1 /********************
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2 * 2004 Jalview Reengineered
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10 package jalview.gui;
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12 import jalview.gui.*;
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13 import jalview.io.*;
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14 import jalview.datamodel.*;
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15 import javax.swing.*;
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17 import java.awt.event.*;
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18 import java.awt.dnd.*;
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19 import javax.swing.*;
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20 import java.awt.datatransfer.*;
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21 import jalview.bin.Cache;
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24 public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
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26 public static JDesktopPane desktop;
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27 static int openFrameCount = 0;
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28 static final int xOffset = 30, yOffset = 30;
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34 java.net.URL url = getClass().getResource("/images/logo.gif");
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37 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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38 MediaTracker mt = new MediaTracker(this);
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39 mt.addImage(image, 0);
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41 setIconImage(image);
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44 }catch(Exception ex){}
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46 setTitle("Jalview 2005");
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47 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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48 desktop = new JDesktopPane();
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49 desktop.setBackground(Color.white);
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50 setContentPane(desktop);
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51 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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54 // This line prevents Windows Look&Feel resizing all new windows to maximum
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55 // if previous window was maximised
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56 desktop.setDesktopManager( new DefaultDesktopManager() );
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59 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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60 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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61 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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62 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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63 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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65 if(x!=null && y!=null && width!=null && height!=null)
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67 setBounds( Integer.parseInt(x), Integer.parseInt(y),
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68 Integer.parseInt(width), Integer.parseInt(height));
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71 setBounds( (int)(screenSize.width-900)/2,
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72 (int)(screenSize.height-650)/2,
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76 this.addWindowListener(new WindowAdapter()
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78 public void windowClosing(WindowEvent evt)
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80 jalview.bin.Cache.setProperty("SCREEN_X",
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81 getBounds().x + "");
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82 jalview.bin.Cache.setProperty("SCREEN_Y",
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83 getBounds().y + "");
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84 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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85 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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90 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
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92 /////////Add a splashscreen on startup
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93 /////////Add a splashscreen on startup
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94 JInternalFrame frame = new JInternalFrame();
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96 SplashScreen splash = new SplashScreen(frame, image);
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97 frame.setContentPane(splash);
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98 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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99 addInternalFrame(frame, "", 750,160, false);
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100 frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
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102 public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
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104 addInternalFrame(frame, title, w, h, true);
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107 public static void addInternalFrame(final JInternalFrame frame, String title,
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110 boolean resizable )
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112 desktop.add(frame);
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115 frame.setSelected(true);
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116 } catch (java.beans.PropertyVetoException e) {}
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117 frame.setTitle(title);
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118 frame.setSize(w,h);
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119 frame.setClosable(true);
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120 frame.setResizable(resizable);
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121 frame.setMaximizable(resizable);
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122 frame.setIconifiable(resizable);
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123 frame.setFrameIcon(null);
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124 frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
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126 final JMenuItem menuItem = new JMenuItem(title);
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127 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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129 public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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132 windowMenu.remove(menuItem);
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136 menuItem.addActionListener(new ActionListener()
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138 public void actionPerformed(ActionEvent e)
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140 try{ frame.setSelected(true); frame.setIcon(false); }
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141 catch(java.beans.PropertyVetoException ex){};
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145 frame.setVisible(true);
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146 windowMenu.add(menuItem);
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149 public void dragEnter(DropTargetDragEvent evt){}
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150 public void dragExit(DropTargetEvent evt){}
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151 public void dragOver(DropTargetDragEvent evt){}
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152 public void dropActionChanged(DropTargetDragEvent evt){}
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153 public void drop(DropTargetDropEvent evt)
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155 Transferable t = evt.getTransferable();
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156 if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
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159 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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161 java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
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163 for (int i = 0; i < files.size(); i++)
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165 String file = files.get(i).toString();
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166 String protocol = "File";
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167 if(file.endsWith(".jar"))
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168 Jalview2XML.LoadJalviewAlign(file);
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171 String format = jalview.io.IdentifyFile.Identify(file, protocol);
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172 LoadFile(file, protocol, format);
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176 }catch(Exception ex){ex.printStackTrace();}
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180 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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182 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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183 new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},
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184 new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}
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185 ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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187 chooser.setFileView(new JalviewFileView());
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188 chooser.setDialogTitle("Open local file");
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189 chooser.setToolTipText("Open");
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190 int value = chooser.showOpenDialog(this);
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191 if(value == JalviewFileChooser.APPROVE_OPTION)
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193 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
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194 String choice = chooser.getSelectedFile().getPath();
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195 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
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196 if(chooser.getSelectedFormat().equals("Jalview"))
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198 Jalview2XML.LoadJalviewAlign(choice);
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202 String format = IdentifyFile.Identify(choice, "File");
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203 LoadFile(choice, "File", format);
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208 public void LoadFile(String file, String protocol, String format)
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210 LoadingThread loader = new LoadingThread(file, protocol, format);
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214 class LoadingThread extends Thread
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216 String file, protocol, format;
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218 public LoadingThread(String file, String protocol, String format)
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221 this.protocol = protocol;
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222 this.format = format;
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226 SequenceI [] sequences = null;
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228 if (FormatAdapter.formats.contains(format))
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229 sequences = FormatAdapter.readFile(file, protocol, format);
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231 if (sequences != null && sequences.length>0)
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233 AlignFrame af = new AlignFrame(new Alignment(sequences));
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234 addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
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235 af.currentFileFormat = format;
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236 af.statusBar.setText("Successfully loaded file " + file);
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238 af.setMaximum(Preferences.showFullscreen);
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239 }catch(Exception ex){}
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243 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"
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244 + "Formats currently supported are\n"
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245 + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
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246 ,"Error loading file",
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247 JOptionPane.WARNING_MESSAGE);
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253 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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255 String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
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256 "Input alignment from URL",
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257 JOptionPane.QUESTION_MESSAGE,
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259 "http://www.").toString();
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263 String format = IdentifyFile.Identify(url, "URL");
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265 if (format.equals("URL NOT FOUND"))
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267 JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
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269 JOptionPane.WARNING_MESSAGE);
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273 LoadFile(url, "URL", format);
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276 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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278 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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279 int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
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280 JOptionPane.YES_NO_CANCEL_OPTION,
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281 JOptionPane.PLAIN_MESSAGE,
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283 new Object[]{"Accept", "Cancel", }, null);
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286 if(accept == JOptionPane.YES_OPTION)
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288 String format = IdentifyFile.Identify(cap.getText(), "Paste");
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289 SequenceI [] sequences = null;
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291 if (FormatAdapter.formats.contains( format ))
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292 sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);
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295 if(sequences!=null)
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297 AlignFrame af = new AlignFrame(new Alignment(sequences));
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298 af.currentFileFormat = format;
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299 addInternalFrame(af, "Cut & Paste input - "+format,
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300 AlignFrame.NEW_WINDOW_WIDTH,
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301 AlignFrame.NEW_WINDOW_HEIGHT);
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302 af.statusBar.setText("Successfully pasted alignment file");
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305 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
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306 +"Formats currently supported are\n"
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307 +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
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308 "Error parsing text", JOptionPane.WARNING_MESSAGE);
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316 public void quit_actionPerformed(ActionEvent e)
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318 if(jalview.bin.Jalview.applet!=null)
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319 jalview.bin.Jalview.applet.destroy();
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326 public void aboutMenuItem_actionPerformed(ActionEvent e)
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328 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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329 "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
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330 +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
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331 +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
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332 +"\nIf you use JalView, please cite:"
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333 +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
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334 +"\nBioinformatics, 2004 12;426-7.",
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336 JOptionPane.INFORMATION_MESSAGE);
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339 public void documentationMenuItem_actionPerformed(ActionEvent e)
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343 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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344 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
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345 javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
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347 javax.help.HelpBroker hb = hs.createHelpBroker();
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348 hb.setLocation(new Point(200, 50));
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349 hb.setSize(new Dimension(800,700));
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350 hb.setCurrentID("home");
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351 hb.setDisplayed(true);
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353 catch (Exception ex)
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355 ex.printStackTrace();
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359 protected void preferences_actionPerformed(ActionEvent e)
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361 Preferences pref = new Preferences();
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364 public void saveState_actionPerformed(ActionEvent e)
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366 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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367 getProperty("LAST_DIRECTORY"),
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369 {"jar"}, new String[]{"Jalview Project"}, "Jalview Project");
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371 chooser.setFileView(new JalviewFileView());
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372 chooser.setDialogTitle("Save State");
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373 int value = chooser.showSaveDialog(this);
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374 if (value == JalviewFileChooser.APPROVE_OPTION)
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376 java.io.File choice = chooser.getSelectedFile();
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377 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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378 Jalview2XML.SaveState(choice);
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384 public void loadState_actionPerformed(ActionEvent e)
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386 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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387 new String[]{"jar"}, new String[]{"Jalview Project"}, "Jalview Project");
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388 chooser.setFileView(new JalviewFileView());
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389 chooser.setDialogTitle("Restore state");
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390 int value = chooser.showOpenDialog(this);
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391 if(value == JalviewFileChooser.APPROVE_OPTION)
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393 String choice = chooser.getSelectedFile().getAbsolutePath();
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394 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
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395 Jalview2XML.LoadJalviewAlign(choice);
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