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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21 public class Desktop extends jalview.jbgui.GDesktop
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23 public static JDesktopPane desktop;
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24 static int openFrameCount = 0;
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25 static final int xOffset = 30, yOffset = 30;
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31 java.net.URL url = getClass().getResource("/BartonGroupBanner.gif");
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34 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
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35 MediaTracker mt = new MediaTracker(this);
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36 mt.addImage(image, 0);
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38 setIconImage(image);
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41 }catch(Exception ex){}
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43 setTitle("Jalview 2005");
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44 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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46 desktop = new JDesktopPane();
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47 setContentPane(desktop);
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48 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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50 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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51 int width = 1200, height = 800;
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52 if(screenSize.getWidth()<width)
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53 width = screenSize.width;
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54 if(screenSize.getHeight()<height)
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55 height = screenSize.height;
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57 setBounds( (int)(screenSize.width-width)/2,
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58 (int)(screenSize.height-height)/2,
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63 /////////Add a splashscreen on startup
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64 JInternalFrame frame = new JInternalFrame();
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66 SplashScreen splash = new SplashScreen(frame, image);
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67 frame.setContentPane(splash);
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69 frame.setVisible(true);
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73 frame.setSelected(true);
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75 catch (java.beans.PropertyVetoException e)
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77 frame.setResizable(true);
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78 frame.setSize(845, 200);
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79 frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
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80 frame.setClosable(false);
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81 frame.setIconifiable(false);
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82 frame.setMaximizable(false);
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83 frame.setFrameIcon(null);
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87 public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
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90 frame.setVisible(true);
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93 frame.setSelected(true);
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94 } catch (java.beans.PropertyVetoException e) {}
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95 frame.setTitle(title);
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96 frame.setResizable(true);
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98 frame.setClosable(true);
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99 frame.setMaximizable(true);
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100 frame.setIconifiable(true);
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101 frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
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103 final JMenuItem menuItem = new JMenuItem(title);
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104 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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105 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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108 windowMenu.remove(menuItem);
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112 menuItem.addActionListener(new ActionListener()
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114 public void actionPerformed(ActionEvent e)
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116 try{ frame.setSelected(true); frame.setIcon(false); }
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117 catch(java.beans.PropertyVetoException ex){};
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121 windowMenu.add(menuItem);
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126 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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128 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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129 chooser.setDialogTitle("Open local file");
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130 chooser.setToolTipText("Open");
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131 int value = chooser.showOpenDialog(this);
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132 if(value == JFileChooser.APPROVE_OPTION)
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134 String choice = chooser.getSelectedFile().getPath();
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135 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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136 String format = IdentifyFile.Identify(choice, "File");
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137 LoadFile(choice, "File", format);
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141 public void LoadFile(String file, String protocol, String format)
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143 SequenceI [] sequences = null;
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145 if (FormatProperties.contains(format))
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146 sequences = FormatAdapter.read(file, protocol, format);
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148 if (sequences != null)
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150 AlignFrame af = new AlignFrame(new Alignment(sequences));
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151 addInternalFrame(af, file, 700, 500);
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152 af.statusBar.setText("Successfully loaded file " + file);
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157 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"
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158 + "Formats currently supported are\n"
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159 + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"
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160 ,"Error loading file",
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161 JOptionPane.WARNING_MESSAGE);
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165 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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167 String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
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168 "Input alignment from URL",
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169 JOptionPane.QUESTION_MESSAGE);
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173 String format = IdentifyFile.Identify(url, "URL");
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175 System.out.println(format +" format");
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176 if (format.equals("URL NOT FOUND"))
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178 JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
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180 JOptionPane.WARNING_MESSAGE);
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184 LoadFile(url, "URL", format);
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187 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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189 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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190 int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
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191 JOptionPane.YES_NO_CANCEL_OPTION,
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192 JOptionPane.PLAIN_MESSAGE,
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194 new Object[]{"Accept", "Cancel", }, null);
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197 if(accept == JOptionPane.YES_OPTION)
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199 String format = IdentifyFile.Identify(cap.getText(), "Paste");
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200 SequenceI [] sequences = null;
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202 if (FormatProperties.contains( format ))
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203 sequences = FormatAdapter.read(cap.getText(), "Paste", format);
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206 if(sequences!=null)
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208 AlignFrame af = new AlignFrame(new Alignment(sequences));
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209 addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
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210 af.statusBar.setText("Successfully pasted alignment file");
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213 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
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214 +"Formats currently supported are\n"
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215 +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
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216 "Error parsing text", JOptionPane.WARNING_MESSAGE);
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224 public void quit_actionPerformed(ActionEvent e)
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226 if(jalview.bin.Jalview.applet!=null)
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227 jalview.bin.Jalview.applet.destroy();
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234 public void aboutMenuItem_actionPerformed(ActionEvent e)
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236 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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238 +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
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239 +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
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240 +"\nIf you use JalView, please cite: \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
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242 JOptionPane.INFORMATION_MESSAGE);
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245 public void documentationMenuItem_actionPerformed(ActionEvent e)
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249 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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250 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
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251 javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
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253 javax.help.HelpBroker hb = hs.createHelpBroker();
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254 hb.setLocation(new Point(200, 50));
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255 hb.setSize(new Dimension(800,700));
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256 hb.setCurrentID("home");
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257 hb.setDisplayed(true);
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259 catch (Exception ex)
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261 ex.printStackTrace();
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265 static JInternalFrame conservationSlider;
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266 static JInternalFrame PIDSlider;
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267 public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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269 SliderPanel sp = null;
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271 if(conservationSlider == null)
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273 sp = new SliderPanel(ap, 30, true, cs);
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274 conservationSlider = new JInternalFrame();
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275 conservationSlider.setContentPane(sp);
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276 conservationSlider.setResizable(false);
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277 addInternalFrame(conservationSlider, "Conservation Colour Increment ("+source+")", 420, 90);
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278 conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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280 public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
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282 conservationSlider = null;
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288 conservationSlider.setTitle("Conservation Colour Increment ("+source+")");
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289 sp = (SliderPanel)conservationSlider.getContentPane();
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293 if(ap.av.alignment.getGroups()!=null)
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294 sp.setAllGroupsCheckEnabled( true );
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296 sp.setAllGroupsCheckEnabled( false);
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298 return sp.getValue();
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302 public static void hideConservationSlider()
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305 conservationSlider.setClosed(true);
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306 conservationSlider = null;
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307 }catch(Exception ex){}
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311 public static void hidePIDSlider()
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314 PIDSlider.setClosed(true);
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316 }catch(Exception ex){}
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319 public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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321 SliderPanel pid = null;
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322 if(PIDSlider == null)
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324 pid = new SliderPanel(ap, 50, false, cs);
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325 PIDSlider = new JInternalFrame();
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326 PIDSlider.setContentPane(pid);
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327 PIDSlider.setResizable(false);
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328 addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
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332 PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
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333 pid = (SliderPanel)PIDSlider.getContentPane();
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337 if (ap.av.alignment.getGroups() != null)
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338 pid.setAllGroupsCheckEnabled(true);
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340 pid.setAllGroupsCheckEnabled(false);
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343 return pid.getValue();
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