X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=5825382fb70421defc9c1ec931ffe719018f2c8a;hb=134576f5b34894218bdc4c5ce5e27fa18ad973bd;hp=88d5acbb2a493739d2b68c247d63258aec6b60dc;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 88d5acb..5825382 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -629,97 +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();
-      if (seq != null && urlLink.isDynamic())
-      {
 
-        // collect matching db-refs
-        DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
-                new String[] { urlLink.getTarget() });
-        // collect id string too
-        String id = seq.getName();
-        String descr = seq.getDescription();
-        if (descr != null && descr.length() < 1)
-        {
-          descr = null;
-        }
+      urlLink.createLinksFromSeq(seq, linkset);
+    }
 
-        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
-            String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), 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]);
-                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
-                }
-              }
-            }
-          }
-        }
-        if (id != null)
-        {
-          // create Bare ID link for this URL
-          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]);
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
-        }
-        // 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
-          String[] urls = urlLink.makeUrls(descr, 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]);
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
-        }
-      }
-      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);
@@ -728,8 +659,11 @@ public class PopupMenu extends JPopupMenu
     {
       add(linkMenu);
     }
+
   }
 
+
+
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -1004,6 +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
    * 
@@ -1734,7 +1677,7 @@ public class PopupMenu extends JPopupMenu
   public void createSequenceDetailsReport(SequenceI[] sequences)
   {
     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
-    StringBuffer contents = new StringBuffer();
+    StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
       contents.append("<p><h2>"
@@ -1749,7 +1692,6 @@ public class PopupMenu extends JPopupMenu
                       seq,
                       true,
                       true,
-                      false,
                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
                               .getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);
@@ -2037,7 +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);