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 jalview.schemes.*;
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16 import javax.swing.*;
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18 import java.awt.event.*;
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19 import java.awt.dnd.*;
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20 import javax.swing.*;
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21 import java.awt.datatransfer.*;
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25 public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
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27 public static JDesktopPane desktop;
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28 static int openFrameCount = 0;
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29 static final int xOffset = 30, yOffset = 30;
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35 java.net.URL url = getClass().getResource("/images/logo.gif");
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38 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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39 MediaTracker mt = new MediaTracker(this);
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40 mt.addImage(image, 0);
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42 setIconImage(image);
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45 }catch(Exception ex){}
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47 setTitle("Jalview 2005");
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48 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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49 desktop = new JDesktopPane();
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50 // desktop.setBackground(Color.white);
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51 setContentPane(desktop);
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52 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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55 // This line prevents Windows Look&Feel resizing all new windows to maximum
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56 // if previous window was maximised
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57 desktop.setDesktopManager( new DefaultDesktopManager() );
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60 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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61 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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62 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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63 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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64 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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66 if(x!=null && y!=null && width!=null && height!=null)
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68 setBounds( Integer.parseInt(x), Integer.parseInt(y),
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69 Integer.parseInt(width), Integer.parseInt(height));
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72 setBounds( (int)(screenSize.width-900)/2,
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73 (int)(screenSize.height-650)/2,
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77 this.addWindowListener(new WindowAdapter()
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79 public void windowClosing(WindowEvent evt)
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81 jalview.bin.Cache.setProperty("SCREEN_X",
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82 getBounds().x + "");
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83 jalview.bin.Cache.setProperty("SCREEN_Y",
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84 getBounds().y + "");
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85 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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86 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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91 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
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94 /////////Add a splashscreen on startup
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95 JInternalFrame frame = new JInternalFrame();
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97 SplashScreen splash = new SplashScreen(frame, image);
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98 frame.setContentPane(splash);
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104 frame.setSelected(true);
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106 catch (java.beans.PropertyVetoException e)
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108 frame.setResizable(true);
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109 frame.setSize(750, 160);
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110 frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
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111 frame.setClosable(false);
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112 frame.setIconifiable(false);
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113 frame.setMaximizable(false);
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114 frame.setFrameIcon(null);
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115 frame.setVisible(true);
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119 public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
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121 desktop.add(frame);
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124 frame.setSelected(true);
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125 } catch (java.beans.PropertyVetoException e) {}
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126 frame.setTitle(title);
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127 frame.setResizable(true);
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128 frame.setSize(w,h);
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129 frame.setClosable(true);
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130 frame.setMaximizable(true);
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131 frame.setIconifiable(true);
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132 frame.setFrameIcon(null);
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133 frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
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135 final JMenuItem menuItem = new JMenuItem(title);
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136 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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137 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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140 windowMenu.remove(menuItem);
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144 menuItem.addActionListener(new ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 try{ frame.setSelected(true); frame.setIcon(false); }
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149 catch(java.beans.PropertyVetoException ex){};
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153 frame.setVisible(true);
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154 windowMenu.add(menuItem);
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157 public void dragEnter(DropTargetDragEvent evt){}
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158 public void dragExit(DropTargetEvent evt){}
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159 public void dragOver(DropTargetDragEvent evt){}
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160 public void dropActionChanged(DropTargetDragEvent evt){}
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161 public void drop(DropTargetDropEvent evt)
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163 Transferable t = evt.getTransferable();
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164 if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
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167 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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169 java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
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171 for (int i = 0; i < files.size(); i++)
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173 String file = files.get(i).toString();
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174 String protocol = "File";
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175 String format = jalview.io.IdentifyFile.Identify(file, protocol);
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176 LoadFile(file, protocol, format);
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179 }catch(Exception ex){ex.printStackTrace();}
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182 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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184 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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185 new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");
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186 chooser.setFileView(new JalviewFileView());
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187 chooser.setDialogTitle("Open local file");
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188 chooser.setToolTipText("Open");
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189 int value = chooser.showOpenDialog(this);
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190 if(value == JalviewFileChooser.APPROVE_OPTION)
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192 String choice = chooser.getSelectedFile().getPath();
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193 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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194 String format = IdentifyFile.Identify(choice, "File");
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195 LoadFile(choice, "File", format);
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199 public void LoadFile(String file, String protocol, String format)
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201 SequenceI [] sequences = null;
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203 if (FormatProperties.contains(format))
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204 sequences = FormatAdapter.read(file, protocol, format);
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206 if (sequences != null && sequences.length>0)
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208 AlignFrame af = new AlignFrame(new Alignment(sequences));
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209 addInternalFrame(af, file, 700, 500);
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210 af.statusBar.setText("Successfully loaded file " + file);
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214 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"
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215 + "Formats currently supported are\n"
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216 + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!
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217 ,"Error loading file",
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218 JOptionPane.WARNING_MESSAGE);
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222 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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224 String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
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225 "Input alignment from URL",
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226 JOptionPane.QUESTION_MESSAGE);
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230 String format = IdentifyFile.Identify(url, "URL");
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232 if (format.equals("URL NOT FOUND"))
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234 JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
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236 JOptionPane.WARNING_MESSAGE);
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240 LoadFile(url, "URL", format);
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243 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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245 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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246 int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
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247 JOptionPane.YES_NO_CANCEL_OPTION,
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248 JOptionPane.PLAIN_MESSAGE,
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250 new Object[]{"Accept", "Cancel", }, null);
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253 if(accept == JOptionPane.YES_OPTION)
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255 String format = IdentifyFile.Identify(cap.getText(), "Paste");
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256 SequenceI [] sequences = null;
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258 if (FormatProperties.contains( format ))
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259 sequences = FormatAdapter.read(cap.getText(), "Paste", format);
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262 if(sequences!=null)
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264 AlignFrame af = new AlignFrame(new Alignment(sequences));
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265 addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
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266 af.statusBar.setText("Successfully pasted alignment file");
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269 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
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270 +"Formats currently supported are\n"
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271 +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
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272 "Error parsing text", JOptionPane.WARNING_MESSAGE);
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280 public void quit_actionPerformed(ActionEvent e)
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282 if(jalview.bin.Jalview.applet!=null)
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283 jalview.bin.Jalview.applet.destroy();
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290 public void aboutMenuItem_actionPerformed(ActionEvent e)
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292 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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293 "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
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294 +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
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295 +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
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296 +"\nIf you use JalView, please cite: Bioinformatics, 2004 12;426-7."
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297 +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
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299 JOptionPane.INFORMATION_MESSAGE);
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302 public void documentationMenuItem_actionPerformed(ActionEvent e)
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306 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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307 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
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308 javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
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310 javax.help.HelpBroker hb = hs.createHelpBroker();
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311 hb.setLocation(new Point(200, 50));
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312 hb.setSize(new Dimension(800,700));
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313 hb.setCurrentID("home");
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314 hb.setDisplayed(true);
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316 catch (Exception ex)
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318 ex.printStackTrace();
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322 static JInternalFrame conservationSlider;
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323 static JInternalFrame PIDSlider;
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324 public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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326 SliderPanel sp = null;
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327 ConservationColourScheme ccs = (ConservationColourScheme)cs;
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328 int value = ccs.inc;
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330 if(conservationSlider == null)
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332 sp = new SliderPanel(ap, value, true, cs);
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333 conservationSlider = new JInternalFrame();
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334 conservationSlider.setContentPane(sp);
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335 addInternalFrame(conservationSlider, "Conservation Colour Increment ("+source+")", 420, 90);
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336 conservationSlider.setResizable(false);
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337 conservationSlider.setMaximizable(false);
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338 conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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340 public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
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342 conservationSlider = null;
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349 conservationSlider.setTitle("Conservation Colour Increment ("+source+")");
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350 sp = (SliderPanel)conservationSlider.getContentPane();
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352 sp.setValue(value);
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355 if(ap.av.alignment.getGroups()!=null)
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356 sp.setAllGroupsCheckEnabled( true );
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358 sp.setAllGroupsCheckEnabled( false);
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360 return sp.getValue();
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364 public static void hideConservationSlider()
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367 conservationSlider.setClosed(true);
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368 conservationSlider = null;
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369 }catch(Exception ex){}
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373 public static void hidePIDSlider()
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376 PIDSlider.setClosed(true);
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378 }catch(Exception ex){}
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381 public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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383 SliderPanel pid = null;
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384 if(PIDSlider == null)
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386 pid = new SliderPanel(ap, 50, false, cs);
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387 PIDSlider = new JInternalFrame();
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388 PIDSlider.setContentPane(pid);
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389 addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
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390 PIDSlider.setResizable(false);
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391 PIDSlider.setMaximizable(false);
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395 PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
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396 pid = (SliderPanel)PIDSlider.getContentPane();
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400 if (ap.av.alignment.getGroups() != null)
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401 pid.setAllGroupsCheckEnabled(true);
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403 pid.setAllGroupsCheckEnabled(false);
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406 return pid.getValue();
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