JAL-2316 Refactoring of functionality to provide urls to gui

[jalview.git] / src / jalview / gui / IdPanel.java

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index e321a74..7170d04 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -27,7 +27,6 @@ import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.util.UrlLink;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
@@ -199,56 +198,10 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    Vector links = Preferences.sequenceURLLinks;
-    if (links == null || links.size() < 1)
-    {
-      return;
-    }
-
     int seq = alignPanel.getSeqPanel().findSeq(e);
-    String url = null;
-    int i = 0;
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    while (url == null && i < links.size())
-    {
-      // DEFAULT LINK IS FIRST IN THE LINK LIST
-      // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
-      url = links.elementAt(i++).toString();
-      jalview.util.UrlLink urlLink = null;
-      try
-      {
-        urlLink = new UrlLink(url);
-      } catch (Exception foo)
-      {
-        jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
-                foo);
-        url = null;
-        continue;
-      }
+    String url = Preferences.sequenceUrlLinks.getDefaultUrl(id);
 
-      if (urlLink.usesDBAccession())
-      {
-        // this URL requires an accession id, not the name of a sequence
-        url = null;
-        continue;
-      }
-
-      if (!urlLink.isValid())
-      {
-        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
-        url = null;
-        continue;
-      }
-
-      String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0] == null || urls[0].length() < 4)
-      {
-        url = null;
-        continue;
-      }
-      // just take first URL made from regex
-      url = urls[1];
-    }
     try
     {
       jalview.util.BrowserLauncher.openURL(url);
@@ -375,7 +328,9 @@ public class IdPanel extends JPanel implements MouseListener,
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
     // build a new links menu based on the current links + any non-positional
     // features
-    Vector<String> nlinks = new Vector<String>(Preferences.sequenceURLLinks);
+    Vector<String> nlinks = Preferences.sequenceUrlLinks
+            .getLinksForDisplay(); // new
+                                   // Vector<String>(Preferences.sequenceURLLinks);
     SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
     if (sfs != null)
     {