Merge branch 'develop' into menard

diff --cc src/jalview/bin/Jalview.java
index 772f99e,efaf86d..65b32af
--- 1/src/jalview/bin/Jalview.java
--- 2/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@@ -512,31 -515,14 +520,34 @@@ public class Jalvie
      // We'll only open the default file if the desktop is visible.
      // And the user
      // ////////////////////
 +  
 +    JFrame Typechooser =new JFrame("choose molecule type"); 
 +    FlowLayout fl = new FlowLayout();
 +    Typechooser.setLayout(fl);
 +    Typechooser.setSize(400,400);
 +    Typechooser.setDefaultCloseOperation(Typechooser.DISPOSE_ON_CLOSE);
 +    JLabel label = new JLabel("What would you open ? ");
 +    JButton rnabutton = new JButton("RNA molecule");
 +    JButton pbutton = new JButton("Proteine molecule");
 +    
 +    pbutton.addActionListener(new pbuttonlistener());
 +    rnabutton.addActionListener(new rnabuttonlistener());
 +    Typechooser.getContentPane().add(label);
 +    Typechooser.getContentPane().add(rnabutton);
 +    Typechooser.getContentPane().add(pbutton);
 +    Typechooser.setVisible(true);
 +    
 +    
 +
 +    
      if (!headless && file == null && vamsasImport == null
 -            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
 +            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && proteine == true)
      {
-       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
-               jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.jar");
+       file = jalview.bin.Cache.getDefault(
+               "STARTUP_FILE",
+               jalview.bin.Cache.getDefault("www.jalview.org",
+                       "http://www.jalview.org")
+                       + "/examples/exampleFile_2_7.jar");
        if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
        {
          // hardwire upgrade of the startup file