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(new Color(220,220,230));
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51 setContentPane(desktop);
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52 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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53 desktop.setDesktopManager( new DefaultDesktopManager() );
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55 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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56 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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57 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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58 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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59 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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61 if(x!=null && y!=null && width!=null && height!=null)
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63 setBounds( Integer.parseInt(x), Integer.parseInt(y),
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64 Integer.parseInt(width), Integer.parseInt(height));
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67 setBounds( (int)(screenSize.width-900)/2,
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68 (int)(screenSize.height-650)/2,
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72 this.addWindowListener(new WindowAdapter()
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74 public void windowClosing(WindowEvent evt)
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76 jalview.bin.Cache.setProperty("SCREEN_X",
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77 getBounds().x + "");
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78 jalview.bin.Cache.setProperty("SCREEN_Y",
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79 getBounds().y + "");
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80 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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81 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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86 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
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89 /////////Add a splashscreen on startup
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90 JInternalFrame frame = new JInternalFrame();
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92 SplashScreen splash = new SplashScreen(frame, image);
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93 frame.setContentPane(splash);
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99 frame.setSelected(true);
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101 catch (java.beans.PropertyVetoException e)
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103 frame.setResizable(true);
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104 frame.setSize(750, 160);
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105 frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
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106 frame.setClosable(false);
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107 frame.setIconifiable(false);
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108 frame.setMaximizable(false);
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109 frame.setFrameIcon(null);
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110 frame.setVisible(true);
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114 public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
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116 desktop.add(frame);
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119 frame.setSelected(true);
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120 } catch (java.beans.PropertyVetoException e) {}
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121 frame.setTitle(title);
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122 frame.setResizable(true);
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123 frame.setSize(w,h);
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124 frame.setClosable(true);
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125 frame.setMaximizable(true);
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126 frame.setIconifiable(true);
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127 frame.setFrameIcon(null);
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128 frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
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130 final JMenuItem menuItem = new JMenuItem(title);
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131 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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132 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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135 windowMenu.remove(menuItem);
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139 menuItem.addActionListener(new ActionListener()
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141 public void actionPerformed(ActionEvent e)
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143 try{ frame.setSelected(true); frame.setIcon(false); }
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144 catch(java.beans.PropertyVetoException ex){};
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148 frame.setVisible(true);
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149 windowMenu.add(menuItem);
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152 public void dragEnter(DropTargetDragEvent evt){}
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153 public void dragExit(DropTargetEvent evt){}
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154 public void dragOver(DropTargetDragEvent evt){}
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155 public void dropActionChanged(DropTargetDragEvent evt){}
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156 public void drop(DropTargetDropEvent evt)
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158 Transferable t = evt.getTransferable();
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159 if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
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162 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
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164 java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
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166 for (int i = 0; i < files.size(); i++)
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168 String file = files.get(i).toString();
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169 String protocol = "File";
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170 String format = jalview.io.IdentifyFile.Identify(file, protocol);
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171 LoadFile(file, protocol, format);
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174 }catch(Exception ex){ex.printStackTrace();}
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177 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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179 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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180 new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");
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181 chooser.setFileView(new JalviewFileView());
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182 chooser.setDialogTitle("Open local file");
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183 chooser.setToolTipText("Open");
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184 int value = chooser.showOpenDialog(this);
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185 if(value == JalviewFileChooser.APPROVE_OPTION)
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187 String choice = chooser.getSelectedFile().getPath();
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188 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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189 String format = IdentifyFile.Identify(choice, "File");
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190 LoadFile(choice, "File", format);
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194 public void LoadFile(String file, String protocol, String format)
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196 SequenceI [] sequences = null;
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198 if (FormatProperties.contains(format))
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199 sequences = FormatAdapter.read(file, protocol, format);
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201 if (sequences != null && sequences.length>0)
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203 AlignFrame af = new AlignFrame(new Alignment(sequences));
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204 addInternalFrame(af, file, 700, 500);
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205 af.statusBar.setText("Successfully loaded file " + file);
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209 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"
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210 + "Formats currently supported are\n"
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211 + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!
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212 ,"Error loading file",
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213 JOptionPane.WARNING_MESSAGE);
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217 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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219 String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
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220 "Input alignment from URL",
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221 JOptionPane.QUESTION_MESSAGE);
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225 String format = IdentifyFile.Identify(url, "URL");
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227 if (format.equals("URL NOT FOUND"))
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229 JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
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231 JOptionPane.WARNING_MESSAGE);
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235 LoadFile(url, "URL", format);
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238 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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240 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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241 int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
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242 JOptionPane.YES_NO_CANCEL_OPTION,
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243 JOptionPane.PLAIN_MESSAGE,
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245 new Object[]{"Accept", "Cancel", }, null);
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248 if(accept == JOptionPane.YES_OPTION)
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250 String format = IdentifyFile.Identify(cap.getText(), "Paste");
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251 SequenceI [] sequences = null;
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253 if (FormatProperties.contains( format ))
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254 sequences = FormatAdapter.read(cap.getText(), "Paste", format);
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257 if(sequences!=null)
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259 AlignFrame af = new AlignFrame(new Alignment(sequences));
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260 addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
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261 af.statusBar.setText("Successfully pasted alignment file");
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264 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
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265 +"Formats currently supported are\n"
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266 +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
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267 "Error parsing text", JOptionPane.WARNING_MESSAGE);
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275 public void quit_actionPerformed(ActionEvent e)
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277 if(jalview.bin.Jalview.applet!=null)
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278 jalview.bin.Jalview.applet.destroy();
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285 public void aboutMenuItem_actionPerformed(ActionEvent e)
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287 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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288 "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
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289 +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
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290 +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
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291 +"\nIf you use JalView, please cite: Bioinformatics, 2004 12;426-7."
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292 +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
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294 JOptionPane.INFORMATION_MESSAGE);
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297 public void documentationMenuItem_actionPerformed(ActionEvent e)
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301 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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302 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
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303 javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
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305 javax.help.HelpBroker hb = hs.createHelpBroker();
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306 hb.setLocation(new Point(200, 50));
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307 hb.setSize(new Dimension(800,700));
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308 hb.setCurrentID("home");
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309 hb.setDisplayed(true);
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311 catch (Exception ex)
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313 ex.printStackTrace();
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317 static JInternalFrame conservationSlider;
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318 static JInternalFrame PIDSlider;
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319 public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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321 SliderPanel sp = null;
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322 ConservationColourScheme ccs = (ConservationColourScheme)cs;
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323 int value = ccs.inc;
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325 if(conservationSlider == null)
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327 sp = new SliderPanel(ap, value, true, cs);
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328 conservationSlider = new JInternalFrame();
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329 conservationSlider.setContentPane(sp);
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330 addInternalFrame(conservationSlider, "Conservation Colour Increment ("+source+")", 420, 90);
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331 conservationSlider.setResizable(false);
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332 conservationSlider.setMaximizable(false);
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333 conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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335 public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
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337 conservationSlider = null;
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344 conservationSlider.setTitle("Conservation Colour Increment ("+source+")");
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345 sp = (SliderPanel)conservationSlider.getContentPane();
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347 sp.setValue(value);
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350 if(ap.av.alignment.getGroups()!=null)
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351 sp.setAllGroupsCheckEnabled( true );
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353 sp.setAllGroupsCheckEnabled( false);
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355 return sp.getValue();
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359 public static void hideConservationSlider()
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362 conservationSlider.setClosed(true);
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363 conservationSlider = null;
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364 }catch(Exception ex){}
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368 public static void hidePIDSlider()
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371 PIDSlider.setClosed(true);
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373 }catch(Exception ex){}
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376 public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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378 SliderPanel pid = null;
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379 if(PIDSlider == null)
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381 pid = new SliderPanel(ap, 50, false, cs);
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382 PIDSlider = new JInternalFrame();
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383 PIDSlider.setContentPane(pid);
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384 addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
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385 PIDSlider.setResizable(false);
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386 PIDSlider.setMaximizable(false);
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390 PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
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391 pid = (SliderPanel)PIDSlider.getContentPane();
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395 if (ap.av.alignment.getGroups() != null)
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396 pid.setAllGroupsCheckEnabled(true);
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398 pid.setAllGroupsCheckEnabled(false);
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401 return pid.getValue();
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