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("/images/logo.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 desktop.setBackground(Color.white);
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48 setContentPane(desktop);
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49 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
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51 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
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52 String x = jalview.bin.Cache.getProperty("SCREEN_X");
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53 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
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54 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
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55 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
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57 if(x!=null && y!=null && width!=null && height!=null)
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59 setBounds( Integer.parseInt(x), Integer.parseInt(y),
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60 Integer.parseInt(width), Integer.parseInt(height));
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63 setBounds( (int)(screenSize.width-900)/2,
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64 (int)(screenSize.height-650)/2,
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68 this.addWindowListener(new WindowAdapter()
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70 public void windowClosing(WindowEvent evt)
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72 jalview.bin.Cache.setProperty("SCREEN_X",
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73 getBounds().x + "");
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74 jalview.bin.Cache.setProperty("SCREEN_Y",
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75 getBounds().y + "");
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76 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
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77 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
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81 /////////Add a splashscreen on startup
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84 /////////Add a splashscreen on startup
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85 JInternalFrame frame = new JInternalFrame();
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87 SplashScreen splash = new SplashScreen(frame, image);
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88 frame.setContentPane(splash);
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90 frame.setVisible(true);
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94 frame.setSelected(true);
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96 catch (java.beans.PropertyVetoException e)
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98 frame.setResizable(true);
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99 frame.setSize(750, 160);
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100 frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
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101 frame.setClosable(false);
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102 frame.setIconifiable(false);
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103 frame.setMaximizable(false);
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104 frame.setFrameIcon(null);
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108 public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
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110 desktop.add(frame);
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111 frame.setVisible(true);
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114 frame.setSelected(true);
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115 } catch (java.beans.PropertyVetoException e) {}
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116 frame.setTitle(title);
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117 frame.setResizable(true);
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118 frame.setSize(w,h);
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119 frame.setClosable(true);
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120 frame.setMaximizable(true);
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121 frame.setIconifiable(true);
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122 frame.setFrameIcon(null);
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123 frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
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125 final JMenuItem menuItem = new JMenuItem(title);
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126 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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127 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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130 windowMenu.remove(menuItem);
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134 menuItem.addActionListener(new ActionListener()
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136 public void actionPerformed(ActionEvent e)
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138 try{ frame.setSelected(true); frame.setIcon(false); }
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139 catch(java.beans.PropertyVetoException ex){};
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143 windowMenu.add(menuItem);
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148 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
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150 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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151 new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");
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152 chooser.setFileView(new JalviewFileView());
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153 chooser.setDialogTitle("Open local file");
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154 chooser.setToolTipText("Open");
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155 int value = chooser.showOpenDialog(this);
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156 if(value == JalviewFileChooser.APPROVE_OPTION)
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158 String choice = chooser.getSelectedFile().getPath();
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159 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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160 String format = IdentifyFile.Identify(choice, "File");
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161 LoadFile(choice, "File", format);
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165 public void LoadFile(String file, String protocol, String format)
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167 SequenceI [] sequences = null;
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169 if (FormatProperties.contains(format))
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170 sequences = FormatAdapter.read(file, protocol, format);
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172 if (sequences != null)
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174 AlignFrame af = new AlignFrame(new Alignment(sequences));
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175 addInternalFrame(af, file, 700, 500);
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176 af.statusBar.setText("Successfully loaded file " + file);
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181 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"
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182 + "Formats currently supported are\n"
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183 + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"
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184 ,"Error loading file",
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185 JOptionPane.WARNING_MESSAGE);
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189 public void inputURLMenuItem_actionPerformed(ActionEvent e)
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191 String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
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192 "Input alignment from URL",
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193 JOptionPane.QUESTION_MESSAGE);
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197 String format = IdentifyFile.Identify(url, "URL");
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199 System.out.println(format +" format");
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200 if (format.equals("URL NOT FOUND"))
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202 JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
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204 JOptionPane.WARNING_MESSAGE);
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208 LoadFile(url, "URL", format);
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211 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
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213 CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
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214 int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
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215 JOptionPane.YES_NO_CANCEL_OPTION,
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216 JOptionPane.PLAIN_MESSAGE,
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218 new Object[]{"Accept", "Cancel", }, null);
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221 if(accept == JOptionPane.YES_OPTION)
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223 String format = IdentifyFile.Identify(cap.getText(), "Paste");
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224 SequenceI [] sequences = null;
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226 if (FormatProperties.contains( format ))
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227 sequences = FormatAdapter.read(cap.getText(), "Paste", format);
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230 if(sequences!=null)
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232 AlignFrame af = new AlignFrame(new Alignment(sequences));
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233 addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
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234 af.statusBar.setText("Successfully pasted alignment file");
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237 JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
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238 +"Formats currently supported are\n"
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239 +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
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240 "Error parsing text", JOptionPane.WARNING_MESSAGE);
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248 public void quit_actionPerformed(ActionEvent e)
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250 if(jalview.bin.Jalview.applet!=null)
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251 jalview.bin.Jalview.applet.destroy();
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258 public void aboutMenuItem_actionPerformed(ActionEvent e)
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260 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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261 "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
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262 +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
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263 +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
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264 +"\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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266 JOptionPane.INFORMATION_MESSAGE);
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269 public void documentationMenuItem_actionPerformed(ActionEvent e)
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273 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
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274 java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
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275 javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
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277 javax.help.HelpBroker hb = hs.createHelpBroker();
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278 hb.setLocation(new Point(200, 50));
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279 hb.setSize(new Dimension(800,700));
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280 hb.setCurrentID("home");
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281 hb.setDisplayed(true);
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283 catch (Exception ex)
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285 ex.printStackTrace();
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289 static JInternalFrame conservationSlider;
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290 static JInternalFrame PIDSlider;
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291 public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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293 SliderPanel sp = null;
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295 if(conservationSlider == null)
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297 sp = new SliderPanel(ap, 30, true, cs);
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298 conservationSlider = new JInternalFrame();
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299 conservationSlider.setContentPane(sp);
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300 conservationSlider.setResizable(false);
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301 addInternalFrame(conservationSlider, "Conservation Colour Increment ("+source+")", 420, 90);
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302 conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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304 public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
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306 conservationSlider = null;
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312 conservationSlider.setTitle("Conservation Colour Increment ("+source+")");
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313 sp = (SliderPanel)conservationSlider.getContentPane();
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317 if(ap.av.alignment.getGroups()!=null)
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318 sp.setAllGroupsCheckEnabled( true );
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320 sp.setAllGroupsCheckEnabled( false);
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322 return sp.getValue();
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326 public static void hideConservationSlider()
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329 conservationSlider.setClosed(true);
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330 conservationSlider = null;
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331 }catch(Exception ex){}
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335 public static void hidePIDSlider()
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338 PIDSlider.setClosed(true);
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340 }catch(Exception ex){}
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343 public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
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345 SliderPanel pid = null;
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346 if(PIDSlider == null)
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348 pid = new SliderPanel(ap, 50, false, cs);
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349 PIDSlider = new JInternalFrame();
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350 PIDSlider.setContentPane(pid);
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351 PIDSlider.setResizable(false);
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352 addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
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356 PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
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357 pid = (SliderPanel)PIDSlider.getContentPane();
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361 if (ap.av.alignment.getGroups() != null)
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362 pid.setAllGroupsCheckEnabled(true);
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364 pid.setAllGroupsCheckEnabled(false);
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367 return pid.getValue();
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