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.bin.*;
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23 import jalview.io.*;
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25 import jalview.jbgui.*;
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27 import jalview.schemes.*;
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30 import java.awt.event.*;
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32 import javax.swing.*;
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36 import jalview.bin.Cache;
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43 * @version $Revision$
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45 public class Preferences extends GPreferences
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47 /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
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48 public static Vector sequenceURLLinks = new Vector();
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49 static { sequenceURLLinks.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");}
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50 Vector nameLinks, urlLinks;
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52 JInternalFrame frame;
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56 * Creates a new Preferences object.
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58 public Preferences()
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61 frame = new JInternalFrame();
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62 frame.setContentPane(this);
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63 Desktop.addInternalFrame(frame, "Preferences", 480, 390);
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64 frame.setMinimumSize(new Dimension(480,390));
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66 fullID.setSelected( Cache.getDefault("SHOW_FULL_ID", true));
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67 fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));
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68 annotations.setSelected( Cache.getDefault("SHOW_FULL_ID", true));
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69 conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
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71 quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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72 identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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74 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
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75 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
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76 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
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78 for (int i = 0; i < 12; i++)
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80 colour.addItem(ColourSchemeProperty.getColourName(i));
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83 String string = Cache.getProperty("DEFAULT_COLOUR");
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87 colour.setSelectedItem(string);
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91 colour.setSelectedIndex(11);
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94 String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
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95 .getAvailableFontFamilyNames();
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97 for (int i = 0; i < fonts.length; i++)
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99 fontNameCB.addItem(fonts[i]);
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102 for (int i = 1; i < 31; i++)
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104 fontSizeCB.addItem(i + "");
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107 fontStyleCB.addItem("plain");
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108 fontStyleCB.addItem("bold");
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109 fontStyleCB.addItem("italic");
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111 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
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112 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
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113 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
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115 gapSymbolCB.addItem("-");
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116 gapSymbolCB.addItem(".");
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118 gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
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120 startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
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121 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
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122 "http://www.jalview.org/examples/exampleFile.jar"));
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124 /****************************************************
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125 * Set up Connections
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128 string = Cache.getDefault("SEQUENCE_LINKS",
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129 "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
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130 sequenceURLLinks = new Vector();
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133 StringTokenizer st = new StringTokenizer(string, "|");
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134 while (st.hasMoreElements())
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136 sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
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138 }catch(Exception ex)
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139 {System.out.println(ex+"\nError parsing sequence links");}
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141 nameLinks = new Vector();
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142 urlLinks = new Vector();
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143 for(int i=0; i<sequenceURLLinks.size(); i++)
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145 String link = sequenceURLLinks.elementAt(i).toString();
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146 nameLinks.addElement(link.substring(0, link.indexOf("|")) );
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147 urlLinks.addElement(link.substring(link.indexOf("|")+1));
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152 useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
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153 proxyServerTB.setEnabled(useProxy.isSelected());
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154 proxyPortTB.setEnabled(useProxy.isSelected());
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155 proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
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156 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
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158 defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
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163 catch (Exception ex)
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165 ex.printStackTrace();
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174 * @param e DOCUMENT ME!
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176 public void ok_actionPerformed(ActionEvent e)
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179 Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));
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180 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
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182 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
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183 Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
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184 Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
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185 Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
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187 Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
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188 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
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190 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
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191 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
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192 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
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194 Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
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195 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));
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197 if(defaultBrowser.getText().trim().length()<1)
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198 Cache.applicationProperties.remove("DEFAULT_BROWSER");
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200 Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
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201 defaultBrowser.getText());
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203 jalview.util.BrowserLauncher.resetBrowser();
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205 if(nameLinks.size()>0)
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207 StringBuffer links = new StringBuffer();
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208 sequenceURLLinks = new Vector();
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209 for (int i = 0; i < nameLinks.size(); i++)
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211 sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
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212 links.append(sequenceURLLinks.elementAt(i).toString());
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216 links.setLength( links.length()-1 );
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217 Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
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220 Cache.applicationProperties.remove("SEQUENCE_LINKS");
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223 Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
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225 if (proxyServerTB.getText().trim().length() < 1)
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226 Cache.applicationProperties.remove("PROXY_SERVER");
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228 Cache.applicationProperties.setProperty("PROXY_SERVER",
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229 proxyServerTB.getText());
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231 if (proxyPortTB.getText().trim().length() < 1)
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232 Cache.applicationProperties.remove("PROXY_PORT");
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234 Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
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236 if(useProxy.isSelected())
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238 System.setProperty("http.proxyHost", proxyServerTB.getText());
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239 System.setProperty("http.proxyPort", proxyPortTB.getText());
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243 System.setProperty("http.proxyHost","");
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244 System.setProperty("http.proxyPort","");
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249 Cache.saveProperties();
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252 frame.setClosed(true);
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254 catch (Exception ex)
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262 public void startupFileTextfield_mouseClicked()
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264 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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268 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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273 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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274 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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275 chooser.setFileView(new JalviewFileView());
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276 chooser.setDialogTitle("Select startup file");
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278 int value = chooser.showOpenDialog(this);
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280 if (value == JalviewFileChooser.APPROVE_OPTION)
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282 jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
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283 chooser.getSelectedFormat());
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284 startupFileTextfield.setText(chooser.getSelectedFile()
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285 .getAbsolutePath());
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292 * @param e DOCUMENT ME!
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294 public void cancel_actionPerformed(ActionEvent e)
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298 frame.setClosed(true);
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300 catch (Exception ex)
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308 * @param e DOCUMENT ME!
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310 public void annotations_actionPerformed(ActionEvent e)
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312 conservation.setEnabled(annotations.isSelected());
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313 quality.setEnabled(annotations.isSelected());
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314 identity.setEnabled(annotations.isSelected());
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318 public void newLink_actionPerformed(ActionEvent e) {
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320 GSequenceLink link = new GSequenceLink();
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321 boolean valid = false;
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324 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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325 "New sequence URL link",
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326 JOptionPane.OK_CANCEL_OPTION
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328 == JOptionPane.OK_OPTION)
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330 if (link.checkValid())
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332 nameLinks.addElement(link.getName());
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333 urlLinks.addElement(link.getURL());
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343 public void editLink_actionPerformed(ActionEvent e) {
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344 GSequenceLink link = new GSequenceLink();
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346 int index = linkNameList.getSelectedIndex();
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349 JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
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350 ,"No link selected", JOptionPane.WARNING_MESSAGE);
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354 link.setName( nameLinks.elementAt(index).toString() );
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355 link.setURL( urlLinks.elementAt(index).toString() );
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357 boolean valid = false;
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361 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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362 "New sequence URL link",
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363 JOptionPane.OK_CANCEL_OPTION
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365 == JOptionPane.OK_OPTION)
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367 if (link.checkValid())
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369 nameLinks.setElementAt(link.getName(), index);
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370 urlLinks.setElementAt(link.getURL(), index);
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381 public void deleteLink_actionPerformed(ActionEvent e) {
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382 int index = linkNameList.getSelectedIndex();
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385 JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
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386 ,"No link selected", JOptionPane.WARNING_MESSAGE);
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389 nameLinks.removeElementAt(index);
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390 urlLinks.removeElementAt(index);
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394 void updateLinkData()
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396 linkNameList.setListData(nameLinks);
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397 linkURLList.setListData(urlLinks);
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400 public void defaultBrowser_mouseClicked(MouseEvent e)
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402 JFileChooser chooser = new JFileChooser(".");
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403 chooser.setDialogTitle("Select default web browser");
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405 int value = chooser.showOpenDialog(this);
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407 if (value == JFileChooser.APPROVE_OPTION)
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409 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
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414 private void jbInit()
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