2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.io.*;
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24 import java.awt.datatransfer.*;
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25 import java.awt.dnd.*;
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26 import java.awt.event.*;
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28 import javax.swing.*;
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35 * @version $Revision$
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37 public class Desktop extends jalview.jbgui.GDesktop
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38 implements DropTargetListener, ClipboardOwner
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40 /** DOCUMENT ME!! */
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41 public static Desktop instance;
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42 public static JDesktopPane desktop;
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43 static int openFrameCount = 0;
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44 static final int xOffset = 30;
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45 static final int yOffset = 30;
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46 public static jalview.ws.Discoverer discoverer;
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48 public static Object [] jalviewClipboard;
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52 * Creates a new Desktop object.
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62 java.net.URL url = getClass().getResource("/images/logo.gif");
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66 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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68 MediaTracker mt = new MediaTracker(this);
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69 mt.addImage(image, 0);
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71 setIconImage(image);
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74 catch (Exception ex)
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78 setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
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79 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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80 desktop = new JDesktopPane();
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81 desktop.setBackground(Color.white);
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82 setContentPane(desktop);
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83 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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85 // This line prevents Windows Look&Feel resizing all new windows to maximum
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86 // if previous window was maximised
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87 desktop.setDesktopManager(new DefaultDesktopManager());
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89 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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90 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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91 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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92 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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93 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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95 if ((x != null) && (y != null) && (width != null) && (height != null))
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97 setBounds(Integer.parseInt(x), Integer.parseInt(y),
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98 Integer.parseInt(width), Integer.parseInt(height));
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102 setBounds((int) (screenSize.width - 900) / 2,
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103 (int) (screenSize.height - 650) / 2, 900, 650);
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106 this.addWindowListener(new WindowAdapter()
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108 public void windowClosing(WindowEvent evt)
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114 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
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116 /////////Add a splashscreen on startup
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117 /////////Add a splashscreen on startup
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118 JInternalFrame frame = new JInternalFrame();
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120 SplashScreen splash = new SplashScreen(frame, image);
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121 frame.setContentPane(splash);
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122 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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123 frame.setLocation((int) ((getWidth() - 750) / 2),
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124 (int) ((getHeight() - 160) / 2));
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126 addInternalFrame(frame, "", 750, 160, false);
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128 discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
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135 * @param frame DOCUMENT ME!
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136 * @param title DOCUMENT ME!
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137 * @param w DOCUMENT ME!
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138 * @param h DOCUMENT ME!
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140 public static synchronized void addInternalFrame(final JInternalFrame frame,
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141 String title, int w, int h)
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143 addInternalFrame(frame, title, w, h, true);
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149 * @param frame DOCUMENT ME!
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150 * @param title DOCUMENT ME!
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151 * @param w DOCUMENT ME!
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152 * @param h DOCUMENT ME!
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153 * @param resizable DOCUMENT ME!
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155 public static synchronized void addInternalFrame(final JInternalFrame frame,
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156 String title, int w, int h, boolean resizable)
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159 frame.setTitle(title);
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160 if(frame.getWidth()<1 || frame.getHeight()<1)
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162 frame.setSize(w, h);
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164 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
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165 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
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166 // IF JALVIEW IS RUNNING HEADLESS
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167 /////////////////////////////////////////////////
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168 if (System.getProperty("java.awt.headless") != null
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169 && System.getProperty("java.awt.headless").equals("true"))
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177 frame.setVisible(true);
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178 frame.setClosable(true);
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179 frame.setResizable(resizable);
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180 frame.setMaximizable(resizable);
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181 frame.setIconifiable(resizable);
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182 frame.setFrameIcon(null);
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184 if (frame.getX()<1 && frame.getY()<1)
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186 frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
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189 final JMenuItem menuItem = new JMenuItem(title);
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190 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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192 public void internalFrameActivated(javax.swing.event.
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193 InternalFrameEvent evt)
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195 JInternalFrame itf = desktop.getSelectedFrame();
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197 itf.requestFocus();
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201 public void internalFrameClosed(
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202 javax.swing.event.InternalFrameEvent evt)
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205 windowMenu.remove(menuItem);
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206 JInternalFrame itf = desktop.getSelectedFrame();
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208 itf.requestFocus();
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213 menuItem.addActionListener(new ActionListener()
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215 public void actionPerformed(ActionEvent e)
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219 frame.setSelected(true);
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220 frame.setIcon(false);
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222 catch (java.beans.PropertyVetoException ex)
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229 windowMenu.add(menuItem);
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231 desktop.add(frame);
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234 frame.setSelected(true);
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235 frame.requestFocus();
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236 }catch(java.beans.PropertyVetoException ve)
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240 public void lostOwnership(Clipboard clipboard, Transferable contents)
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242 Desktop.jalviewClipboard = null;
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245 public void dragEnter(DropTargetDragEvent evt)
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248 public void dragExit(DropTargetEvent evt)
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251 public void dragOver(DropTargetDragEvent evt)
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254 public void dropActionChanged(DropTargetDragEvent evt)
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260 * @param evt DOCUMENT ME!
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262 public void drop(DropTargetDropEvent evt)
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264 Transferable t = evt.getTransferable();
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265 java.util.List files = null;
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269 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
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270 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
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272 //Works on Windows and MacOSX
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273 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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274 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
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276 else if (t.isDataFlavorSupported(uriListFlavor))
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278 // This is used by Unix drag system
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279 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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280 String data = (String) t.getTransferData(uriListFlavor);
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281 files = new java.util.ArrayList(1);
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282 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
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285 st.hasMoreTokens(); )
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287 String s = st.nextToken();
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288 if (s.startsWith("#"))
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290 // the line is a comment (as per the RFC 2483)
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294 java.net.URI uri = new java.net.URI(s);
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295 java.io.File file = new java.io.File(uri);
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300 catch (Exception e)
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302 e.printStackTrace();
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309 for (int i = 0; i < files.size(); i++)
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311 String file = files.get(i).toString();
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312 String protocol = FormatAdapter.FILE;
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313 String format = null;
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315 if (file.endsWith(".jar"))
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317 format = "Jalview";
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322 format = new IdentifyFile().Identify(file,
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325 LoadFile(file, protocol, format);
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328 catch (Exception ex)
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330 ex.printStackTrace();
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338 * @param e DOCUMENT ME!
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340 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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342 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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346 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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351 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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352 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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354 chooser.setFileView(new JalviewFileView());
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355 chooser.setDialogTitle("Open local file");
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356 chooser.setToolTipText("Open");
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358 int value = chooser.showOpenDialog(this);
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360 if (value == JalviewFileChooser.APPROVE_OPTION)
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362 String choice = chooser.getSelectedFile().getPath();
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363 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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364 chooser.getSelectedFile().getParent());
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366 String format = null;
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367 if (chooser.getSelectedFormat().equals("Jalview"))
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369 format = "Jalview";
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373 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
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376 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
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377 LoadFile(choice, FormatAdapter.FILE, format);
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384 * @param file DOCUMENT ME!
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385 * @param protocol DOCUMENT ME!
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386 * @param format DOCUMENT ME!
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388 public void LoadFile(String file, String protocol, String format)
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390 FileLoader fileLoader = new FileLoader();
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391 fileLoader.LoadFile(file, protocol, format);
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397 * @param e DOCUMENT ME!
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399 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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401 // This construct allows us to have a wider textfield
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403 JLabel label = new JLabel("Enter URL of Input File");
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404 JTextField textinput = new JTextField("http://www.", 40);
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405 JPanel panel = new JPanel(new BorderLayout());
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406 panel.add(label, BorderLayout.NORTH);
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407 panel.add(textinput, BorderLayout.SOUTH);
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410 int reply = JOptionPane.showInternalConfirmDialog(desktop,
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411 panel, "Input Alignment From URL",
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412 JOptionPane.OK_CANCEL_OPTION );
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415 if (reply != JOptionPane.OK_OPTION )
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420 String url = textinput.getText();
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422 if (url.toLowerCase().endsWith(".jar"))
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424 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
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425 new Jalview2XML().LoadJalviewAlign(url);
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430 String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
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432 if (format.equals("URL NOT FOUND"))
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434 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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435 "Couldn't locate " + url,
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437 JOptionPane.WARNING_MESSAGE);
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442 LoadFile(url, FormatAdapter.URL, format);
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449 * @param e DOCUMENT ME!
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451 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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453 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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455 Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
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463 jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
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464 jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
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465 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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466 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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473 * @param e DOCUMENT ME!
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475 public void aboutMenuItem_actionPerformed(ActionEvent e)
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477 StringBuffer message = new StringBuffer("JalView version " +
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478 jalview.bin.Cache.getProperty(
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480 "; last updated: " +
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482 Cache.getDefault("BUILD_DATE", "unknown"));
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484 if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
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485 jalview.bin.Cache.getProperty("VERSION")))
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487 message.append("\n\n!! Jalview version "
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488 + jalview.bin.Cache.getProperty("LATEST_VERSION")
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489 + " is available for download from http://www.jalview.org !!\n");
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493 message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
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494 "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
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495 "\nFor all issues relating to Jalview, email help@jalview.org" +
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496 "\n\nIf you use JalView, please cite:" +
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497 "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
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498 "\nBioinformatics, 2004 12;426-7.");
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500 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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502 message.toString(), "About Jalview",
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503 JOptionPane.INFORMATION_MESSAGE);
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509 * @param e DOCUMENT ME!
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511 public void documentationMenuItem_actionPerformed(ActionEvent e)
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515 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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516 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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517 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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519 javax.help.HelpBroker hb = hs.createHelpBroker();
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520 hb.setCurrentID("home");
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521 hb.setDisplayed(true);
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523 catch (Exception ex)
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525 ex.printStackTrace();
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532 * @param e DOCUMENT ME!
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534 protected void preferences_actionPerformed(ActionEvent e)
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542 * @param e DOCUMENT ME!
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544 public void saveState_actionPerformed(ActionEvent e)
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546 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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547 "LAST_DIRECTORY"), new String[] { "jar" },
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548 new String[] { "Jalview Project" }, "Jalview Project");
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550 chooser.setFileView(new JalviewFileView());
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551 chooser.setDialogTitle("Save State");
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553 int value = chooser.showSaveDialog(this);
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555 if (value == JalviewFileChooser.APPROVE_OPTION)
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557 java.io.File choice = chooser.getSelectedFile();
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558 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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559 new Jalview2XML().SaveState(choice);
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566 * @param e DOCUMENT ME!
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568 public void loadState_actionPerformed(ActionEvent e)
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570 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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571 "LAST_DIRECTORY"), new String[] { "jar" },
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572 new String[] { "Jalview Project" }, "Jalview Project");
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573 chooser.setFileView(new JalviewFileView());
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574 chooser.setDialogTitle("Restore state");
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576 int value = chooser.showOpenDialog(this);
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578 if (value == JalviewFileChooser.APPROVE_OPTION)
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580 String choice = chooser.getSelectedFile().getAbsolutePath();
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581 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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582 chooser.getSelectedFile().getParent());
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583 new Jalview2XML().LoadJalviewAlign(choice);
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587 /* public void vamsasLoad_actionPerformed(ActionEvent e)
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589 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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590 getProperty("LAST_DIRECTORY"));
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592 chooser.setFileView(new JalviewFileView());
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593 chooser.setDialogTitle("Load Vamsas file");
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594 chooser.setToolTipText("Import");
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596 int value = chooser.showOpenDialog(this);
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598 if (value == JalviewFileChooser.APPROVE_OPTION)
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600 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
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602 chooser.getSelectedFile().getAbsolutePath()
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609 public void inputSequence_actionPerformed(ActionEvent e)
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611 SequenceFetcher sf = new SequenceFetcher(null);
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