Put alignmentProperties in scrollpane

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 0304ea1..0310f2a 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -23,6 +23,7 @@ import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.lang.reflect.Constructor;
 import java.util.*;
 
 import javax.swing.*;
@@ -63,6 +64,7 @@ public class Desktop
   {
     instance = this;
     doVamsasClientCheck();
+    doGroovyCheck();
     Image image = null;
 
 
@@ -1104,5 +1106,87 @@ public class Desktop
       }
     }
   }*/
+  protected JMenuItem groovyShell;
+  public void doGroovyCheck() {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText("Groovy Shell...");
+      groovyShell.addActionListener(new ActionListener() 
+      {
+          public void actionPerformed(ActionEvent e) {
+              groovyShell_actionPerformed(e);
+          }  
+      });
+      toolsMenu.add(groovyShell);
+      groovyShell.setVisible(true);
+    }
+  }
+  /** 
+   * Accessor method to quickly get all the AlignmentFrames
+   * loaded.  
+   */    
+  protected AlignFrame[] getAlignframes() {
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    
+    if (frames == null)
+    {
+      return null;
+      }
+      Vector avp=new Vector();
+      try
+      {
+          //REVERSE ORDER
+          for (int i = frames.length - 1; i > -1; i--)
+          {
+              if (frames[i] instanceof AlignFrame)
+              {
+                  AlignFrame af = (AlignFrame) frames[i];
+                  avp.addElement(af);
+              }
+          }
+      }
+      catch (Exception ex)
+      {
+          ex.printStackTrace();
+      }
+      if (avp.size()==0)
+      {
+          return null;
+      }
+      AlignFrame afs[] = new AlignFrame[avp.size()];
+      for (int i=0,j=avp.size(); i<j; i++) {
+          afs[i] = (AlignFrame) avp.elementAt(i);
+      }
+      avp.clear();
+      return afs;
+  }
 
+  /**
+    * Add Groovy Support to Jalview
+    */
+  public void groovyShell_actionPerformed(ActionEvent e) {
+    // use reflection to avoid creating compilation dependency.
+    if (!jalview.bin.Cache.groovyJarsPresent())
+    {
+      throw new Error("Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+    }
+    try {
+    Class gcClass = Desktop.class.getClassLoader().loadClass("groovy.ui.Console");
+    Constructor gccons = gcClass.getConstructor(null);
+    java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class} );
+    java.lang.reflect.Method run = gcClass.getMethod("run", null);
+    Object gc = gccons.newInstance(null);
+    setvar.invoke(gc, new Object[] { "Jalview", this});
+    run.invoke(gc, null);
+    }
+    catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+              "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
+              JOptionPane.ERROR_MESSAGE);
+    }
   }
+}