Merge branch 'develop' into develop_m2_8_1_2

diff --combined src/jalview/bin/Jalview.java
index df9501d,94206c2..c3d674b
--- 1/src/jalview/bin/Jalview.java
--- 2/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@@ -70,11 -70,7 +70,11 @@@ public class Jalvie
        }
      });
    }
 -  protected static boolean proteine;
 +  /**
 +   * Put protein=true for get a protein example
 +   */
 +  private static boolean protein=false;
 +
  
    /**
     * main class for Jalview application
@@@ -137,6 -133,11 +137,11 @@@
                        + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
        System.exit(0);
      }
+     if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless"))
+     {
+       System.setProperty("java.awt.headless", "true");
+       headless=true;
+     }
      Cache.loadProperties(aparser.getValue("props")); // must do this before
      // anything else!
      String defs = aparser.getValue("setprop");
@@@ -156,10 -157,6 +161,6 @@@
        }
        defs = aparser.getValue("setprop");
      }
-     if (aparser.contains("nodisplay"))
-     {
-       System.setProperty("java.awt.headless", "true");
-     }
      if (System.getProperty("java.awt.headless") != null
              && System.getProperty("java.awt.headless").equals("true"))
      {
@@@ -525,14 -522,27 +526,14 @@@
      // 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) && proteine == true)
 +            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && protein == true)
      {
        file = jalview.bin.Cache.getDefault(
                "STARTUP_FILE",