X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=8d3de7d4e25255a553bad3c2f923b7f51a6b800a;hb=0a871d8258ce41f9293615771b1c3dcf447f0eb6;hp=dda9e0ea48e1e994d58669aa2154e0596747b55d;hpb=b22e1863f9c10dbff13ca8bc889255b91f0c4d1c;p=jalview.git

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index dda9e0e..8d3de7d 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -46,11 +46,17 @@ import java.util.Vector;
  */
 public class UrlLink
 {
+  private static final String SEQUENCEID_PLACEHOLDER = DELIM + SEQUENCE_ID
+          + DELIM;
+
+  private static final String ACCESSION_PLACEHOLDER = DELIM + DB_ACCESSION
+          + DELIM;
+
   /**
    * 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.
+   * links, and otherwise orders by link name + url (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>()
   {
@@ -61,29 +67,17 @@ public class UrlLink
       {
         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))
+      if (link1.contains(SEQUENCEID_PLACEHOLDER)
+              && link2.contains(ACCESSION_PLACEHOLDER))
       {
         return -1;
       }
-      if (pattern2.contains(UrlConstants.SEQUENCE_ID)
-              && pattern1.contains(UrlConstants.DB_ACCESSION))
+      if (link2.contains(SEQUENCEID_PLACEHOLDER)
+              && link1.contains(ACCESSION_PLACEHOLDER))
       {
         return 1;
       }
-      return String.CASE_INSENSITIVE_ORDER.compare(name1, name2);
-
+      return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
     }
   };
 
@@ -328,8 +322,8 @@ public class UrlLink
             // debug
             for (int s = 0; s <= rg.numSubs(); s++)
             {
-              System.err.println("Sub " + s + " : " + rg.matchedFrom(s)
-                      + " : " + rg.matchedTo(s) + " : '"
+              jalview.bin.Console.errPrintln("Sub " + s + " : "
+                      + rg.matchedFrom(s) + " : " + rg.matchedTo(s) + " : '"
                       + rg.stringMatched(s) + "'");
             }
             // try to collate subgroup matches
@@ -618,17 +612,17 @@ public class UrlLink
     if (usesDBAccession()) // link is ID
     {
       // collect matching db-refs
-      DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
+      List<DBRefEntry> dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
               new String[]
               { target });
 
       // if there are any dbrefs which match up with the link
       if (dbr != null)
       {
-        for (int r = 0; r < dbr.length; r++)
+        for (int r = 0, nd = dbr.size(); r < nd; r++)
         {
           // create Bare ID link for this URL
-          createBareURLLink(dbr[r].getAccessionId(), true, linkset);
+          createBareURLLink(dbr.get(r).getAccessionId(), true, linkset);
         }
       }
     }