JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben-2 and updated develop

diff --cc authors.props
index 0000000,0000000..3c06708
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/authors.props
@@@ -1,0 -1,0 +1,4 @@@
++YEAR=2018
++AUTHORS=J Procter, M Carstairs, B Soares, K Mourao, TC Ofoegbu, AM Waterhouse, J Engelhardt, LM Lui, A Menard, D Barton, N Sherstnev, D Roldan-Martinez, M Clamp, S Searle, G Barton
++AUTHORFNAMES=Jim Procter, Mungo Carstairs, Ben Soares, Kira Mourao, Tochukwu 'Charles' Ofoegbu, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Anne Menard, Daniel Barton, Natasha Sherstnev, David Roldan-Martinez, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
++ 

diff --cc build-j11.xml
Simple merge

diff --cc resources/lang/Messages.properties
index 6b56f07,7a89b71..2d48fac
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -30,8 -30,8 +30,9 @@@ action.minimize_associated_windows = Mi
  action.close_all = Close all
  action.load_project = Load Project
  action.save_project = Save Project
 +action.save_project_as = Save Project as...
  action.quit = Quit
+ label.quit_jalview = Quit Jalview?
  action.expand_views = Expand Views
  action.gather_views = Gather Views
  action.page_setup = Page Setup...

diff --cc resources/lang/Messages_es.properties
index c367eea,756d1c9..ade37ff
--- 1/resources/lang/Messages_es.properties
--- 2/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@@ -30,8 -30,8 +30,9 @@@ action.minimize_associated_windows = Mi
  action.close_all = Cerrar todo
  action.load_project = Cargar proyecto
  action.save_project = Guardar proyecto
 +action.save_project_as = Guardar proyecto como...
  action.quit = Salir
+ label.quit_jalview = Salir Javliew?
  action.expand_views = Expandir vistas
  action.gather_views = Capturar vistas
  action.page_setup = Configuración de la página

diff --cc src/jalview/gui/AlignFrame.java
index a587ac3,2b6d868..bd9f661
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1195,15 -1187,28 +1195,31 @@@ public class AlignFrame extends GAlignF
        }
        else
        {
 +        // create backupfiles object and get new temp filename destination
 +        BackupFiles backupfiles = new BackupFiles(file);
 +
          try
          {
 -          // PrintWriter out = new PrintWriter(new FileWriter(file));
 -          PrintWriter out = new PrintWriter(new FileWriter(file), true);
 +          PrintWriter out = new PrintWriter(
 +                  new FileWriter(backupfiles.getTempFilePath()));
  
+           // TESTING code here
+           boolean TESTING = true;
+           if (TESTING)
+           {
+             out.print("; TESTSTART\n");
+             int count = 20;
+             for (int i = 0; i < count; i++)
+             {
+               // Thread.sleep(1000);
+               out.println("; TEST: " + (count - 1 - i));
+             }
+           }
            out.print(output);
+           if (TESTING)
+           {
+             out.print("; TESTEND\n");
+           }
            out.close();
            this.setTitle(file);
            statusBar.setText(MessageManager.formatMessage(

diff --cc src/jalview/gui/Desktop.java
Simple merge

diff --cc src/jalview/io/FileLoader.java
Simple merge

diff --cc src/jalview/jbgui/GDesktop.java
Simple merge

diff --cc test/jalview/bin/CommandLineOperations.java
index 0424acc,4017931..483bb8b
--- 1/test/jalview/bin/CommandLineOperations.java
--- 2/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@@ -279,14 -281,13 +281,12 @@@ public class CommandLineOperation
              "Failed command : -open examples/uniref50.fa" },
          { "CMD [-nosortbytree] executed successfully!",
              "Failed command : -nosortbytree" },
 -        { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 -            "Failed command : -dasserver nickname=www.test.com" },
 -        { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 +        {
 +            "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
              "Failed command : -features examples/testdata/plantfdx.features" },
-         {
-             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
+         { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
              "Failed command : -annotations examples/testdata/plantfdx.annotations" },
-         {
-             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
+         { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
              "Failed command : -tree examples/testdata/uniref50_test_tree" },
          // non headless mode input operations
          { "CMD [-nousagestats] executed successfully!",