2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
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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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70 DasSourceBrowser dasSource;
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74 * Creates a new Preferences object.
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76 public Preferences()
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79 frame = new JInternalFrame();
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80 frame.setContentPane(this);
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81 dasSource = new DasSourceBrowser();
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82 dasPanel.add(dasSource, BorderLayout.CENTER);
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84 int width = 500, height = 420;
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85 if(System.getProperty("os.name").startsWith("Mac"))
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91 Desktop.addInternalFrame(frame, "Preferences", width, height);
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92 frame.setMinimumSize(new Dimension(width, height));
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94 seqLimit.setSelected( Cache.getDefault("SHOW_JVSUFFIX", true));
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95 rightAlign.setSelected( Cache.getDefault("RIGHT_ALIGN_IDS", false));
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96 fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));
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97 annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
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99 conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
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100 quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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101 identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
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103 conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
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104 quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
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105 identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
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107 for (int i = 0; i < 13; i++)
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109 colour.addItem(ColourSchemeProperty.getColourName(i));
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112 String string = Cache.getDefault("DEFAULT_COLOUR", "None");
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114 colour.setSelectedItem(string);
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116 String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
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117 .getAvailableFontFamilyNames();
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119 for (int i = 0; i < fonts.length; i++)
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121 fontNameCB.addItem(fonts[i]);
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124 for (int i = 1; i < 31; i++)
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126 fontSizeCB.addItem(i + "");
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129 fontStyleCB.addItem("plain");
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130 fontStyleCB.addItem("bold");
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131 fontStyleCB.addItem("italic");
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133 fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
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134 fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
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135 fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
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137 smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
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139 idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
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141 wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
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143 gapSymbolCB.addItem("-");
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144 gapSymbolCB.addItem(".");
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146 gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
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148 startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
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149 startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
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150 "http://www.jalview.org/examples/exampleFile.jar"));
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152 sortby.addItem("No sort");
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153 sortby.addItem("Id");
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154 sortby.addItem("Pairwise Identity");
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155 sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
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157 epsRendering.addItem("Prompt each time");
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158 epsRendering.addItem("Lineart");
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159 epsRendering.addItem("Text");
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160 epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
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162 blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
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163 clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
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164 fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
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165 msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
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166 pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
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167 pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
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168 pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
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170 modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
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172 autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
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173 padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
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175 /****************************************************
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176 * Set up Connections
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178 nameLinks = new Vector();
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179 urlLinks = new Vector();
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180 for(int i=0; i<sequenceURLLinks.size(); i++)
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182 String link = sequenceURLLinks.elementAt(i).toString();
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183 nameLinks.addElement(link.substring(0, link.indexOf("|")) );
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184 urlLinks.addElement(link.substring(link.indexOf("|")+1));
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189 useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
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190 proxyServerTB.setEnabled(useProxy.isSelected());
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191 proxyPortTB.setEnabled(useProxy.isSelected());
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192 proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
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193 proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
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195 defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
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200 catch (Exception ex)
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202 ex.printStackTrace();
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211 * @param e DOCUMENT ME!
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213 public void ok_actionPerformed(ActionEvent e)
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216 Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
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217 Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.isSelected()));
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218 Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
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220 Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
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221 Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
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222 Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
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223 Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
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225 Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
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226 Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
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228 Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
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229 Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
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230 Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
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232 Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected()));
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234 Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
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236 Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));
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238 Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
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239 Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));
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241 Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
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243 if(epsRendering.getSelectedItem().equals("Prompt each time"))
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244 Cache.applicationProperties.remove("EPS_RENDERING");
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246 Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
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248 if(defaultBrowser.getText().trim().length()<1)
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249 Cache.applicationProperties.remove("DEFAULT_BROWSER");
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251 Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
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252 defaultBrowser.getText());
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254 jalview.util.BrowserLauncher.resetBrowser();
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256 if(nameLinks.size()>0)
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258 StringBuffer links = new StringBuffer();
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259 sequenceURLLinks = new Vector();
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260 for (int i = 0; i < nameLinks.size(); i++)
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262 sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
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263 links.append(sequenceURLLinks.elementAt(i).toString());
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267 links.setLength( links.length()-1 );
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268 Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
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271 Cache.applicationProperties.remove("SEQUENCE_LINKS");
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274 Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
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276 if (proxyServerTB.getText().trim().length() < 1)
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277 Cache.applicationProperties.remove("PROXY_SERVER");
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279 Cache.applicationProperties.setProperty("PROXY_SERVER",
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280 proxyServerTB.getText());
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282 if (proxyPortTB.getText().trim().length() < 1)
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283 Cache.applicationProperties.remove("PROXY_PORT");
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285 Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
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287 if(useProxy.isSelected())
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289 System.setProperty("http.proxyHost", proxyServerTB.getText());
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290 System.setProperty("http.proxyPort", proxyPortTB.getText());
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294 System.setProperty("http.proxyHost","");
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295 System.setProperty("http.proxyPort","");
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299 Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
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300 Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
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301 Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
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302 Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
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303 Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
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304 Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
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305 Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
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306 Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
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307 jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
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309 Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
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310 Boolean.toString(autoCalculateConsCheck.isSelected()));
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311 Cache.applicationProperties.setProperty("PAD_GAPS",
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312 Boolean.toString(padGaps.isSelected()));
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314 dasSource.saveProperties(Cache.applicationProperties);
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316 Cache.saveProperties();
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319 frame.setClosed(true);
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321 catch (Exception ex)
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329 public void startupFileTextfield_mouseClicked()
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331 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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335 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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340 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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341 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
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342 chooser.setFileView(new JalviewFileView());
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343 chooser.setDialogTitle("Select startup file");
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345 int value = chooser.showOpenDialog(this);
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347 if (value == JalviewFileChooser.APPROVE_OPTION)
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349 jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
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350 chooser.getSelectedFormat());
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351 startupFileTextfield.setText(chooser.getSelectedFile()
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352 .getAbsolutePath());
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359 * @param e DOCUMENT ME!
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361 public void cancel_actionPerformed(ActionEvent e)
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365 frame.setClosed(true);
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367 catch (Exception ex)
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375 * @param e DOCUMENT ME!
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377 public void annotations_actionPerformed(ActionEvent e)
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379 conservation.setEnabled(annotations.isSelected());
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380 quality.setEnabled(annotations.isSelected());
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381 identity.setEnabled(annotations.isSelected());
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385 public void newLink_actionPerformed(ActionEvent e) {
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387 GSequenceLink link = new GSequenceLink();
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388 boolean valid = false;
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391 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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392 "New sequence URL link",
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393 JOptionPane.OK_CANCEL_OPTION
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395 == JOptionPane.OK_OPTION)
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397 if (link.checkValid())
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399 nameLinks.addElement(link.getName());
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400 urlLinks.addElement(link.getURL());
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410 public void editLink_actionPerformed(ActionEvent e) {
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411 GSequenceLink link = new GSequenceLink();
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413 int index = linkNameList.getSelectedIndex();
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416 JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
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417 ,"No link selected", JOptionPane.WARNING_MESSAGE);
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421 link.setName( nameLinks.elementAt(index).toString() );
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422 link.setURL( urlLinks.elementAt(index).toString() );
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424 boolean valid = false;
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428 if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
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429 "New sequence URL link",
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430 JOptionPane.OK_CANCEL_OPTION
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432 == JOptionPane.OK_OPTION)
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434 if (link.checkValid())
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436 nameLinks.setElementAt(link.getName(), index);
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437 urlLinks.setElementAt(link.getURL(), index);
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448 public void deleteLink_actionPerformed(ActionEvent e) {
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449 int index = linkNameList.getSelectedIndex();
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452 JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
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453 ,"No link selected", JOptionPane.WARNING_MESSAGE);
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456 nameLinks.removeElementAt(index);
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457 urlLinks.removeElementAt(index);
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461 void updateLinkData()
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463 linkNameList.setListData(nameLinks);
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464 linkURLList.setListData(urlLinks);
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467 public void defaultBrowser_mouseClicked(MouseEvent e)
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469 JFileChooser chooser = new JFileChooser(".");
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470 chooser.setDialogTitle("Select default web browser");
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472 int value = chooser.showOpenDialog(this);
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474 if (value == JFileChooser.APPROVE_OPTION)
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476 defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
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481 private void jbInit()
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