Load and Save State added

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 95c08a1..29eea5f 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -46,7 +46,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListene
     setTitle("Jalview 2005");\r
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
     desktop = new JDesktopPane();\r
- //   desktop.setBackground(Color.white);\r
+    desktop.setBackground(Color.white);\r
     setContentPane(desktop);\r
     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
 \r
@@ -125,12 +125,13 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
    frame.toFront();\r
    final JMenuItem menuItem = new JMenuItem(title);\r
    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
-                                   { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
-                                     {\r
-                                       openFrameCount--;\r
-                                       windowMenu.remove(menuItem);\r
-                                     };\r
-                                   });\r
+   {\r
+     public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
+     {\r
+       openFrameCount--;\r
+       windowMenu.remove(menuItem);\r
+     };\r
+   });\r
 \r
    menuItem.addActionListener(new ActionListener()\r
     {\r
@@ -163,8 +164,13 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
      {\r
        String file = files.get(i).toString();\r
        String protocol = "File";\r
-       String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-       LoadFile(file, protocol, format);\r
+       if(file.endsWith(".jar"))\r
+                Jalview2XML.LoadJalviewAlign(file);\r
+      else\r
+      {\r
+        String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+        LoadFile(file, protocol, format);\r
+      }\r
      }\r
 \r
    }catch(Exception ex){ex.printStackTrace();}\r
@@ -174,7 +180,10 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
  {\r
    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
-       new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");\r
+       new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},\r
+       new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview Archive"}\r
+       ,null);\r
+\r
    chooser.setFileView(new JalviewFileView());\r
    chooser.setDialogTitle("Open local file");\r
    chooser.setToolTipText("Open");\r
@@ -182,9 +191,16 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
    if(value == JalviewFileChooser.APPROVE_OPTION)\r
    {\r
      String choice =  chooser.getSelectedFile().getPath();\r
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
-     String format = IdentifyFile.Identify(choice, "File");\r
-     LoadFile(choice, "File", format);\r
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
+     if(chooser.getSelectedFormat().equals("Jalview"))\r
+     {\r
+       Jalview2XML.LoadJalviewAlign(choice);\r
+     }\r
+     else\r
+     {\r
+       String format = IdentifyFile.Identify(choice, "File");\r
+       LoadFile(choice, "File", format);\r
+     }\r
    }\r
  }\r
 \r
@@ -215,6 +231,7 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
      {\r
        AlignFrame af = new AlignFrame(new Alignment(sequences));\r
        addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
+       af.currentFileFormat = format;\r
        af.statusBar.setText("Successfully loaded file " + file);\r
        try{\r
            af.setMaximum(Preferences.showFullscreen);\r
@@ -224,7 +241,7 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
      else\r
        JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
                             + "Formats currently supported are\n"\r
-                            + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!\r
+                            + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
                             ,"Error loading file",\r
                                      JOptionPane.WARNING_MESSAGE);\r
 \r
@@ -234,8 +251,6 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 \r
  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
  {\r
-   JOptionPane op = new JOptionPane();\r
-\r
    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
                                             "Input alignment from URL",\r
                                             JOptionPane.QUESTION_MESSAGE,\r
@@ -279,6 +294,7 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
       if(sequences!=null)\r
       {\r
         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+        af.currentFileFormat = format;\r
         addInternalFrame(af, "Cut & Paste input - "+format,\r
                          AlignFrame.NEW_WINDOW_WIDTH,\r
                          AlignFrame.NEW_WINDOW_HEIGHT);\r
@@ -287,7 +303,7 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
       else\r
         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
                                       +"Formats currently supported are\n"\r
-                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
+                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",\r
                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 \r
    }\r
@@ -344,6 +360,40 @@ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
    Preferences pref = new Preferences();\r
  }\r
 \r
+ public void saveState_actionPerformed(ActionEvent e)\r
+ {\r
+   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+       getProperty("LAST_DIRECTORY"),\r
+       new String[]\r
+       {"xml"}, new String[]{"Jalview Project"}, "Jalview Project");\r
+\r
+   chooser.setFileView(new JalviewFileView());\r
+   chooser.setDialogTitle("Save State");\r
+   int value = chooser.showSaveDialog(this);\r
+   if (value == JalviewFileChooser.APPROVE_OPTION)\r
+   {\r
+     java.io.File choice = chooser.getSelectedFile();\r
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+     Jalview2XML.SaveState(choice);\r
+   }\r
+\r
+ }\r
+\r
+\r
+ public void loadState_actionPerformed(ActionEvent e)\r
+ {\r
+   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
+       new String[]{"xml"}, new String[]{"Jalview Project"}, "Jalview Project");\r
+   chooser.setFileView(new JalviewFileView());\r
+   chooser.setDialogTitle("Restore state");\r
+   int value = chooser.showOpenDialog(this);\r
+   if(value == JalviewFileChooser.APPROVE_OPTION)\r
+   {\r
+     String choice =  chooser.getSelectedFile().getAbsolutePath();\r
+     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
+     Jalview2XML.LoadState(choice);\r
+   }\r
+ }\r
 }\r
 \r
 \r