Tooltips for features, links for features added

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 8f6e49f..1c9b3cd 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -87,6 +87,11 @@ public class APopupMenu
       showText.setState(sg.getDisplayText());\r
       showColourText.setState(sg.getColourText());\r
       showBoxes.setState(sg.getDisplayBoxes());\r
+      if (!ap.av.alignment.getGroups().contains(sg))\r
+      {\r
+        groupMenu.remove(unGroupMenuItem);\r
+      }\r
+\r
     }\r
     else\r
     {\r
@@ -94,12 +99,7 @@ public class APopupMenu
       remove(editMenu);\r
     }\r
 \r
-    if (!ap.av.alignment.getGroups().contains(sg))\r
-    {\r
-      groupMenu.remove(unGroupMenuItem);\r
-    }\r
-\r
-    if (seq != null && links!=null)\r
+    if (links!=null)\r
     {\r
       Menu linkMenu = new Menu("Link");\r
       MenuItem item;\r
@@ -109,13 +109,22 @@ public class APopupMenu
         link = links.elementAt(i).toString();\r
         final String target = link.substring(0, link.indexOf("|"));\r
         item = new MenuItem(target);\r
-        String id = seq.getName();\r
-        if(id.indexOf("|")>-1)\r
-             id = id.substring(id.lastIndexOf("|")+1);\r
 \r
-        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
-               + id +\r
-               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+        final String url;\r
+\r
+        if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+        {\r
+          String id = seq.getName();\r
+          if (id.indexOf("|") > -1)\r
+            id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
+          url = link.substring(link.indexOf("|") + 1,\r
+                               link.indexOf("$SEQUENCE_ID$"))\r
+              + id +\r
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+        }\r
+        else\r
+          url = link.substring(link.lastIndexOf("|")+1);\r
 \r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
@@ -128,18 +137,19 @@ public class APopupMenu
       }\r
       add(linkMenu);\r
 \r
-      item = new MenuItem("Show PDB Structure");\r
-      item.addActionListener(new java.awt.event.ActionListener()\r
-           {\r
-               public void actionPerformed(ActionEvent e)\r
-               {\r
-                  addPDB(seq);\r
-               }\r
-           });\r
-\r
-      add(item);\r
-\r
+      if(seq!=null)\r
+      {\r
+        item = new MenuItem("Show PDB Structure");\r
+        item.addActionListener(new java.awt.event.ActionListener()\r
+        {\r
+          public void actionPerformed(ActionEvent e)\r
+          {\r
+            addPDB(seq);\r
+          }\r
+        });\r
 \r
+        add(item);\r
+      }\r
     }\r
   }\r
 \r