-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-package jalview.gui;\r
-\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.datamodel.*;\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class Desktop extends jalview.jbgui.GDesktop\r
-{\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30, yOffset = 30;\r
- static boolean splashScreenVisible = false;\r
-\r
- public Desktop()\r
- {\r
- Image image =null;\r
- try{\r
- java.net.URL url = getClass().getResource("/BartonGroupBanner.gif");\r
- if(url!=null)\r
- {\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- mt.waitForID(0);\r
- setIconImage(image);\r
- }\r
-\r
- }catch(Exception ex){}\r
-\r
- setTitle("Jalview 2005");\r
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- setVisible(true);\r
- desktop = new JDesktopPane();\r
- setContentPane(desktop);\r
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
-\r
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
- setBounds( (int)(screenSize.getWidth()-1200)/2,\r
- (int)(screenSize.getHeight()-800)/2,\r
- 1200 ,\r
- 800);\r
-\r
-\r
- /////////Add a splashscreen on startup\r
- /* JInternalFrame frame = new JInternalFrame();\r
-\r
- SplashScreen splash = new SplashScreen(frame, image);\r
- frame.setContentPane(splash);\r
- addInternalFrame(frame, "",820,200);\r
- splashScreenVisible = true;\r
-\r
- frame.setLocation( (int)((getWidth()-820) /2), (int)((getHeight()-240) /2));\r
- frame.setClosable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
- frame.setFrameIcon(null);*/\r
- }\r
-\r
- public static void splashScreenClosing()\r
- {\r
- splashScreenVisible = false;\r
- JInternalFrame [] frames = desktop.getAllFrames();\r
- for(int i=0; i<frames.length; i++)\r
- frames[i].setVisible(true);\r
- }\r
-\r
- public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
- {\r
- if(!splashScreenVisible)\r
- frame.setVisible(true); //necessary as of 1.3\r
- desktop.add(frame);\r
- openFrameCount++;\r
- try {\r
- frame.setSelected(true);\r
- } catch (java.beans.PropertyVetoException e) {}\r
- frame.setTitle(title);\r
- frame.setResizable(true);\r
- frame.setSize(w,h);\r
- frame.setClosable(true);\r
- frame.setMaximizable(true);\r
- frame.setIconifiable(true);\r
- frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
- 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
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- try{ frame.setSelected(true); frame.setIcon(false); }\r
- catch(java.beans.PropertyVetoException ex){};\r
- }\r
- });\r
-\r
- windowMenu.add(menuItem);\r
- }\r
-\r
-\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
- String format = IdentifyFile.Identify(choice, "File");\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains(format))\r
- sequences = FormatAdapter.read(file, protocol, format);\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, 700, 500);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\r
-\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(this, "Couldn't open file.\n"\r
- + "Formats currently supported are\n"\r
- + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
-\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(this,"Enter url of input file",\r
- "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE);\r
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- System.out.println(format +" format");\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(this,"Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- LoadFile(url, "URL", format);\r
- }\r
-\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
- int accept = JOptionPane.showInternalOptionDialog(desktop, cap, "Cut & paste Alignment File",\r
- JOptionPane.YES_NO_CANCEL_OPTION,\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- new Object[]{"Accept", "Cancel", }, null);\r
-\r
-\r
- if(accept == JOptionPane.YES_OPTION)\r
- {\r
- String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains( format ))\r
- sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
-\r
-\r
- if(sequences!=null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(this, "Couldn't read the pasted text.\n"\r
- +"Formats currently supported are\n"\r
- +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
- "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
-\r
-\r
- }\r
- }\r
-\r
-/*\r
-* Exit the program\r
-*/\r
- public void quit_actionPerformed(ActionEvent e)\r
- {\r
- this.setVisible(false);\r
- System.exit(0);\r
- }\r
-\r
-\r
- protected void colourIndexMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColourKey colourKey = new ColourKey(null);\r
- addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
- }\r
-\r
-\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showInternalMessageDialog(desktop,\r
- "JalView 2005"\r
- +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse and Geoff Barton."\r
- +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
- +"\nIf you use JalView, please cite: \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
- "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- jalview.util.BrowserLauncher.openURL("http://jalview.org/documentation.html");\r
- }catch(Exception ex){}\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.io.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop extends jalview.jbgui.GDesktop
+ implements DropTargetListener
+{
+ /** DOCUMENT ME!! */
+ public static JDesktopPane desktop;
+ static int openFrameCount = 0;
+ static final int xOffset = 30;
+ static final int yOffset = 30;
+ public static jalview.ws.Discoverer discoverer;
+
+ public static Object [] jalviewClipboard;
+
+
+ /**
+ * Creates a new Desktop object.
+ */
+ public Desktop()
+ {
+ Image image = null;
+
+
+ try
+ {
+ java.net.URL url = getClass().getResource("/images/logo.gif");
+
+ if (url != null)
+ {
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(image, 0);
+ mt.waitForID(0);
+ setIconImage(image);
+ }
+ }
+ catch (Exception ex)
+ {
+ }
+
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ desktop = new JDesktopPane();
+ desktop.setBackground(Color.white);
+ setContentPane(desktop);
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
+ // This line prevents Windows Look&Feel resizing all new windows to maximum
+ // if previous window was maximised
+ desktop.setDesktopManager(new DefaultDesktopManager());
+
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ String x = jalview.bin.Cache.getProperty("SCREEN_X");
+ String y = jalview.bin.Cache.getProperty("SCREEN_Y");
+ String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
+ String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
+
+ if ((x != null) && (y != null) && (width != null) && (height != null))
+ {
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),
+ Integer.parseInt(width), Integer.parseInt(height));
+ }
+ else
+ {
+ setBounds((int) (screenSize.width - 900) / 2,
+ (int) (screenSize.height - 650) / 2, 900, 650);
+ }
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
+
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+
+ /////////Add a splashscreen on startup
+ /////////Add a splashscreen on startup
+ JInternalFrame frame = new JInternalFrame();
+
+ SplashScreen splash = new SplashScreen(frame, image);
+ frame.setContentPane(splash);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.setLocation((int) ((getWidth() - 750) / 2),
+ (int) ((getHeight() - 160) / 2));
+
+ addInternalFrame(frame, "", 750, 160, false);
+
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame,
+ String title, int w, int h)
+ {
+ addInternalFrame(frame, title, w, h, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param resizable DOCUMENT ME!
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame,
+ String title, int w, int h, boolean resizable)
+ {
+
+ frame.setTitle(title);
+ if(frame.getWidth()<1 || frame.getHeight()<1)
+ {
+ frame.setSize(w, h);
+ }
+ // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
+ // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
+ // IF JALVIEW IS RUNNING HEADLESS
+ /////////////////////////////////////////////////
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ return;
+ }
+
+
+ openFrameCount++;
+
+ frame.setVisible(true);
+ frame.setClosable(true);
+ frame.setResizable(resizable);
+ frame.setMaximizable(resizable);
+ frame.setIconifiable(resizable);
+ frame.setFrameIcon(null);
+
+ if (frame.getX()<1 && frame.getY()<1)
+ {
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
+ }
+
+ final JMenuItem menuItem = new JMenuItem(title);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ openFrameCount--;
+ windowMenu.remove(menuItem);
+ JInternalFrame itf = desktop.getSelectedFrame();
+ if (itf != null)
+ itf.requestFocus();
+ }
+ ;
+ });
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setSelected(true);
+ frame.setIcon(false);
+ }
+ catch (java.beans.PropertyVetoException ex)
+ {
+
+ }
+ }
+ });
+
+ windowMenu.add(menuItem);
+
+ desktop.add(frame);
+ frame.toFront();
+ try{
+ frame.setSelected(true);
+ frame.requestFocus();
+ }catch(java.beans.PropertyVetoException ve)
+ {}
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dragEnter(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dragExit(DropTargetEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dragOver(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void drop(DropTargetDropEvent evt)
+ {
+ Transferable t = evt.getTransferable();
+
+ if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ return;
+ }
+
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+
+ try
+ {
+ java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+
+ for (int i = 0; i < files.size(); i++)
+ {
+ String file = files.get(i).toString();
+ String protocol = "File";
+ String format = null;
+
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+
+ }
+ else
+ {
+ format = jalview.io.IdentifyFile.Identify(file,
+ protocol);
+ }
+ LoadFile(file, protocol, format);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"),
+ new String[]
+ {
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+ "jar"
+ },
+ new String[]
+ {
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Open local file");
+ chooser.setToolTipText("Open");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ String format = null;
+ if (chooser.getSelectedFormat().equals("Jalview"))
+ {
+ format = "Jalview";
+ }
+ else
+ {
+ format = IdentifyFile.Identify(choice, "File");
+ }
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+ LoadFile(choice, "File", format);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ * @param protocol DOCUMENT ME!
+ * @param format DOCUMENT ME!
+ */
+ public void LoadFile(String file, String protocol, String format)
+ {
+ FileLoader fileLoader = new FileLoader();
+ fileLoader.LoadFile(file, protocol, format);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)
+ {
+ Object reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ "Enter url of input file", "Input alignment from URL",
+ JOptionPane.QUESTION_MESSAGE, null, null, "http://www.");
+
+ if (reply == null)
+ {
+ return;
+ }
+
+ String url = reply.toString().trim();
+
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
+ Jalview2XML.LoadJalviewAlign(url);
+ }
+ else
+ {
+
+ String format = IdentifyFile.Identify(url, "URL");
+
+ if (format.equals("URL NOT FOUND"))
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + url,
+ "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ LoadFile(url, "URL", format);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput();
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+ }
+
+ /*
+ * Exit the program
+ */
+ public void quit()
+ {
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+ System.exit(0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void aboutMenuItem_actionPerformed(ActionEvent e)
+ {
+ StringBuffer message = new StringBuffer("JalView 2005 version " +
+ jalview.bin.Cache.getProperty(
+ "VERSION") +
+ "; last updated: " +
+ jalview.bin.
+ Cache.getDefault("BUILD_DATE", "unknown"));
+
+ if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+ jalview.bin.Cache.getProperty("VERSION")))
+ {
+ message.append("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from http://www.jalview.org !!\n");
+
+ }
+
+ message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
+ "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
+ "\nFor all issues relating to Jalview, email help@jalview.org" +
+ "\n\nIf you use JalView, please cite:" +
+ "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
+ "\nBioinformatics, 2004 12;426-7.");
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ message.toString(), "About Jalview",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void documentationMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+ new Preferences();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveState_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "jar" },
+ new String[] { "Jalview Project" }, "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save State");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ Jalview2XML.SaveState(choice);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void loadState_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "jar" },
+ new String[] { "Jalview Project" }, "Jalview Project");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Restore state");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getAbsolutePath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+ Jalview2XML.LoadJalviewAlign(choice);
+ }
+ }
+
+ /* public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Vamsas file");
+ chooser.setToolTipText("Import");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+ vs.load(
+ chooser.getSelectedFile().getAbsolutePath()
+ );
+ }
+
+ }*/
+
+
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
+ SequenceFetcher sf = new SequenceFetcher(null);
+ }
+}
+