import jalview.datamodel.SequenceI;
import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Vector;
+/**
+ * A helper class to parse URL Link strings taken from applet parameters or
+ * jalview properties file using the com.stevesoft.pat.Regex implementation.
+ * Jalview 2.4 extension allows regular expressions to be used to parse ID
+ * strings and replace the result in the URL. Regex's operate on the whole ID
+ * string given to the matchURL method, if no regex is supplied, then only text
+ * following the first pipe symbol will be substituted. Usage documentation
+ * todo.
+ */
public class UrlLink
{
/**
- * helper class to parse URL Link strings taken from applet parameters or
- * jalview properties file using the com.stevesoft.pat.Regex implementation.
- * Jalview 2.4 extension allows regular expressions to be used to parse ID
- * strings and replace the result in the URL. Regex's operate on the whole ID
- * string given to the matchURL method, if no regex is supplied, then only
- * text following the first pipe symbol will be substituted. Usage
- * documentation todo.
+ * A comparator that puts SEQUENCE_ID template links before DB_ACCESSION
+ * links, and otherwise orders by link name (not case sensitive). It expects
+ * to compare strings formatted as "Name|URLTemplate" where the template may
+ * include $SEQUENCE_ID$ or $DB_ACCESSION$ or neither.
*/
+ public static final Comparator<String> LINK_COMPARATOR = new Comparator<String>()
+ {
+ @Override
+ public int compare(String link1, String link2)
+ {
+ if (link1 == null || link2 == null)
+ {
+ return 0; // for failsafe only
+ }
+ String[] tokens1 = link1.split("\\|");
+ String[] tokens2 = link2.split("\\|");
+ if (tokens1.length < 2 || tokens2.length < 2)
+ {
+ // for failsafe only
+ return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
+ }
+ String name1 = tokens1[0];
+ String name2 = tokens2[0];
+ String pattern1 = tokens1[1];
+ String pattern2 = tokens2[1];
+ if (pattern1.contains(UrlConstants.SEQUENCE_ID)
+ && pattern2.contains(UrlConstants.DB_ACCESSION))
+ {
+ return -1;
+ }
+ if (pattern2.contains(UrlConstants.SEQUENCE_ID)
+ && pattern1.contains(UrlConstants.DB_ACCESSION))
+ {
+ return 1;
+ }
+ return String.CASE_INSENSITIVE_ORDER.compare(name1, name2);
+
+ }
+ };
private static final String EQUALS = "=";
+ rg.stringMatched(s) + "'");
}
// try to collate subgroup matches
- Vector<String> subs = new Vector<String>();
+ Vector<String> subs = new Vector<>();
// have to loop through submatches, collating them at top level
// match
int s = 0; // 1;
}
}
}
+
+ /**
+ * Sorts links (formatted as LinkName|LinkPattern) suitable for display in a
+ * menu
+ * <ul>
+ * <li>SEQUENCE_ID links precede DB_ACCESSION links (i.e. canonical lookup
+ * before cross-references)</li>
+ * <li>otherwise by Link name (case insensitive)</li>
+ * </ul>
+ *
+ * @param nlinks
+ */
+ public static void sort(List<String> nlinks)
+ {
+ Collections.sort(nlinks, LINK_COMPARATOR);
+ }
}