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.io.*;
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23 import jalview.jbgui.*;
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25 import jalview.schemes.*;
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28 import java.awt.event.*;
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30 import javax.swing.*;
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34 import jalview.bin.Cache;
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41 * @version $Revision$
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43 public class Preferences extends GPreferences
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45 /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
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46 public static Vector sequenceURLLinks;
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49 String string = Cache.getDefault("SEQUENCE_LINKS",
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50 "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
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51 sequenceURLLinks = new Vector();
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55 StringTokenizer st = new StringTokenizer(string, "|");
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56 while (st.hasMoreElements())
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58 sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
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61 catch (Exception ex)
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63 System.out.println(ex + "\nError parsing sequence links");
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66 Vector nameLinks, urlLinks;
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68 JInternalFrame frame;
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72 * Creates a new Preferences object.
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74 public Preferences()
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77 frame = new JInternalFrame();
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78 frame.setContentPane(this);
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79 Desktop.addInternalFrame(frame, "Preferences", 480, 390);
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80 frame.setMinimumSize(new Dimension(480,390));
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82 dbRef.setSelected( Cache.getDefault("SHOW_DBREF", true));
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83 seqLimit.setSelected( Cache.getDefault("SHOW_JVSUFFIX", true));
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84 fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));
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85 annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
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87 conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
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88 quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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89 identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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91 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
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92 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
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93 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
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95 for (int i = 0; i < 13; i++)
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97 colour.addItem(ColourSchemeProperty.getColourName(i));
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100 String string = Cache.getDefault("DEFAULT_COLOUR", "None");
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102 colour.setSelectedItem(string);
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104 String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
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105 .getAvailableFontFamilyNames();
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107 for (int i = 0; i < fonts.length; i++)
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109 fontNameCB.addItem(fonts[i]);
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112 for (int i = 1; i < 31; i++)
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114 fontSizeCB.addItem(i + "");
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117 fontStyleCB.addItem("plain");
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118 fontStyleCB.addItem("bold");
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119 fontStyleCB.addItem("italic");
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121 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
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122 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
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123 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
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125 gapSymbolCB.addItem("-");
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126 gapSymbolCB.addItem(".");
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128 gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
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130 startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
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131 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
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132 "http://www.jalview.org/examples/exampleFile.jar"));
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134 sortby.addItem("No sort");
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135 sortby.addItem("Id");
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136 sortby.addItem("Pairwise Identity");
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137 sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
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139 epsRendering.addItem("Prompt each time");
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140 epsRendering.addItem("Lineart");
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141 epsRendering.addItem("Text");
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142 epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
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144 blcdb.setSelected( Cache.getDefault("BLC_DBPREFIX", false) );
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145 blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
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146 clustaldb.setSelected( Cache.getDefault("CLUSTAL_DBPREFIX", false) );
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147 clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
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148 fastadb.setSelected( Cache.getDefault("FASTA_DBPREFIX", false) );
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149 fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
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150 msfdb.setSelected( Cache.getDefault("MSF_DBPREFIX", false) );
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151 msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
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152 pfamdb.setSelected( Cache.getDefault("PFAM_DBPREFIX", false) );
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153 pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
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154 pileupdb.setSelected( Cache.getDefault("PILEUP_DBPREFIX", false) );
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155 pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
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156 pirdb.setSelected( Cache.getDefault("PIR_DBPREFIX", false) );
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157 pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
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159 /****************************************************
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160 * Set up Connections
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162 nameLinks = new Vector();
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163 urlLinks = new Vector();
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164 for(int i=0; i<sequenceURLLinks.size(); i++)
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166 String link = sequenceURLLinks.elementAt(i).toString();
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167 nameLinks.addElement(link.substring(0, link.indexOf("|")) );
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168 urlLinks.addElement(link.substring(link.indexOf("|")+1));
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173 useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
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174 proxyServerTB.setEnabled(useProxy.isSelected());
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175 proxyPortTB.setEnabled(useProxy.isSelected());
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176 proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
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177 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
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179 defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
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184 catch (Exception ex)
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186 ex.printStackTrace();
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195 * @param e DOCUMENT ME!
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197 public void ok_actionPerformed(ActionEvent e)
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200 Cache.applicationProperties.setProperty("SHOW_DBREF", Boolean.toString(dbRef.isSelected()));
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201 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
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202 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
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204 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
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205 Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
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206 Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
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207 Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
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209 Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
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210 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
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212 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
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213 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
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214 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
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216 Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
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217 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));
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219 Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
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221 if(epsRendering.getSelectedItem().equals("Prompt each time"))
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222 Cache.applicationProperties.remove("EPS_RENDERING");
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224 Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
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226 if(defaultBrowser.getText().trim().length()<1)
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227 Cache.applicationProperties.remove("DEFAULT_BROWSER");
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229 Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
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230 defaultBrowser.getText());
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232 jalview.util.BrowserLauncher.resetBrowser();
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234 if(nameLinks.size()>0)
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236 StringBuffer links = new StringBuffer();
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237 sequenceURLLinks = new Vector();
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238 for (int i = 0; i < nameLinks.size(); i++)
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240 sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
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241 links.append(sequenceURLLinks.elementAt(i).toString());
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245 links.setLength( links.length()-1 );
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246 Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
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249 Cache.applicationProperties.remove("SEQUENCE_LINKS");
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252 Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
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254 if (proxyServerTB.getText().trim().length() < 1)
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255 Cache.applicationProperties.remove("PROXY_SERVER");
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257 Cache.applicationProperties.setProperty("PROXY_SERVER",
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258 proxyServerTB.getText());
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260 if (proxyPortTB.getText().trim().length() < 1)
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261 Cache.applicationProperties.remove("PROXY_PORT");
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263 Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
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265 if(useProxy.isSelected())
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267 System.setProperty("http.proxyHost", proxyServerTB.getText());
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268 System.setProperty("http.proxyPort", proxyPortTB.getText());
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272 System.setProperty("http.proxyHost","");
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273 System.setProperty("http.proxyPort","");
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277 Cache.applicationProperties.setProperty("BLC_DBPREFIX", Boolean.toString(blcdb.isSelected()) );
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278 Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
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279 Cache.applicationProperties.setProperty("CLUSTAL_DBPREFIX", Boolean.toString(clustaldb.isSelected()) );
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280 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
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281 Cache.applicationProperties.setProperty("FASTA_DBPREFIX", Boolean.toString(fastadb.isSelected()) );
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282 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
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283 Cache.applicationProperties.setProperty("MSF_DBPREFIX", Boolean.toString(msfdb.isSelected()) );
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284 Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
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285 Cache.applicationProperties.setProperty("PFAM_DBPREFIX", Boolean.toString(pfamdb.isSelected()) );
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286 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
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287 Cache.applicationProperties.setProperty("PILEUP_DBPREFIX", Boolean.toString(pileupdb.isSelected()) );
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288 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
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289 Cache.applicationProperties.setProperty("PIR_DBPREFIX", Boolean.toString(pirdb.isSelected()) );
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290 Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
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293 Cache.saveProperties();
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296 frame.setClosed(true);
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298 catch (Exception ex)
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306 public void startupFileTextfield_mouseClicked()
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308 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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312 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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317 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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318 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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319 chooser.setFileView(new JalviewFileView());
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320 chooser.setDialogTitle("Select startup file");
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322 int value = chooser.showOpenDialog(this);
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324 if (value == JalviewFileChooser.APPROVE_OPTION)
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326 jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
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327 chooser.getSelectedFormat());
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328 startupFileTextfield.setText(chooser.getSelectedFile()
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329 .getAbsolutePath());
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336 * @param e DOCUMENT ME!
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338 public void cancel_actionPerformed(ActionEvent e)
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342 frame.setClosed(true);
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344 catch (Exception ex)
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352 * @param e DOCUMENT ME!
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354 public void annotations_actionPerformed(ActionEvent e)
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356 conservation.setEnabled(annotations.isSelected());
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357 quality.setEnabled(annotations.isSelected());
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358 identity.setEnabled(annotations.isSelected());
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362 public void newLink_actionPerformed(ActionEvent e) {
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364 GSequenceLink link = new GSequenceLink();
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365 boolean valid = false;
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368 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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369 "New sequence URL link",
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370 JOptionPane.OK_CANCEL_OPTION
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372 == JOptionPane.OK_OPTION)
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374 if (link.checkValid())
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376 nameLinks.addElement(link.getName());
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377 urlLinks.addElement(link.getURL());
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387 public void editLink_actionPerformed(ActionEvent e) {
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388 GSequenceLink link = new GSequenceLink();
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390 int index = linkNameList.getSelectedIndex();
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393 JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
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394 ,"No link selected", JOptionPane.WARNING_MESSAGE);
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398 link.setName( nameLinks.elementAt(index).toString() );
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399 link.setURL( urlLinks.elementAt(index).toString() );
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401 boolean valid = false;
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405 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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406 "New sequence URL link",
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407 JOptionPane.OK_CANCEL_OPTION
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409 == JOptionPane.OK_OPTION)
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411 if (link.checkValid())
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413 nameLinks.setElementAt(link.getName(), index);
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414 urlLinks.setElementAt(link.getURL(), index);
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425 public void deleteLink_actionPerformed(ActionEvent e) {
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426 int index = linkNameList.getSelectedIndex();
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429 JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
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430 ,"No link selected", JOptionPane.WARNING_MESSAGE);
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433 nameLinks.removeElementAt(index);
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434 urlLinks.removeElementAt(index);
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438 void updateLinkData()
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440 linkNameList.setListData(nameLinks);
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441 linkURLList.setListData(urlLinks);
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444 public void defaultBrowser_mouseClicked(MouseEvent e)
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446 JFileChooser chooser = new JFileChooser(".");
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447 chooser.setDialogTitle("Select default web browser");
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449 int value = chooser.showOpenDialog(this);
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451 if (value == JFileChooser.APPROVE_OPTION)
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453 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
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458 private void jbInit()
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