2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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24 import java.awt.event.*;
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25 import javax.swing.*;
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27 import jalview.bin.*;
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28 import jalview.io.*;
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29 import jalview.jbgui.*;
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30 import jalview.schemes.*;
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36 * @version $Revision$
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38 public class Preferences
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39 extends GPreferences
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41 /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
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42 public static Vector sequenceURLLinks;
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45 String string = Cache.getDefault("SEQUENCE_LINKS",
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46 "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
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47 sequenceURLLinks = new Vector();
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51 StringTokenizer st = new StringTokenizer(string, "|");
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52 while (st.hasMoreElements())
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54 sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
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57 catch (Exception ex)
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59 System.out.println(ex + "\nError parsing sequence links");
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63 Vector nameLinks, urlLinks;
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65 JInternalFrame frame;
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67 DasSourceBrowser dasSource;
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70 * Creates a new Preferences object.
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72 public Preferences()
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75 frame = new JInternalFrame();
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76 frame.setContentPane(this);
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77 dasSource = new DasSourceBrowser();
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78 dasPanel.add(dasSource, BorderLayout.CENTER);
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80 int width = 500, height = 420;
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81 if (System.getProperty("os.name").startsWith("Mac"))
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87 Desktop.addInternalFrame(frame, "Preferences", width, height);
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88 frame.setMinimumSize(new Dimension(width, height));
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90 seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
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91 rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
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92 fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
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93 annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
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95 conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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96 quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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97 identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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99 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
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100 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
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101 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
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102 openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
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104 for (int i = 0; i < 13; i++)
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106 colour.addItem(ColourSchemeProperty.getColourName(i));
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109 String string = Cache.getDefault("DEFAULT_COLOUR", "None");
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111 colour.setSelectedItem(string);
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113 String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
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114 .getAvailableFontFamilyNames();
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116 for (int i = 0; i < fonts.length; i++)
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118 fontNameCB.addItem(fonts[i]);
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121 for (int i = 1; i < 31; i++)
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123 fontSizeCB.addItem(i + "");
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126 fontStyleCB.addItem("plain");
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127 fontStyleCB.addItem("bold");
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128 fontStyleCB.addItem("italic");
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130 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
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131 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
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132 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
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134 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
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136 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
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138 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
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140 gapSymbolCB.addItem("-");
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141 gapSymbolCB.addItem(".");
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143 gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
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145 startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
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146 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
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147 "http://www.jalview.org/examples/exampleFile2_3.jar"));
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149 sortby.addItem("No sort");
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150 sortby.addItem("Id");
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151 sortby.addItem("Pairwise Identity");
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152 sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
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154 epsRendering.addItem("Prompt each time");
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155 epsRendering.addItem("Lineart");
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156 epsRendering.addItem("Text");
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157 epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
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158 "Prompt each time"));
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160 blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
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161 clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
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162 fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
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163 msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
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164 pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
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165 pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
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166 pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
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168 modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
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170 autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
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171 padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
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173 /****************************************************
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174 * Set up Connections
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176 nameLinks = new Vector();
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177 urlLinks = new Vector();
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178 for (int i = 0; i < sequenceURLLinks.size(); i++)
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180 String link = sequenceURLLinks.elementAt(i).toString();
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181 nameLinks.addElement(link.substring(0, link.indexOf("|")));
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182 urlLinks.addElement(link.substring(link.indexOf("|") + 1));
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187 useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
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188 proxyServerTB.setEnabled(useProxy.isSelected());
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189 proxyPortTB.setEnabled(useProxy.isSelected());
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190 proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
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191 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
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193 defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
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198 catch (Exception ex)
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200 ex.printStackTrace();
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208 * @param e DOCUMENT ME!
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210 public void ok_actionPerformed(ActionEvent e)
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213 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
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214 Boolean.toString(seqLimit.
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216 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
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217 Boolean.toString(rightAlign.
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219 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
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220 Boolean.toString(fullScreen.
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222 Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
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223 Boolean.toString(openoverv.
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225 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
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227 toString(annotations.isSelected()));
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228 Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
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230 toString(conservation.isSelected()));
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231 Cache.applicationProperties.setProperty("SHOW_QUALITY",
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232 Boolean.toString(quality.isSelected()));
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233 Cache.applicationProperties.setProperty("SHOW_IDENTITY",
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234 Boolean.toString(identity.
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237 Cache.applicationProperties.setProperty("DEFAULT_COLOUR",
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238 colour.getSelectedItem().toString());
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239 Cache.applicationProperties.setProperty("GAP_SYMBOL",
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240 gapSymbolCB.getSelectedItem().
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243 Cache.applicationProperties.setProperty("FONT_NAME",
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244 fontNameCB.getSelectedItem().
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246 Cache.applicationProperties.setProperty("FONT_STYLE",
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247 fontStyleCB.getSelectedItem().
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249 Cache.applicationProperties.setProperty("FONT_SIZE",
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250 fontSizeCB.getSelectedItem().
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253 Cache.applicationProperties.setProperty("ID_ITALICS",
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254 Boolean.toString(idItalics.
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257 Cache.applicationProperties.setProperty("ANTI_ALIAS",
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258 Boolean.toString(smoothFont.
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261 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
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262 Boolean.toString(wrap.isSelected()));
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264 Cache.applicationProperties.setProperty("STARTUP_FILE",
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265 startupFileTextfield.getText());
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266 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
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268 toString(startupCheckbox.isSelected()));
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270 Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
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271 sortby.getSelectedItem().toString());
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273 if (epsRendering.getSelectedItem().equals("Prompt each time"))
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275 Cache.applicationProperties.remove("EPS_RENDERING");
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279 Cache.applicationProperties.setProperty("EPS_RENDERING",
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280 epsRendering.getSelectedItem().
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284 if (defaultBrowser.getText().trim().length() < 1)
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286 Cache.applicationProperties.remove("DEFAULT_BROWSER");
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290 Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
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291 defaultBrowser.getText());
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294 jalview.util.BrowserLauncher.resetBrowser();
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296 if (nameLinks.size() > 0)
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298 StringBuffer links = new StringBuffer();
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299 sequenceURLLinks = new Vector();
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300 for (int i = 0; i < nameLinks.size(); i++)
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302 sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +
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303 urlLinks.elementAt(i));
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304 links.append(sequenceURLLinks.elementAt(i).toString());
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308 links.setLength(links.length() - 1);
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309 Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
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313 Cache.applicationProperties.remove("SEQUENCE_LINKS");
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316 Cache.applicationProperties.setProperty("USE_PROXY",
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317 Boolean.toString(useProxy.
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320 if (proxyServerTB.getText().trim().length() < 1)
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322 Cache.applicationProperties.remove("PROXY_SERVER");
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326 Cache.applicationProperties.setProperty("PROXY_SERVER",
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327 proxyServerTB.getText());
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330 if (proxyPortTB.getText().trim().length() < 1)
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332 Cache.applicationProperties.remove("PROXY_PORT");
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336 Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
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339 if (useProxy.isSelected())
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341 System.setProperty("http.proxyHost", proxyServerTB.getText());
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342 System.setProperty("http.proxyPort", proxyPortTB.getText());
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346 System.setProperty("http.proxyHost", "");
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347 System.setProperty("http.proxyPort", "");
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350 Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
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351 Boolean.toString(blcjv.isSelected()));
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352 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
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354 toString(clustaljv.isSelected()));
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355 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
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356 Boolean.toString(fastajv.isSelected()));
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357 Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
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358 Boolean.toString(msfjv.isSelected()));
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359 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
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360 Boolean.toString(pfamjv.isSelected()));
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361 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
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362 Boolean.toString(pileupjv.
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364 Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
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365 Boolean.toString(pirjv.isSelected()));
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366 Cache.applicationProperties.setProperty("PIR_MODELLER",
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367 Boolean.toString(modellerOutput.
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369 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
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371 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
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373 autoCalculateConsCheck.isSelected()));
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374 Cache.applicationProperties.setProperty("PAD_GAPS",
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375 Boolean.toString(padGaps.isSelected()));
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377 dasSource.saveProperties(Cache.applicationProperties);
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379 Cache.saveProperties();
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382 frame.setClosed(true);
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384 catch (Exception ex)
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392 public void startupFileTextfield_mouseClicked()
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394 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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399 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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404 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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405 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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406 chooser.setFileView(new JalviewFileView());
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407 chooser.setDialogTitle("Select startup file");
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409 int value = chooser.showOpenDialog(this);
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411 if (value == JalviewFileChooser.APPROVE_OPTION)
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413 jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
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414 chooser.getSelectedFormat());
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415 startupFileTextfield.setText(chooser.getSelectedFile()
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416 .getAbsolutePath());
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423 * @param e DOCUMENT ME!
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425 public void cancel_actionPerformed(ActionEvent e)
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429 frame.setClosed(true);
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431 catch (Exception ex)
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439 * @param e DOCUMENT ME!
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441 public void annotations_actionPerformed(ActionEvent e)
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443 conservation.setEnabled(annotations.isSelected());
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444 quality.setEnabled(annotations.isSelected());
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445 identity.setEnabled(annotations.isSelected());
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448 public void newLink_actionPerformed(ActionEvent e)
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451 GSequenceLink link = new GSequenceLink();
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452 boolean valid = false;
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455 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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456 "New sequence URL link",
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457 JOptionPane.OK_CANCEL_OPTION
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459 == JOptionPane.OK_OPTION)
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461 if (link.checkValid())
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463 nameLinks.addElement(link.getName());
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464 urlLinks.addElement(link.getURL());
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476 public void editLink_actionPerformed(ActionEvent e)
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478 GSequenceLink link = new GSequenceLink();
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480 int index = linkNameList.getSelectedIndex();
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483 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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484 "No link selected!"
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485 , "No link selected",
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486 JOptionPane.WARNING_MESSAGE);
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490 link.setName(nameLinks.elementAt(index).toString());
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491 link.setURL(urlLinks.elementAt(index).toString());
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493 boolean valid = false;
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497 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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498 "New sequence URL link",
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499 JOptionPane.OK_CANCEL_OPTION
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501 == JOptionPane.OK_OPTION)
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503 if (link.checkValid())
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505 nameLinks.setElementAt(link.getName(), index);
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506 urlLinks.setElementAt(link.getURL(), index);
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519 public void deleteLink_actionPerformed(ActionEvent e)
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521 int index = linkNameList.getSelectedIndex();
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524 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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525 "No link selected!"
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526 , "No link selected",
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527 JOptionPane.WARNING_MESSAGE);
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530 nameLinks.removeElementAt(index);
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531 urlLinks.removeElementAt(index);
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535 void updateLinkData()
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537 linkNameList.setListData(nameLinks);
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538 linkURLList.setListData(urlLinks);
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541 public void defaultBrowser_mouseClicked(MouseEvent e)
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543 JFileChooser chooser = new JFileChooser(".");
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544 chooser.setDialogTitle("Select default web browser");
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546 int value = chooser.showOpenDialog(this);
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548 if (value == JFileChooser.APPROVE_OPTION)
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550 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
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555 private void jbInit()
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