Merge branch 'features/JAL-1723_sequenceReport' into develop

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3b79fdc..5825382 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -54,7 +54,6 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
-import jalview.util.DBRefUtils;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -63,8 +62,8 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
@@ -617,7 +616,8 @@ public class PopupMenu extends JPopupMenu
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    List<String> linkset = new ArrayList<String>();
+    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
     for (String link : links)
     {
       UrlLink urlLink = null;
@@ -629,80 +629,28 @@ public class PopupMenu extends JPopupMenu
         Cache.log.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
-      ;
+
       if (!urlLink.isValid())
       {
         Cache.log.error(urlLink.getInvalidMessage());
         continue;
       }
-      final String label = urlLink.getLabel();
-
-      // collect id string too
-      String id = seq.getName();
-      String descr = seq.getDescription();
-      if (descr != null && descr.length() < 1)
-      {
-        descr = null;
-      }
 
-      if (seq != null && urlLink.usesSeqId()) // link is ID
-      {
-        // collect matching db-refs
-        DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
-                new String[] { urlLink.getTarget() });
-
-        // if there are any dbrefs which match up with the link
-        if (dbr != null)
-        {
-          for (int r = 0; r < dbr.length; r++)
-          {
-            if (id != null && dbr[r].getAccessionId().equals(id))
-            {
-              // suppress duplicate link creation for the bare sequence ID
-              // string with this link
-              id = null;
-            }
-            // create Bare ID link for this URL
-            createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset,
-                    linkMenu, label, true);
-          }
-        }
+      urlLink.createLinksFromSeq(seq, linkset);
+    }
 
-        // Create urls from description but only for URL links which are regex
-        // links
-        if (descr != null && urlLink.getRegexReplace() != null)
-        {
-          // create link for this URL from description where regex matches
-          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
-        }
-
-      }
-      else if (seq != null && !urlLink.usesSeqId()) // link is name
-      {
-        if (id != null)
-        {
-          // create Bare ID link for this URL
-          createBareURLLink(urlLink, id, linkset, linkMenu, label, false);
-        }
-        // Create urls from description but only for URL links which are regex
-        // links
-        if (descr != null && urlLink.getRegexReplace() != null)
-        {
-          // create link for this URL from description where regex matches
-          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
-        }
-      }
-      else
-      {
-        if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
-        {
-          linkset.add(label + "|" + urlLink.getUrl_prefix());
-          // Add a non-dynamic link
-          addshowLink(linkMenu, label, urlLink.getUrl_prefix());
-        }
-      }
+    addshowLinks(linkMenu, linkset.values());
 
+    // disable link menu if there are no valid entries
+    if (linkMenu.getItemCount() > 0)
+    {
+      linkMenu.setEnabled(true);
     }
+    else
+    {
+      linkMenu.setEnabled(false);
+    }
+
     if (sequence != null)
     {
       sequenceMenu.add(linkMenu);
@@ -711,36 +659,11 @@ public class PopupMenu extends JPopupMenu
     {
       add(linkMenu);
     }
-  }
 
-  /*
-   * Create a bare URL Link
-   */
-  private void createBareURLLink(UrlLink urlLink, String id,
-          List<String> linkset, JMenu linkMenu, String label,
-          Boolean addSepToLabel)
-  {
-    String[] urls = urlLink.makeUrls(id, true);
-    if (urls != null)
-    {
-      for (int u = 0; u < urls.length; u += 2)
-      {
-        if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-        {
-          linkset.add(urls[u] + "|" + urls[u + 1]);
-          if (addSepToLabel)
-          {
-            addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
-          }
-          else
-          {
-            addshowLink(linkMenu, label, urls[u + 1]);
-          }
-        }
-      }
-    }
   }
 
+
+
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -1015,6 +938,15 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
+  {
+    for (List<String> linkstrset : linkset)
+    {
+      // split linkstr into label and url
+      addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+    }
+  }
+
   /**
    * add a show URL menu item to the given linkMenu
    * 
@@ -2047,7 +1979,7 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+      Conservation c = new Conservation("Group", sg.getSequences(ap.av
               .getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);