X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=36183bb1f9804df638bec763214e0d3f1d7c197f;hb=0306c5b7a2aa4cc232ad0590a8ef285022eabd51;hp=f92f01c0bb16ee3c81a6194c9764df0e1feebeb0;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index f92f01c..36183bb 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -15,9 +15,13 @@ import jalview.datamodel.*; import javax.swing.*; import java.awt.*; import java.awt.event.*; +import java.awt.dnd.*; +import javax.swing.*; +import java.awt.datatransfer.*; +import jalview.bin.Cache; -public class Desktop extends jalview.jbgui.GDesktop +public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener { public static JDesktopPane desktop; static int openFrameCount = 0; @@ -25,11 +29,12 @@ public class Desktop extends jalview.jbgui.GDesktop public Desktop() { + Image image =null; try{ - java.net.URL url = getClass().getResource("/BartonGroupBanner.gif"); + java.net.URL url = getClass().getResource("/images/logo.gif"); if(url!=null) { - Image image = java.awt.Toolkit.getDefaultToolkit().createImage(url); + image = java.awt.Toolkit.getDefaultToolkit().createImage(url); MediaTracker mt = new MediaTracker(this); mt.addImage(image, 0); mt.waitForID(0); @@ -40,41 +45,93 @@ public class Desktop extends jalview.jbgui.GDesktop setTitle("Jalview 2005"); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - setVisible(true); desktop = new JDesktopPane(); + desktop.setBackground(Color.white); setContentPane(desktop); desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - int inset = 150; + + + // 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(); - setBounds(inset, inset, - screenSize.width - inset*2, - screenSize.height - inset*2); - } + 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) +{ + 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() + ""); +} +}); +setVisible(true); + +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); + addInternalFrame(frame, "", 750,160, false); + frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2)); + } public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h) { - frame.setVisible(true); //necessary as of 1.3 + addInternalFrame(frame, title, w, h, true); + } + + public static void addInternalFrame(final JInternalFrame frame, String title, + int w, + int h, + boolean resizable ) + { desktop.add(frame); openFrameCount++; try { frame.setSelected(true); } catch (java.beans.PropertyVetoException e) {} frame.setTitle(title); - frame.setResizable(true); frame.setSize(w,h); frame.setClosable(true); - frame.setMaximizable(true); - frame.setIconifiable(true); + frame.setResizable(resizable); + frame.setMaximizable(resizable); + frame.setIconifiable(resizable); + frame.setFrameIcon(null); frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount); frame.toFront(); 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); - }; - }); + { + public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt) + { + openFrameCount--; + windowMenu.remove(menuItem); + }; + }); menuItem.addActionListener(new ActionListener() { @@ -85,63 +142,129 @@ public class Desktop extends jalview.jbgui.GDesktop } }); + frame.setVisible(true); windowMenu.add(menuItem); } + public void dragEnter(DropTargetDragEvent evt){} + public void dragExit(DropTargetEvent evt){} + public void dragOver(DropTargetDragEvent evt){} + public void dropActionChanged(DropTargetDragEvent evt){} + 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"; + if(file.endsWith(".jar")) + Jalview2XML.LoadJalviewAlign(file); + else + { + String format = jalview.io.IdentifyFile.Identify(file, protocol); + LoadFile(file, protocol, format); + } + } + + }catch(Exception ex){ex.printStackTrace();} + } public void inputLocalFileMenuItem_actionPerformed(ActionEvent e) { - JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY); + 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 == JFileChooser.APPROVE_OPTION) + if(value == JalviewFileChooser.APPROVE_OPTION) { + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat()); String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.LAST_DIRECTORY = choice; - String format = IdentifyFile.Identify(choice, "File"); - LoadFile(choice, "File", format); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent()); + if(chooser.getSelectedFormat().equals("Jalview")) + { + Jalview2XML.LoadJalviewAlign(choice); + } + else + { + String format = IdentifyFile.Identify(choice, "File"); + LoadFile(choice, "File", format); + } } } public void LoadFile(String file, String protocol, String format) { - SequenceI [] sequences = null; - + LoadingThread loader = new LoadingThread(file, protocol, format); + loader.start(); + } - if (FormatProperties.contains(format)) - sequences = FormatAdapter.read(file, protocol, format); + class LoadingThread extends Thread + { + String file, protocol, format; - if (sequences != null) + public LoadingThread(String file, String protocol, String format) { - AlignFrame af = new AlignFrame(new Alignment(sequences)); - addInternalFrame(af, file, 700, 500); - af.statusBar.setText("Successfully loaded file " + file); + this.file = file; + this.protocol = protocol; + this.format = format; } - else - JOptionPane.showMessageDialog(this, "Couldn't open file.\n" - + "Formats currently supported are\n" - + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" - ,"Error loading file", - JOptionPane.WARNING_MESSAGE); + public void run() + { + SequenceI [] sequences = null; + + if (FormatAdapter.formats.contains(format)) + sequences = FormatAdapter.readFile(file, protocol, format); + + if (sequences != null && sequences.length>0) + { + AlignFrame af = new AlignFrame(new Alignment(sequences)); + addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT); + af.currentFileFormat = format; + af.statusBar.setText("Successfully loaded file " + file); + try{ + af.setMaximum(Preferences.showFullscreen); + }catch(Exception ex){} + + } + else + JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n" + + "Formats currently supported are\n" + + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter! + ,"Error loading file", + JOptionPane.WARNING_MESSAGE); + } } + public void inputURLMenuItem_actionPerformed(ActionEvent e) { - String url = JOptionPane.showInputDialog(this,"Enter url of input file", + String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file", "Input alignment from URL", - JOptionPane.QUESTION_MESSAGE); + JOptionPane.QUESTION_MESSAGE, + null, null, + "http://www.").toString(); if (url == null) return; String format = IdentifyFile.Identify(url, "URL"); - System.out.println(format +" format"); if (format.equals("URL NOT FOUND")) { - JOptionPane.showMessageDialog(this,"Couldn't locate " + url, + JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url, "URL not found", JOptionPane.WARNING_MESSAGE); return; @@ -153,7 +276,7 @@ public class Desktop extends jalview.jbgui.GDesktop public void inputTextboxMenuItem_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(true); - int accept = JOptionPane.showInternalOptionDialog(desktop, cap, "Cut & paste Alignment File", + int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, @@ -165,23 +288,25 @@ public class Desktop extends jalview.jbgui.GDesktop String format = IdentifyFile.Identify(cap.getText(), "Paste"); SequenceI [] sequences = null; - if (FormatProperties.contains( format )) - sequences = FormatAdapter.read(cap.getText(), "Paste", format); + if (FormatAdapter.formats.contains( format )) + sequences = FormatAdapter.readFile(cap.getText(), "Paste", format); if(sequences!=null) { AlignFrame af = new AlignFrame(new Alignment(sequences)); - addInternalFrame(af, "Cut & Paste input - "+format, 700, 500); + af.currentFileFormat = format; + addInternalFrame(af, "Cut & Paste input - "+format, + AlignFrame.NEW_WINDOW_WIDTH, + AlignFrame.NEW_WINDOW_HEIGHT); af.statusBar.setText("Successfully pasted alignment file"); } else - JOptionPane.showMessageDialog(this, "Couldn't read the pasted text.\n" + JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n" +"Formats currently supported are\n" - +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM", + +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM", "Error parsing text", JOptionPane.WARNING_MESSAGE); - } } @@ -190,33 +315,86 @@ public class Desktop extends jalview.jbgui.GDesktop */ public void quit_actionPerformed(ActionEvent e) { - this.setVisible(false); - System.exit(0); + if(jalview.bin.Jalview.applet!=null) + jalview.bin.Jalview.applet.destroy(); + else + System.exit(0); } - protected void colourIndexMenuItem_actionPerformed(ActionEvent e) - { - ColourKey colourKey = new ColourKey(null); - addInternalFrame(colourKey, "Colour scheme key", 400, 320); - } - public void aboutMenuItem_actionPerformed(ActionEvent e) { - JOptionPane.showInternalMessageDialog(desktop, - "Jalview 1998-2005\n" - +"Sequence Alignment viewer & editor", + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE + +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." + +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." + +"\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.", "About Jalview", JOptionPane.INFORMATION_MESSAGE); } public void documentationMenuItem_actionPerformed(ActionEvent e) { - try{ - jalview.util.BrowserLauncher.openURL("http://jalview.org/documentation.html"); - }catch(Exception ex){} + 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.setLocation(new Point(200, 50)); + hb.setSize(new Dimension(800,700)); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + protected void preferences_actionPerformed(ActionEvent e) + { + Preferences pref = new Preferences(); + } + + public void saveState_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY"), + new String[] + {"xml"}, 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); + } + } + public void loadState_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[]{"xml"}, 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.LoadState(choice); + } + } } + +