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
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40 /** DOCUMENT ME!! */
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41 public static JDesktopPane desktop;
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42 static int openFrameCount = 0;
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43 static final int xOffset = 30;
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44 static final int yOffset = 30;
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45 public static jalview.ws.Discoverer discoverer;
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47 public static Object [] jalviewClipboard;
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51 * Creates a new Desktop object.
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60 java.net.URL url = getClass().getResource("/images/logo.gif");
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64 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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66 MediaTracker mt = new MediaTracker(this);
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67 mt.addImage(image, 0);
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69 setIconImage(image);
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72 catch (Exception ex)
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76 setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
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77 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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78 desktop = new JDesktopPane();
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79 desktop.setBackground(Color.white);
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80 setContentPane(desktop);
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81 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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83 // This line prevents Windows Look&Feel resizing all new windows to maximum
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84 // if previous window was maximised
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85 desktop.setDesktopManager(new DefaultDesktopManager());
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87 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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88 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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89 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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90 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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91 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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93 if ((x != null) && (y != null) && (width != null) && (height != null))
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95 setBounds(Integer.parseInt(x), Integer.parseInt(y),
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96 Integer.parseInt(width), Integer.parseInt(height));
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100 setBounds((int) (screenSize.width - 900) / 2,
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101 (int) (screenSize.height - 650) / 2, 900, 650);
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104 this.addWindowListener(new WindowAdapter()
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106 public void windowClosing(WindowEvent evt)
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112 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
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114 /////////Add a splashscreen on startup
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115 /////////Add a splashscreen on startup
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116 JInternalFrame frame = new JInternalFrame();
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118 SplashScreen splash = new SplashScreen(frame, image);
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119 frame.setContentPane(splash);
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120 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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121 frame.setLocation((int) ((getWidth() - 750) / 2),
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122 (int) ((getHeight() - 160) / 2));
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124 addInternalFrame(frame, "", 750, 160, false);
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126 discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
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133 * @param frame DOCUMENT ME!
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134 * @param title DOCUMENT ME!
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135 * @param w DOCUMENT ME!
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136 * @param h DOCUMENT ME!
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138 public static synchronized void addInternalFrame(final JInternalFrame frame,
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139 String title, int w, int h)
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141 addInternalFrame(frame, title, w, h, true);
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147 * @param frame DOCUMENT ME!
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148 * @param title DOCUMENT ME!
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149 * @param w DOCUMENT ME!
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150 * @param h DOCUMENT ME!
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151 * @param resizable DOCUMENT ME!
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153 public static synchronized void addInternalFrame(final JInternalFrame frame,
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154 String title, int w, int h, boolean resizable)
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157 frame.setTitle(title);
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158 if(frame.getWidth()<1 || frame.getHeight()<1)
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160 frame.setSize(w, h);
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162 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
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163 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
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164 // IF JALVIEW IS RUNNING HEADLESS
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165 /////////////////////////////////////////////////
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166 if (System.getProperty("java.awt.headless") != null
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167 && System.getProperty("java.awt.headless").equals("true"))
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175 frame.setVisible(true);
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176 frame.setClosable(true);
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177 frame.setResizable(resizable);
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178 frame.setMaximizable(resizable);
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179 frame.setIconifiable(resizable);
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180 frame.setFrameIcon(null);
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182 if (frame.getX()<1 && frame.getY()<1)
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184 frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
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187 final JMenuItem menuItem = new JMenuItem(title);
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188 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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190 public void internalFrameActivated(javax.swing.event.
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191 InternalFrameEvent evt)
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193 JInternalFrame itf = desktop.getSelectedFrame();
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195 itf.requestFocus();
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199 public void internalFrameClosed(
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200 javax.swing.event.InternalFrameEvent evt)
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203 windowMenu.remove(menuItem);
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204 JInternalFrame itf = desktop.getSelectedFrame();
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206 itf.requestFocus();
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211 menuItem.addActionListener(new ActionListener()
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213 public void actionPerformed(ActionEvent e)
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217 frame.setSelected(true);
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218 frame.setIcon(false);
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220 catch (java.beans.PropertyVetoException ex)
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227 windowMenu.add(menuItem);
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229 desktop.add(frame);
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232 frame.setSelected(true);
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233 frame.requestFocus();
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234 }catch(java.beans.PropertyVetoException ve)
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238 public void dragEnter(DropTargetDragEvent evt)
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241 public void dragExit(DropTargetEvent evt)
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244 public void dragOver(DropTargetDragEvent evt)
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247 public void dropActionChanged(DropTargetDragEvent evt)
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253 * @param evt DOCUMENT ME!
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255 public void drop(DropTargetDropEvent evt)
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257 Transferable t = evt.getTransferable();
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258 java.util.List files = null;
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262 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
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263 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
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265 //Works on Windows and MacOSX
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266 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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267 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
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269 else if (t.isDataFlavorSupported(uriListFlavor))
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271 // This is used by Unix drag system
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272 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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273 String data = (String) t.getTransferData(uriListFlavor);
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274 files = new java.util.ArrayList(1);
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275 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
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278 st.hasMoreTokens(); )
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280 String s = st.nextToken();
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281 if (s.startsWith("#"))
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283 // the line is a comment (as per the RFC 2483)
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287 java.net.URI uri = new java.net.URI(s);
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288 java.io.File file = new java.io.File(uri);
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293 catch (Exception e)
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295 e.printStackTrace();
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302 for (int i = 0; i < files.size(); i++)
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304 String file = files.get(i).toString();
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305 String protocol = FormatAdapter.FILE;
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306 String format = null;
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308 if (file.endsWith(".jar"))
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310 format = "Jalview";
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315 format = new IdentifyFile().Identify(file,
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318 LoadFile(file, protocol, format);
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321 catch (Exception ex)
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323 ex.printStackTrace();
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331 * @param e DOCUMENT ME!
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333 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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335 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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339 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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344 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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345 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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347 chooser.setFileView(new JalviewFileView());
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348 chooser.setDialogTitle("Open local file");
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349 chooser.setToolTipText("Open");
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351 int value = chooser.showOpenDialog(this);
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353 if (value == JalviewFileChooser.APPROVE_OPTION)
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355 String choice = chooser.getSelectedFile().getPath();
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356 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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357 chooser.getSelectedFile().getParent());
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359 String format = null;
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360 if (chooser.getSelectedFormat().equals("Jalview"))
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362 format = "Jalview";
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366 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
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369 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
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370 LoadFile(choice, FormatAdapter.FILE, format);
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377 * @param file DOCUMENT ME!
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378 * @param protocol DOCUMENT ME!
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379 * @param format DOCUMENT ME!
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381 public void LoadFile(String file, String protocol, String format)
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383 FileLoader fileLoader = new FileLoader();
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384 fileLoader.LoadFile(file, protocol, format);
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390 * @param e DOCUMENT ME!
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392 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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394 // This construct allows us to have a wider textfield
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396 JLabel label = new JLabel("Enter URL of Input File");
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397 JTextField textinput = new JTextField("http://www.", 40);
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398 JPanel panel = new JPanel(new BorderLayout());
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399 panel.add(label, BorderLayout.NORTH);
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400 panel.add(textinput, BorderLayout.SOUTH);
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403 int reply = JOptionPane.showInternalConfirmDialog(desktop,
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404 panel, "Input Alignment From URL",
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405 JOptionPane.OK_CANCEL_OPTION );
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408 if (reply != JOptionPane.OK_OPTION )
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413 String url = textinput.getText();
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415 if (url.toLowerCase().endsWith(".jar"))
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417 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
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418 Jalview2XML.LoadJalviewAlign(url);
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423 String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
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425 if (format.equals("URL NOT FOUND"))
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427 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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428 "Couldn't locate " + url,
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430 JOptionPane.WARNING_MESSAGE);
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435 LoadFile(url, FormatAdapter.URL, format);
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442 * @param e DOCUMENT ME!
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444 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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446 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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448 Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
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456 jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
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457 jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
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458 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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459 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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466 * @param e DOCUMENT ME!
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468 public void aboutMenuItem_actionPerformed(ActionEvent e)
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470 StringBuffer message = new StringBuffer("JalView version " +
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471 jalview.bin.Cache.getProperty(
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473 "; last updated: " +
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475 Cache.getDefault("BUILD_DATE", "unknown"));
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477 if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
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478 jalview.bin.Cache.getProperty("VERSION")))
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480 message.append("\n\n!! Jalview version "
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481 + jalview.bin.Cache.getProperty("LATEST_VERSION")
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482 + " is available for download from http://www.jalview.org !!\n");
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486 message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
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487 "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
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488 "\nFor all issues relating to Jalview, email help@jalview.org" +
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489 "\n\nIf you use JalView, please cite:" +
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490 "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
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491 "\nBioinformatics, 2004 12;426-7.");
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493 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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495 message.toString(), "About Jalview",
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496 JOptionPane.INFORMATION_MESSAGE);
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502 * @param e DOCUMENT ME!
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504 public void documentationMenuItem_actionPerformed(ActionEvent e)
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508 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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509 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
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510 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
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512 javax.help.HelpBroker hb = hs.createHelpBroker();
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513 hb.setCurrentID("home");
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514 hb.setDisplayed(true);
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516 catch (Exception ex)
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518 ex.printStackTrace();
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525 * @param e DOCUMENT ME!
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527 protected void preferences_actionPerformed(ActionEvent e)
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535 * @param e DOCUMENT ME!
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537 public void saveState_actionPerformed(ActionEvent e)
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539 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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540 "LAST_DIRECTORY"), new String[] { "jar" },
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541 new String[] { "Jalview Project" }, "Jalview Project");
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543 chooser.setFileView(new JalviewFileView());
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544 chooser.setDialogTitle("Save State");
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546 int value = chooser.showSaveDialog(this);
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548 if (value == JalviewFileChooser.APPROVE_OPTION)
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550 java.io.File choice = chooser.getSelectedFile();
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551 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
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552 Jalview2XML.SaveState(choice);
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559 * @param e DOCUMENT ME!
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561 public void loadState_actionPerformed(ActionEvent e)
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563 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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564 "LAST_DIRECTORY"), new String[] { "jar" },
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565 new String[] { "Jalview Project" }, "Jalview Project");
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566 chooser.setFileView(new JalviewFileView());
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567 chooser.setDialogTitle("Restore state");
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569 int value = chooser.showOpenDialog(this);
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571 if (value == JalviewFileChooser.APPROVE_OPTION)
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573 String choice = chooser.getSelectedFile().getAbsolutePath();
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574 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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575 chooser.getSelectedFile().getParent());
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576 Jalview2XML.LoadJalviewAlign(choice);
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580 /* public void vamsasLoad_actionPerformed(ActionEvent e)
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582 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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583 getProperty("LAST_DIRECTORY"));
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585 chooser.setFileView(new JalviewFileView());
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586 chooser.setDialogTitle("Load Vamsas file");
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587 chooser.setToolTipText("Import");
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589 int value = chooser.showOpenDialog(this);
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591 if (value == JalviewFileChooser.APPROVE_OPTION)
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593 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
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595 chooser.getSelectedFile().getAbsolutePath()
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602 public void inputSequence_actionPerformed(ActionEvent e)
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604 SequenceFetcher sf = new SequenceFetcher(null);
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