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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29 import javax.swing.*;
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36 * @version $Revision$
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38 public class Desktop extends jalview.jbgui.GDesktop
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39 implements DropTargetListener, ClipboardOwner
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41 /** DOCUMENT ME!! */
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42 public static Desktop instance;
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43 public static JDesktopPane desktop;
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44 static int openFrameCount = 0;
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45 static final int xOffset = 30;
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46 static final int yOffset = 30;
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47 public static jalview.ws.Discoverer discoverer;
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49 public static Object [] jalviewClipboard;
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53 * Creates a new Desktop object.
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63 java.net.URL url = getClass().getResource("/images/logo.gif");
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67 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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69 MediaTracker mt = new MediaTracker(this);
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70 mt.addImage(image, 0);
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72 setIconImage(image);
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75 catch (Exception ex)
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79 setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
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80 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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81 desktop = new JDesktopPane();
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82 desktop.setBackground(Color.white);
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83 setContentPane(desktop);
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84 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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86 // This line prevents Windows Look&Feel resizing all new windows to maximum
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87 // if previous window was maximised
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88 desktop.setDesktopManager(new DefaultDesktopManager());
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90 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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91 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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92 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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93 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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94 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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96 if ((x != null) && (y != null) && (width != null) && (height != null))
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98 setBounds(Integer.parseInt(x), Integer.parseInt(y),
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99 Integer.parseInt(width), Integer.parseInt(height));
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103 setBounds((int) (screenSize.width - 900) / 2,
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104 (int) (screenSize.height - 650) / 2, 900, 650);
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107 this.addWindowListener(new WindowAdapter()
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109 public void windowClosing(WindowEvent evt)
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115 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
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117 /////////Add a splashscreen on startup
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118 /////////Add a splashscreen on startup
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119 JInternalFrame frame = new JInternalFrame();
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121 SplashScreen splash = new SplashScreen(frame, image);
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122 frame.setContentPane(splash);
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123 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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124 frame.setLocation((int) ((getWidth() - 750) / 2),
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125 (int) ((getHeight() - 160) / 2));
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127 addInternalFrame(frame, "", 750, 160, false);
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129 discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
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136 * @param frame DOCUMENT ME!
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137 * @param title DOCUMENT ME!
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138 * @param w DOCUMENT ME!
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139 * @param h DOCUMENT ME!
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141 public static synchronized void addInternalFrame(final JInternalFrame frame,
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142 String title, int w, int h)
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144 addInternalFrame(frame, title, w, h, true);
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150 * @param frame DOCUMENT ME!
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151 * @param title DOCUMENT ME!
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152 * @param w DOCUMENT ME!
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153 * @param h DOCUMENT ME!
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154 * @param resizable DOCUMENT ME!
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156 public static synchronized void addInternalFrame(final JInternalFrame frame,
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157 String title, int w, int h, boolean resizable)
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160 frame.setTitle(title);
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161 if(frame.getWidth()<1 || frame.getHeight()<1)
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163 frame.setSize(w, h);
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165 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
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166 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
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167 // IF JALVIEW IS RUNNING HEADLESS
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168 /////////////////////////////////////////////////
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169 if (System.getProperty("java.awt.headless") != null
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170 && System.getProperty("java.awt.headless").equals("true"))
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178 frame.setVisible(true);
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179 frame.setClosable(true);
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180 frame.setResizable(resizable);
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181 frame.setMaximizable(resizable);
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182 frame.setIconifiable(resizable);
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183 frame.setFrameIcon(null);
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185 if (frame.getX()<1 && frame.getY()<1)
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187 frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
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190 final JMenuItem menuItem = new JMenuItem(title);
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191 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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193 public void internalFrameActivated(javax.swing.event.
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194 InternalFrameEvent evt)
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196 JInternalFrame itf = desktop.getSelectedFrame();
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198 itf.requestFocus();
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202 public void internalFrameClosed(
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203 javax.swing.event.InternalFrameEvent evt)
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206 windowMenu.remove(menuItem);
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207 JInternalFrame itf = desktop.getSelectedFrame();
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209 itf.requestFocus();
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214 menuItem.addActionListener(new ActionListener()
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216 public void actionPerformed(ActionEvent e)
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220 frame.setSelected(true);
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221 frame.setIcon(false);
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223 catch (java.beans.PropertyVetoException ex)
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230 windowMenu.add(menuItem);
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232 desktop.add(frame);
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235 frame.setSelected(true);
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236 frame.requestFocus();
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237 }catch(java.beans.PropertyVetoException ve)
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241 public void lostOwnership(Clipboard clipboard, Transferable contents)
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243 Desktop.jalviewClipboard = null;
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246 public void dragEnter(DropTargetDragEvent evt)
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249 public void dragExit(DropTargetEvent evt)
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252 public void dragOver(DropTargetDragEvent evt)
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255 public void dropActionChanged(DropTargetDragEvent evt)
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261 * @param evt DOCUMENT ME!
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263 public void drop(DropTargetDropEvent evt)
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265 Transferable t = evt.getTransferable();
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266 java.util.List files = null;
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270 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
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271 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
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273 //Works on Windows and MacOSX
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274 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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275 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
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277 else if (t.isDataFlavorSupported(uriListFlavor))
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279 // This is used by Unix drag system
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280 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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281 String data = (String) t.getTransferData(uriListFlavor);
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282 files = new java.util.ArrayList(1);
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283 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
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286 st.hasMoreTokens(); )
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288 String s = st.nextToken();
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289 if (s.startsWith("#"))
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291 // the line is a comment (as per the RFC 2483)
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295 java.net.URI uri = new java.net.URI(s);
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296 java.io.File file = new java.io.File(uri);
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301 catch (Exception e)
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303 e.printStackTrace();
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310 for (int i = 0; i < files.size(); i++)
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312 String file = files.get(i).toString();
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313 String protocol = FormatAdapter.FILE;
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314 String format = null;
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316 if (file.endsWith(".jar"))
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318 format = "Jalview";
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323 format = new IdentifyFile().Identify(file,
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328 new FileLoader().LoadFile(file, protocol, format);
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332 catch (Exception ex)
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334 ex.printStackTrace();
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342 * @param e DOCUMENT ME!
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344 public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
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346 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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350 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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355 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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356 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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358 chooser.setFileView(new JalviewFileView());
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359 chooser.setDialogTitle("Open local file");
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360 chooser.setToolTipText("Open");
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362 int value = chooser.showOpenDialog(this);
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364 if (value == JalviewFileChooser.APPROVE_OPTION)
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366 String choice = chooser.getSelectedFile().getPath();
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367 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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368 chooser.getSelectedFile().getParent());
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370 String format = null;
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371 if (chooser.getSelectedFormat().equals("Jalview"))
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373 format = "Jalview";
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377 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
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380 if (viewport != null)
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381 new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
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383 new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
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392 * @param e DOCUMENT ME!
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394 public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
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396 // This construct allows us to have a wider textfield
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398 JLabel label = new JLabel("Enter URL of Input File");
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399 final JComboBox history = new JComboBox();
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401 JPanel panel = new JPanel(new GridLayout(2,1));
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403 panel.add(history);
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404 history.setPreferredSize(new Dimension(400,20));
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405 history.setEditable(true);
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406 history.addItem("http://www.");
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408 String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
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410 StringTokenizer st;
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412 if (historyItems != null)
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414 st = new StringTokenizer(historyItems, "\t");
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416 while (st.hasMoreTokens())
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418 history.addItem(st.nextElement());
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422 int reply = JOptionPane.showInternalConfirmDialog(desktop,
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423 panel, "Input Alignment From URL",
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424 JOptionPane.OK_CANCEL_OPTION );
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427 if (reply != JOptionPane.OK_OPTION )
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432 String url = history.getSelectedItem().toString();
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434 if (url.toLowerCase().endsWith(".jar"))
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436 if (viewport != null)
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437 new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
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439 new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
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443 String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
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445 if (format.equals("URL NOT FOUND"))
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447 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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448 "Couldn't locate " + url,
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450 JOptionPane.WARNING_MESSAGE);
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455 if (viewport != null)
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456 new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
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458 new FileLoader().LoadFile(url, FormatAdapter.URL, format);
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465 * @param e DOCUMENT ME!
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467 public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
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469 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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470 cap.setForInput(viewport);
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471 Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
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479 jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
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480 jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
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481 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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482 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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489 * @param e DOCUMENT ME!
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491 public void aboutMenuItem_actionPerformed(ActionEvent e)
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493 StringBuffer message = new StringBuffer("JalView version " +
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494 jalview.bin.Cache.getProperty(
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496 "; last updated: " +
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498 Cache.getDefault("BUILD_DATE", "unknown"));
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500 if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
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501 jalview.bin.Cache.getProperty("VERSION")))
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503 message.append("\n\n!! Jalview version "
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504 + jalview.bin.Cache.getProperty("LATEST_VERSION")
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505 + " is available for download from http://www.jalview.org !!\n");
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509 message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
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510 "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
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511 "\nFor all issues relating to Jalview, email help@jalview.org" +
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512 "\n\nIf you use JalView, please cite:" +
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513 "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
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514 "\nBioinformatics, 2004 12;426-7.");
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516 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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518 message.toString(), "About Jalview",
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519 JOptionPane.INFORMATION_MESSAGE);
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525 * @param e DOCUMENT ME!
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527 public void documentationMenuItem_actionPerformed(ActionEvent e)
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531 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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532 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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533 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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535 javax.help.HelpBroker hb = hs.createHelpBroker();
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536 hb.setCurrentID("home");
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537 hb.setDisplayed(true);
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539 catch (Exception ex)
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541 ex.printStackTrace();
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548 * @param e DOCUMENT ME!
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550 protected void preferences_actionPerformed(ActionEvent e)
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558 * @param e DOCUMENT ME!
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560 public void saveState_actionPerformed(ActionEvent e)
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562 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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563 "LAST_DIRECTORY"), new String[] { "jar" },
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564 new String[] { "Jalview Project" }, "Jalview Project");
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566 chooser.setFileView(new JalviewFileView());
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567 chooser.setDialogTitle("Save State");
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569 int value = chooser.showSaveDialog(this);
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571 if (value == JalviewFileChooser.APPROVE_OPTION)
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573 java.io.File choice = chooser.getSelectedFile();
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574 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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575 new Jalview2XML().SaveState(choice);
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582 * @param e DOCUMENT ME!
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584 public void loadState_actionPerformed(ActionEvent e)
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586 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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587 "LAST_DIRECTORY"), new String[] { "jar" },
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588 new String[] { "Jalview Project" }, "Jalview Project");
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589 chooser.setFileView(new JalviewFileView());
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590 chooser.setDialogTitle("Restore state");
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592 int value = chooser.showOpenDialog(this);
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594 if (value == JalviewFileChooser.APPROVE_OPTION)
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596 String choice = chooser.getSelectedFile().getAbsolutePath();
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597 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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598 chooser.getSelectedFile().getParent());
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599 new Jalview2XML().LoadJalviewAlign(choice);
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603 /* public void vamsasLoad_actionPerformed(ActionEvent e)
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605 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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606 getProperty("LAST_DIRECTORY"));
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608 chooser.setFileView(new JalviewFileView());
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609 chooser.setDialogTitle("Load Vamsas file");
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610 chooser.setToolTipText("Import");
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612 int value = chooser.showOpenDialog(this);
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614 if (value == JalviewFileChooser.APPROVE_OPTION)
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616 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
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618 chooser.getSelectedFile().getAbsolutePath()
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625 public void inputSequence_actionPerformed(ActionEvent e)
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627 SequenceFetcher sf = new SequenceFetcher(null);
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