link strings taken from applet parameters or
29 * jalview properties file using the com.stevesoft.pat.Regex implementation.
30 * Jalview 2.4 extension allows regular expressions to be used to parse ID
31 * strings and replace the result in the URL. Regex's operate on the whole ID
32 * string given to the matchURL method, if no regex is supplied, then only
33 * text following the first pipe symbol will be susbstituted. Usage
36 private String url_suffix, url_prefix, target, label, regexReplace;
38 private boolean dynamic = false;
40 private String invalidMessage = null;
43 * parse the given linkString of the form '<label>|<url>' into parts url may
44 * contain a string $SEQUENCE_ID<=optional regex=>$ where <=optional regex=>
45 * must be of the form =/<perl style regex>/=$
49 public UrlLink(String link)
51 int sep = link.indexOf("|"), psqid = link.indexOf("$SEQUENCE_ID");
59 p = link.indexOf("|", sep + 1);
60 } while (p > sep && p < psqid);
61 // Assuming that the URL itself does not contain any '|' symbols
62 // sep now contains last pipe symbol position prior to any regex symbols
63 label = link.substring(0, sep);
64 if (label.indexOf("|") > -1)
66 // | terminated database name / www target at start of Label
67 target = label.substring(0, label.indexOf("|"));
69 else if (label.indexOf(" ") > 2)
71 // space separated Label - matches database name
72 target = label.substring(0, label.indexOf(" "));
78 // Parse URL : Whole URL string first
79 url_prefix = link.substring(sep + 1, psqid);
80 if (link.indexOf("$SEQUENCE_ID=/") == psqid
81 && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
83 // Extract Regex and suffix
84 url_suffix = link.substring(p + 3);
85 regexReplace = link.substring(psqid + 14, p);
88 com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
89 + regexReplace + "/");
92 invalidMessage = "Invalid Regular Expression : '"
93 + regexReplace + "'\n";
97 invalidMessage = "Invalid Regular Expression : '" + regexReplace
104 // verify format is really correct.
105 if (link.indexOf("$SEQUENCE_ID$") == psqid)
107 url_suffix = link.substring(psqid + 13);
112 invalidMessage = "Warning: invalid regex structure for URL link : "
119 target = link.substring(0, sep);
120 label = link.substring(0, sep = link.lastIndexOf("|"));
121 url_prefix = link.substring(sep + 1);
122 regexReplace = null; // implies we trim any prefix if necessary //
123 // regexReplace=".*\\|?(.*)";
129 * @return the url_suffix
131 public String getUrl_suffix()
137 * @return the url_prefix
139 public String getUrl_prefix()
147 public String getTarget()
155 public String getLabel()
161 * @return the regexReplace
163 public String getRegexReplace()
169 * @return the invalidMessage
171 public String getInvalidMessage()
173 return invalidMessage;
177 * Check if URL string was parsed properly.
179 * @return boolean - if false then <code>getInvalidMessage</code> returns an
182 public boolean isValid()
184 return invalidMessage == null;
188 * return one or more URL strings by applying regex to the given idstring
191 * @param onlyIfMatches
192 * - when true url strings are only made if regex is defined and
194 * @return String[] { part of idstring substituted, full substituted url , ..
195 * next part, next url..}
197 public String[] makeUrls(String idstring, boolean onlyIfMatches)
201 if (regexReplace != null)
203 com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
204 + regexReplace + "/");
205 if (rg.search(idstring))
207 int ns = rg.numSubs();
211 return new String[] { rg.stringMatched(),
212 url_prefix + rg.stringMatched() + url_suffix };
214 * else if (ns==1) { // take only subgroup match return new String[]
215 * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
221 for (int s = 0; s <= rg.numSubs(); s++)
223 System.err.println("Sub " + s + " : " + rg.matchedFrom(s)
224 + " : " + rg.matchedTo(s) + " : '"
225 + rg.stringMatched(s) + "'");
227 // try to collate subgroup matches
228 Vector subs = new Vector();
229 // have to loop through submatches, collating them at top level
234 if (s + 1 <= ns && rg.matchedTo(s) > -1
235 && rg.matchedTo(s + 1) > -1
236 && rg.matchedTo(s + 1) < rg.matchedTo(s))
238 // s is top level submatch. search for submatches enclosed by
242 while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
244 if (rg.matchedFrom(r) > -1)
246 mtch += rg.stringMatched(r);
250 if (mtch.length() > 0)
252 subs.addElement(mtch);
253 subs.addElement(url_prefix + mtch + url_suffix);
259 if (rg.matchedFrom(s) > -1)
261 subs.addElement(rg.stringMatched(s));
262 subs.addElement(url_prefix + rg.stringMatched(s)
269 String[] res = new String[subs.size()];
270 for (int r = 0, rs = subs.size(); r < rs; r++)
272 res[r] = (String) subs.elementAt(r);
274 subs.removeAllElements();
283 /* Otherwise - trim off any 'prefix' - pre 2.4 Jalview behaviour */
284 if (idstring.indexOf("|") > -1)
286 idstring = idstring.substring(idstring.lastIndexOf("|") + 1);
289 // just return simple url substitution.
290 return new String[] { idstring, url_prefix + idstring + url_suffix };
294 return new String[] { "", url_prefix };
298 public String toString()
303 + (dynamic ? ("$SEQUENCE_ID" + ((regexReplace != null) ? "="
304 + regexReplace + "=$" : "$")) : "")
305 + ((url_suffix == null) ? "" : url_suffix);
309 private static void testUrls(UrlLink ul, String idstring, String[] urls)
314 System.out.println("Created NO urls.");
318 System.out.println("Created " + (urls.length / 2) + " Urls.");
319 for (int uls = 0; uls < urls.length; uls += 2)
321 System.out.println("URL Replacement text : " + urls[uls]
322 + " : URL : " + urls[uls + 1]);
327 public static void main(String argv[])
329 String[] links = new String[] {
331 * "AlinkT|Target|http://foo.foo.soo/",
332 * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
333 * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo"
335 * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo"
336 * , "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",
337 * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$"
339 * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$"
341 * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
342 * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
344 "NESTED|http://nested/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
345 String[] idstrings = new String[] {
347 * //"LGUL_human", //"QWIQW_123123", "uniprot|why_do+_12313_foo",
348 * //"123123312", "123123 ABCDE foo", "PFAM:PF23943",
350 "Label:gi|9234|pdb|102L|A" };
351 // TODO: test the setLabel method.
352 for (int i = 0; i < links.length; i++)
354 UrlLink ul = new UrlLink(links[i]);
357 System.out.println("\n\n\n");
358 System.out.println("Link " + i + " " + links[i] + " : "
360 System.out.println(" pref : "
365 + ((ul.getRegexReplace() != null) ? ul.getRegexReplace()
367 for (int ids = 0; ids < idstrings.length; ids++)
369 System.out.println("ID String : " + idstrings[ids]
370 + "\nWithout onlyIfMatches:");
371 String[] urls = ul.makeUrls(idstrings[ids], false);
372 testUrls(ul, idstrings[ids], urls);
373 System.out.println("With onlyIfMatches set.");
374 urls = ul.makeUrls(idstrings[ids], true);
375 testUrls(ul, idstrings[ids], urls);
380 System.err.println("Invalid URLLink : " + links[i] + " : "
381 + ul.getInvalidMessage());
386 public boolean isDynamic()
388 // TODO Auto-generated method stub
392 public void setLabel(String newlabel)
394 this.label = newlabel;