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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 5ff9ad9..40c51cb 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -195,6 +195,35 @@ public class PopupMenu extends JPopupMenu
         {\r
             sequenceMenu.setVisible(false);\r
         }\r
+        else\r
+        {\r
+          java.util.Vector links = Preferences.sequenceURLLinks;\r
+\r
+          JMenu linkMenu = new JMenu("Link");\r
+          JMenuItem item;\r
+          for(int i=0; i<links.size(); i++)\r
+          {\r
+            String link = links.elementAt(i).toString();\r
+\r
+            item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
+\r
+            final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
+                + sequence.getName() +\r
+                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+\r
+\r
+            item.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    showLink(url);\r
+                }\r
+            });\r
+\r
+            linkMenu.add(item);\r
+          }\r
+          add(linkMenu);\r
+        }\r
     }\r
 \r
     /**\r
@@ -310,6 +339,28 @@ public class PopupMenu extends JPopupMenu
         colourMenu.add(buriedColour);\r
         colourMenu.add(nucleotideMenuItem);\r
         colourMenu.add(userDefinedColour);\r
+\r
+        if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
+        {\r
+          java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+              getUserColourSchemes().keys();\r
+\r
+          while (userColours.hasMoreElements())\r
+          {\r
+            JMenuItem item = new JMenuItem(userColours.\r
+                nextElement().toString());\r
+            item.addActionListener(new ActionListener()\r
+            {\r
+              public void actionPerformed(ActionEvent evt)\r
+              {\r
+                userDefinedColour_actionPerformed(evt);\r
+              }\r
+            });\r
+            colourMenu.add(item);\r
+          }\r
+        }\r
+\r
+\r
         colourMenu.addSeparator();\r
         colourMenu.add(abovePIDColour);\r
         colourMenu.add(conservationMenuItem);\r
@@ -394,7 +445,7 @@ public class PopupMenu extends JPopupMenu
                     abovePIDColour_actionPerformed(e);\r
                 }\r
             });\r
-        userDefinedColour.setText("User Defined");\r
+        userDefinedColour.setText("User Defined...");\r
         userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
             {\r
                 public void actionPerformed(ActionEvent e)\r
@@ -434,13 +485,15 @@ public class PopupMenu extends JPopupMenu
     void refresh()\r
     {\r
         SequenceGroup sg = getGroup();\r
-        SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
-        if (superG != null)\r
+        if(sg!=null)\r
         {\r
+          SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
+\r
+          if (superG != null)\r
+          {\r
             superG.setSuperGroupProperties(sg);\r
+          }\r
         }\r
-\r
         ap.seqPanel.repaint();\r
     }\r
 \r
@@ -564,11 +617,11 @@ public class PopupMenu extends JPopupMenu
 \r
             if (sg.cs instanceof ResidueColourScheme)\r
             {\r
-                ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+                ((ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
             }\r
             else if (sg.cs instanceof ScoreColourScheme)\r
             {\r
-                ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+                ((ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
             }\r
 \r
             SliderPanel.showPIDSlider();\r
@@ -576,7 +629,7 @@ public class PopupMenu extends JPopupMenu
         else // remove PIDColouring\r
         {\r
             ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
-            rcs.setThreshold(0);\r
+            rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
             sg.cs = rcs;\r
         }\r
 \r
@@ -590,9 +643,18 @@ public class PopupMenu extends JPopupMenu
      */\r
     protected void userDefinedColour_actionPerformed(ActionEvent e)\r
     {\r
-        new UserDefinedColours(ap, getGroup());\r
-    }\r
-\r
+       SequenceGroup sg = getGroup();\r
+\r
+       if (e.getActionCommand().equals("User Defined..."))\r
+         new UserDefinedColours(ap, sg);\r
+       else\r
+       {\r
+         UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+             getUserColourSchemes().get(e.getActionCommand());\r
+\r
+         sg.cs = udc;\r
+       }\r
+     }\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -724,9 +786,9 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup getGroup()\r
     {\r
         SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
-        // this method won't add a new group if it already exists\r
-        ap.av.alignment.addGroup(sg);\r
+      // this method won't add a new group if it already exists\r
+        if(sg!=null)\r
+          ap.av.alignment.addGroup(sg);\r
 \r
         return sg;\r
     }\r
@@ -856,4 +918,22 @@ public class PopupMenu extends JPopupMenu
         getGroup().setColourText(showColourText.isSelected());\r
         refresh();\r
     }\r
+\r
+    public void showLink(String url)\r
+    {\r
+      try\r
+      {\r
+        jalview.util.BrowserLauncher.openURL(url);\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+            "Unixers: Couldn't find default web browser."\r
+           +"\nAdd the full path to your browser in Preferences.",\r
+           "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
+\r
+\r
+        ex.printStackTrace();\r
+      }\r
+    }\r
 }\r