import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
// Not dynamic
ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
// Not dynamic
ul = new UrlLink(DB + SEP + URL_PREFIX + URL_SUFFIX.substring(1));
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
assertFalse(ul.isDynamic());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX + URL_SUFFIX.substring(1), ul.getUrl_prefix());
assertFalse(ul.isDynamic());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertNull(ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
// invalid regex
assertEquals(REGEX_NESTED.substring(2, REGEX_NESTED.length() - 2),
ul.getRegexReplace());
assertTrue(ul.isValid());
assertNull(ul.getInvalidMessage());
// invalid regex
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(DB, ul.getLabel());
assertEquals(URL_PREFIX, ul.getUrl_prefix());
assertEquals(URL_SUFFIX, ul.getUrl_suffix());
assertTrue(ul.isDynamic());
assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
ul.getRegexReplace());
assertFalse(ul.isValid());
assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
ul.getRegexReplace());
assertFalse(ul.isValid());
+ DELIM + URL_SUFFIX);
String idstring = "FER_CAPAA";
String[] urls = ul.makeUrls(idstring, true);
+ DELIM + URL_SUFFIX);
String idstring = "FER_CAPAA";
String[] urls = ul.makeUrls(idstring, true);
+ REGEX_NESTED + DELIM + URL_SUFFIX);
String idstring = "FER_CAPAA";
String[] urls = ul.makeUrls(idstring, true);
+ REGEX_NESTED + DELIM + URL_SUFFIX);
String idstring = "FER_CAPAA";
String[] urls = ul.makeUrls(idstring, true);
String key = DB + SEP + URL_PREFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
String key = DB + SEP + URL_PREFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
assertEquals(linkset.get(key).get(1), DB);
assertEquals(linkset.get(key).get(2), null);
assertEquals(linkset.get(key).get(3), URL_PREFIX);
assertEquals(linkset.get(key).get(1), DB);
assertEquals(linkset.get(key).get(2), null);
assertEquals(linkset.get(key).get(3), URL_PREFIX);
String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
String key = DB + SEP + URL_PREFIX + URL_SUFFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
assertEquals(linkset.get(key).get(1), DB);
assertEquals(linkset.get(key).get(2), null);
assertEquals(linkset.get(key).get(3), URL_PREFIX + URL_SUFFIX);
assertEquals(linkset.get(key).get(1), DB);
assertEquals(linkset.get(key).get(2), null);
assertEquals(linkset.get(key).get(3), URL_PREFIX + URL_SUFFIX);
// links as might be added into Preferences | Connections dialog
links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
// links as might be added into Preferences | Connections dialog
links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ URL_SUFFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
+ URL_SUFFIX;
assertEquals(1, linkset.size());
assertTrue(linkset.containsKey(key));
assertEquals(linkset.get(key).get(1), DB);
assertEquals(linkset.get(key).get(2), seq0.getName());
assertEquals(linkset.get(key).get(3), URL_PREFIX + seq0.getName()
assertEquals(linkset.get(key).get(1), DB);
assertEquals(linkset.get(key).get(2), seq0.getName());
assertEquals(linkset.get(key).get(3), URL_PREFIX + seq0.getName()
"http://www.ebi.ac.uk/interpro/entry/IPR012675");
// Test where there are no matching dbrefs for the link
"http://www.ebi.ac.uk/interpro/entry/IPR012675");
// Test where there are no matching dbrefs for the link
+ URL_SUFFIX);
linkset = new LinkedHashMap<String, List<String>>();
ul.createLinksFromSeq(seq0, linkset);
+ URL_SUFFIX);
linkset = new LinkedHashMap<String, List<String>>();
ul.createLinksFromSeq(seq0, linkset);