X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=336cdd3dba797975ea52e21dc962802912fa7a2a;hb=f1eef48c0073f03279b444dc297780c26d238cd8;hp=aafd8c0f676307bac0c3b4ed77f774c74a4d2245;hpb=b1bc2a997b0620a85818ed5f6813326c1faae9d3;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index aafd8c0..336cdd3 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -12,12 +12,17 @@ package jalview.gui; import jalview.gui.*; import jalview.io.*; import jalview.datamodel.*; +import jalview.schemes.*; import javax.swing.*; import java.awt.*; import java.awt.event.*; +import java.awt.dnd.*; +import javax.swing.*; +import java.awt.datatransfer.*; +import java.io.*; -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 +30,12 @@ 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); @@ -40,20 +46,72 @@ 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; + 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 + JInternalFrame frame = new JInternalFrame(); + + SplashScreen splash = new SplashScreen(frame, image); + frame.setContentPane(splash); + desktop.add(frame); + + openFrameCount++; + try + { + frame.setSelected(true); + } + catch (java.beans.PropertyVetoException e) + {} + frame.setResizable(true); + frame.setSize(750, 160); + frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2)); + frame.setClosable(false); + frame.setIconifiable(false); + frame.setMaximizable(false); + frame.setFrameIcon(null); + frame.setVisible(true); + } public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h) { - frame.setVisible(true); //necessary as of 1.3 desktop.add(frame); openFrameCount++; try { @@ -65,6 +123,7 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setClosable(true); frame.setMaximizable(true); frame.setIconifiable(true); + frame.setFrameIcon(null); frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount); frame.toFront(); final JMenuItem menuItem = new JMenuItem(title); @@ -85,21 +144,47 @@ 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"; + 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", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files"); + 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) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.LAST_DIRECTORY = choice; + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); String format = IdentifyFile.Identify(choice, "File"); LoadFile(choice, "File", format); } @@ -109,22 +194,20 @@ public class Desktop extends jalview.jbgui.GDesktop { SequenceI [] sequences = null; - if (FormatProperties.contains(format)) sequences = FormatAdapter.read(file, protocol, format); - if (sequences != null) + if (sequences != null && sequences.length>0) { AlignFrame af = new AlignFrame(new Alignment(sequences)); addInternalFrame(af, file, 700, 500); af.statusBar.setText("Successfully loaded file " + file); - } else - JOptionPane.showMessageDialog(this, "Couldn't open file.\n" + JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n" + "Formats currently supported are\n" - + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" + + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter! ,"Error loading file", JOptionPane.WARNING_MESSAGE); @@ -132,7 +215,7 @@ public class Desktop extends jalview.jbgui.GDesktop 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); if (url == null) @@ -140,10 +223,9 @@ public class Desktop extends jalview.jbgui.GDesktop 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; @@ -155,7 +237,7 @@ 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, @@ -178,12 +260,11 @@ public class Desktop extends jalview.jbgui.GDesktop 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", "Error parsing text", JOptionPane.WARNING_MESSAGE); - } } @@ -192,35 +273,130 @@ 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 2005" - +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse and Geoff Barton." + 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: \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", + +"\nIf you use JalView, please cite: Bioinformatics, 2004 12;426-7." + +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", "About Jalview", JOptionPane.INFORMATION_MESSAGE); } 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.setLocation(new Point(200, 50)); + hb.setSize(new Dimension(800,700)); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + static JInternalFrame conservationSlider; + static JInternalFrame PIDSlider; + public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source) + { + SliderPanel sp = null; + ConservationColourScheme ccs = (ConservationColourScheme)cs; + int value = ccs.inc; + + if(conservationSlider == null) + { + sp = new SliderPanel(ap, value, true, cs); + conservationSlider = new JInternalFrame(); + conservationSlider.setContentPane(sp); + addInternalFrame(conservationSlider, "Conservation Colour Increment ("+source+")", 420, 90); + conservationSlider.setResizable(false); + conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed(javax.swing.event.InternalFrameEvent e) + { + conservationSlider = null; + } + }); + } + else + { + + conservationSlider.setTitle("Conservation Colour Increment ("+source+")"); + sp = (SliderPanel)conservationSlider.getContentPane(); + sp.cs = cs; + sp.setValue(value); + } + + if(ap.av.alignment.getGroups()!=null) + sp.setAllGroupsCheckEnabled( true ); + else + sp.setAllGroupsCheckEnabled( false); + + return sp.getValue(); + + } + + public static void hideConservationSlider() + { + try{ + conservationSlider.setClosed(true); + conservationSlider = null; + }catch(Exception ex){} +} + + + public static void hidePIDSlider() + { try{ - jalview.util.BrowserLauncher.openURL("http://jalview.org/documentation.html"); + PIDSlider.setClosed(true); + PIDSlider = null; }catch(Exception ex){} } + public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source) + { + SliderPanel pid = null; + if(PIDSlider == null) + { + pid = new SliderPanel(ap, 50, false, cs); + PIDSlider = new JInternalFrame(); + PIDSlider.setContentPane(pid); + addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90); + PIDSlider.setResizable(false); + } + else + { + PIDSlider.setTitle("Percentage Identity Threshold ("+source+")"); + pid = (SliderPanel)PIDSlider.getContentPane(); + pid.cs = cs; + } + + if (ap.av.alignment.getGroups() != null) + pid.setAllGroupsCheckEnabled(true); + else + pid.setAllGroupsCheckEnabled(false); + + + return pid.getValue(); + + } }