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.jbgui.*;
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22 import javax.swing.table.AbstractTableModel;
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23 import javax.swing.event.*;
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24 import jalview.util.TableSorter;
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25 import java.awt.event.*;
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26 import javax.swing.*;
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30 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
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31 import org.biojava.dasobert.dasregistry.DasSource;
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32 import org.biojava.dasobert.dasregistry.Das1Source;
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33 import java.awt.BorderLayout;
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35 public class DasSourceBrowser extends GDasSourceBrowser
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36 implements Runnable, ListSelectionListener
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38 static DasSource[] dasSources = null;
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40 Hashtable localSources = null;
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42 Vector selectedSources;
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44 public DasSourceBrowser()
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46 registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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47 "http://www.spice-3d.org/dasregistry/das1/sources") );
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49 setSelectedFromProperties();
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51 displayFullDetails(null);
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52 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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54 filter1.addListSelectionListener(this);
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55 filter2.addListSelectionListener(this);
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56 filter3.addListSelectionListener(this);
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58 //Ask to be notified of selection changes.
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59 ListSelectionModel rowSM = table.getSelectionModel();
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60 rowSM.addListSelectionListener(new ListSelectionListener()
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62 public void valueChanged(ListSelectionEvent e)
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64 //Ignore extra messages.
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65 if (e.getValueIsAdjusting())
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68 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
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69 if (!lsm.isSelectionEmpty())
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71 int selectedRow = lsm.getMinSelectionIndex();
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72 displayFullDetails(table.getValueAt(selectedRow, 0).toString());
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77 table.addMouseListener(new MouseAdapter()
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79 public void mouseClicked(MouseEvent evt)
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81 if(evt.getClickCount()==2
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82 || SwingUtilities.isRightMouseButton(evt))
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83 editRemoveLocalSource(evt);
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87 if(dasSources==null)
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89 Thread worker = new Thread(this);
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100 int dSize = dasSources.length;
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101 Object[][] data = new Object[dSize][2];
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102 for (int i = 0; i < dSize; i++)
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104 data[i][0] = dasSources[i].getNickname();
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105 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
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109 refreshTableData(data);
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110 setCapabilities(dasSources);
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112 javax.swing.SwingUtilities.invokeLater(new Runnable()
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116 TableSorter sorter = (TableSorter)table.getModel();
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117 sorter.setSortingStatus(1, TableSorter.DESCENDING);
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118 sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
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122 progressBar.setIndeterminate(false);
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123 progressBar.setVisible(false);
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124 addLocal.setVisible(true);
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125 refresh.setVisible(true);
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129 public void refreshTableData(Object[][] data)
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131 TableSorter sorter = new TableSorter(new DASTableModel(data));
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132 sorter.setTableHeader(table.getTableHeader());
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133 table.setModel(sorter);
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136 void displayFullDetails(String nickName)
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139 StringBuffer text = new StringBuffer(
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140 "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
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142 if (nickName == null)
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144 fullDetails.setText(text +
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145 "Select a DAS service from the table"
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146 + " to read a full description here.</font></html>");
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150 int dSize = dasSources.length;
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151 for (int i = 0; i < dSize; i++)
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153 if (!dasSources[i].getNickname().equals(nickName))
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156 DasSource ds = dasSources[i];
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158 text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
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160 text.append("<font color=\"#0000FF\">Nickname:</font> " +
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161 dasSources[i].getNickname() + "<br>");
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162 text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
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165 text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
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166 +dasSources[i].getAdminemail()
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167 +"\">"+dasSources[i].getAdminemail()+"</a>" +
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171 text.append("<font color=\"#0000FF\">Registered at:</font> " + dasSources[i].getRegisterDate() +
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174 text.append("<font color=\"#0000FF\">Last successful test:</font> " + dasSources[i].getLeaseDate() +
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177 text.append("<font color=\"#0000FF\">Labels:</font> ");
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178 for(int s=0; s<dasSources[i].getLabels().length; s++)
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180 text.append( dasSources[i].getLabels()[s]);
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181 if(s<dasSources[i].getLabels().length-1)
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185 text.append("<br>");
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189 text.append("<font color=\"#0000FF\">Capabilities:</font> ");
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190 String[] scap = dasSources[i].getCapabilities();
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191 for (int j = 0; j < scap.length; j++)
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193 text.append(scap[j]);
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194 if (j < scap.length - 1)
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197 text.append("<br>");
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199 text.append("<font color=\"#0000FF\">Coordinates:</font> ");
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200 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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201 for (int j = 0; j < dcs.length; j++)
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203 text.append("(" + dcs[j].getUniqueId() + ") "
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204 + dcs[j].getCategory() + ", " + dcs[j].getName());
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205 if (dcs[j].getNCBITaxId() != 0)
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206 text.append(", " + dcs[j].getNCBITaxId());
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207 if (dcs[j].getOrganismName().length() > 0)
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208 text.append(", " + dcs[j].getOrganismName());
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210 text.append("<br>");
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213 text.append("<font color=\"#0000FF\">Description:</font> " +
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214 dasSources[i].getDescription() + "<br>");
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217 if (dasSources[i].getHelperurl()!=null
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218 && dasSources[i].getHelperurl().length() > 0)
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220 text.append("<font color=\"#0000FF\"><a href=\"" +
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221 dasSources[i].getHelperurl()
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222 + "\">Go to site</a></font<br>");
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225 text.append("</font></html>");
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230 fullDetails.setText(text.toString());
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231 javax.swing.SwingUtilities.invokeLater(new Runnable()
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235 fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
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243 System.out.println("das source browser running");
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244 addLocal.setVisible(false);
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245 refresh.setVisible(false);
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246 progressBar.setVisible(true);
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247 progressBar.setIndeterminate(true);
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249 dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
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251 appendLocalSources();
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256 public Vector getSelectedSources()
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258 Vector selected = new Vector();
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259 for (int r = 0; r < selectedSources.size(); r++)
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261 for (int i = 0; i < dasSources.length; i++)
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263 if (dasSources[i].getNickname().equals(
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264 selectedSources.elementAt(r)))
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266 selected.addElement(dasSources[i]);
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275 public DasSource[] getDASSource()
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277 if(dasSources==null)
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279 dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
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280 appendLocalSources();
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286 public void refresh_actionPerformed(ActionEvent e)
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288 saveProperties(jalview.bin.Cache.applicationProperties);
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290 Thread worker = new Thread(this);
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294 private void setCapabilities(DasSource[] sources)
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296 Vector authority = new Vector();
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297 Vector type = new Vector();
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298 Vector label = new Vector();
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300 authority.addElement("Any");
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301 type.addElement("Any");
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302 label.addElement("Any");
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303 label.addElement("NOT IMPLEMENTED YET");
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304 filter3.setEnabled(false);
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306 for (int i = 0; i < sources.length; i++)
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308 DasSource ds = sources[i];
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310 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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312 for (int j = 0; j < dcs.length; j++)
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314 if (!type.contains(dcs[j].getCategory()))
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315 type.addElement(dcs[j].getCategory());
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317 if (!authority.contains(dcs[j].getName()))
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318 authority.addElement(dcs[j].getName());
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321 String[] slabels = ds.getLabels();
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322 for (int s = 0; s < slabels.length; s++)
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324 if (!label.contains(slabels[s]))
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326 label.addElement(slabels[s]);
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332 filter1.setListData(authority);
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333 filter2.setListData(type);
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334 filter3.setListData(label);
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336 javax.swing.SwingUtilities.invokeLater(new Runnable()
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340 filter1.setSelectedIndex(0);
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341 filter2.setSelectedIndex(0);
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342 filter3.setSelectedIndex(0);
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347 public void amendLocal(boolean newSource)
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349 String url = "http://localhost:8080/", nickname = "";
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353 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
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354 nickname = table.getValueAt(selectedRow, 0).toString();
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355 url = ((DasSource)localSources.get(nickname)).getUrl();
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358 JTextField nametf = new JTextField(nickname, 40);
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359 JTextField urltf = new JTextField(url, 40);
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361 JPanel panel = new JPanel(new BorderLayout());
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362 JPanel pane12 = new JPanel(new BorderLayout());
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363 pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
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364 pane12.add(nametf, BorderLayout.EAST);
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365 panel.add(pane12, BorderLayout.NORTH);
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366 pane12 = new JPanel(new BorderLayout());
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367 pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
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368 pane12.add(urltf, BorderLayout.EAST);
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369 panel.add(pane12, BorderLayout.SOUTH);
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372 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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373 panel, "Enter Nickname & URL of Local DAS Source",
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374 JOptionPane.OK_CANCEL_OPTION);
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376 if (reply != JOptionPane.OK_OPTION )
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381 if(!urltf.getText().endsWith("/"))
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382 urltf.setText(urltf.getText()+"/");
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384 Das1Source local = new Das1Source();
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386 local.setUrl(urltf.getText());
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387 local.setNickname(nametf.getText());
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390 if(localSources==null)
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391 localSources = new Hashtable();
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393 localSources.put(local.getNickname(), local);
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395 if(!newSource && !nickname.equals(nametf.getText()))
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397 localSources.remove(nickname);
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400 int size = dasSources.length;
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401 int adjust = newSource ? 1 : 0;
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403 Object[][] data = new Object[size+adjust][2];
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404 for (int i = 0; i < size; i++)
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406 if(!newSource && dasSources[i].getNickname().equals(nickname))
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408 ((DasSource)dasSources[i]).setNickname(local.getNickname());
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409 ((DasSource)dasSources[i]).setUrl(local.getUrl());
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410 data[i][0] = local.getNickname();
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411 data[i][1] = new Boolean(true);
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415 data[i][0] = dasSources[i].getNickname();
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416 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
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423 data[size][0] = local.getNickname();
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424 data[size][1] = new Boolean(true);
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425 selectedSources.add(local.getNickname());
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428 DasSource [] tmp = new DasSource[size+adjust];
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430 System.arraycopy(dasSources, 0, tmp, 0, size);
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437 refreshTableData(data);
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439 SwingUtilities.invokeLater(new Runnable()
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443 scrollPane.getVerticalScrollBar().setValue(
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444 scrollPane.getVerticalScrollBar().getMaximum()
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449 displayFullDetails(local.getNickname());
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452 public void editRemoveLocalSource(MouseEvent evt)
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454 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
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455 if(selectedRow==-1)
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458 String nickname = table.getValueAt(selectedRow, 0).toString();
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460 if (!localSources.containsKey(nickname))
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462 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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463 "You can only edit or remove local DAS Sources!",
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464 "Public DAS source - not editable",
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465 JOptionPane.WARNING_MESSAGE);
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470 Object[] options = {"Edit", "Remove", "Cancel"};
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471 int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
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472 "Do you want to edit or remove "+nickname+"?",
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473 "Edit / Remove Local DAS Source",
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474 JOptionPane.YES_NO_CANCEL_OPTION,
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475 JOptionPane.QUESTION_MESSAGE,
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482 case 0: amendLocal(false); break;
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484 localSources.remove(nickname);
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485 selectedSources.remove(nickname);
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486 Object[][] data = new Object[dasSources.length-1][2];
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487 DasSource [] tmp = new DasSource[dasSources.length-1];
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489 for (int i = 0; i < dasSources.length; i++)
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491 if (dasSources[i].getNickname().equals(nickname))
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497 tmp[index] = dasSources[i];
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498 data[index][0] = dasSources[i].getNickname();
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499 data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
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505 refreshTableData(data);
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506 SwingUtilities.invokeLater(new Runnable()
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510 scrollPane.getVerticalScrollBar().setValue(
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511 scrollPane.getVerticalScrollBar().getMaximum()
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520 void appendLocalSources()
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522 if(localSources==null)
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525 int size = dasSources!=null ? dasSources.length : 0;
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526 int lsize = localSources.size();
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528 Object[][] data = new Object[size+lsize][2];
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529 for (int i = 0; i < size; i++)
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531 data[i][0] = dasSources[i].getNickname();
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532 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
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536 DasSource [] tmp = new DasSource[size+lsize];
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537 if(dasSources!=null)
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538 System.arraycopy(dasSources, 0, tmp, 0, size);
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540 Enumeration en = localSources.keys();
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542 while(en.hasMoreElements())
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544 String key = en.nextElement().toString();
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545 data[index][0] = key;
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546 data[index][1] = new Boolean(false);
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547 tmp[index] = new Das1Source();
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548 tmp[index].setNickname(key);
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549 tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
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556 refreshTableData(data);
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559 public void valueChanged(ListSelectionEvent evt)
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561 //Called when the MainTable selection changes
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562 if (evt.getValueIsAdjusting())
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567 displayFullDetails(null);
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569 // Filter the displayed data sources
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570 int dSize = dasSources.length;
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571 ArrayList names = new ArrayList();
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572 ArrayList selected = new ArrayList();
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575 //The features filter is not visible, but we must still
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576 //filter the das source list here.
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577 //July 2006 - only 6 sources fo not serve features
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578 Object [] dummyFeatureList = new Object[]{"features"};
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580 // capabilities.get
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581 for (int i = 0; i < dSize; i++)
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583 ds = dasSources[i];
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585 if (!selectedInList(dummyFeatureList, ds.getCapabilities())
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586 || !selectedInList(filter3.getSelectedValues(),
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592 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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593 for (int j = 0; j < dcs.length; j++)
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595 if (selectedInList(dummyFeatureList,ds.getCapabilities())
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597 selectedInList(filter1.getSelectedValues(),
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599 {dcs[j].getName()})
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600 && selectedInList(filter2.getSelectedValues(),
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602 {dcs[j].getCategory()}))
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604 names.add(ds.getNickname());
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605 selected.add(new Boolean(
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606 selectedSources.contains(ds.getNickname())));
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612 dSize = names.size();
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613 Object[][] data = new Object[dSize][2];
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614 for (int d = 0; d < dSize; d++)
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616 data[d][0] = names.get(d);
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617 data[d][1] = selected.get(d);
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620 refreshTableData(data);
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623 boolean selectedInList(Object [] selection, String[] items)
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625 for (int i = 0; i < selection.length; i++)
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627 if (selection[i].equals("Any"))
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630 for (int j = 0; j < items.length; j++)
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632 if (selection[i].equals(items[j]))
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640 void setSelectedFromProperties()
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642 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
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643 StringTokenizer st = new StringTokenizer(active, "\t");
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644 selectedSources = new Vector();
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645 while(st.hasMoreTokens())
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647 selectedSources.addElement(st.nextToken());
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650 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
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653 if(localSources == null)
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654 localSources = new Hashtable();
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656 st = new StringTokenizer(local, "\t");
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657 while(st.hasMoreTokens())
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659 String token = st.nextToken();
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660 int bar = token.indexOf("|");
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661 Das1Source source = new Das1Source();
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663 source.setUrl(token.substring(bar + 1));
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664 source.setNickname(token.substring(0, bar));
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666 localSources.put(source.getNickname(), source);
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671 public void saveProperties(Properties properties)
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673 properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
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675 StringBuffer sb = new StringBuffer();
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676 for(int r=0; r<table.getModel().getRowCount(); r++)
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678 if( ((Boolean)table.getValueAt(r,1)).booleanValue())
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680 sb.append(table.getValueAt(r,0)+"\t");
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684 properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );
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686 if(localSources!=null)
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688 sb = new StringBuffer();
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689 Enumeration en = localSources.keys();
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690 while(en.hasMoreElements())
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692 String token = en.nextElement().toString();
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693 sb.append(token+"|"
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694 + ((DasSource)localSources.get(token)).getUrl()
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698 properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
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703 class DASTableModel
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704 extends AbstractTableModel
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707 public DASTableModel(Object[][] data)
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712 private String[] columnNames = new String[] {"Nickname", "Use Source"};
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714 private Object[][] data;
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716 public int getColumnCount()
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718 return columnNames.length;
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721 public int getRowCount()
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723 return data.length;
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726 public String getColumnName(int col)
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728 return columnNames[col];
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731 public Object getValueAt(int row, int col)
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733 return data[row][col];
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737 * JTable uses this method to determine the default renderer/
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738 * editor for each cell. If we didn't implement this method,
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739 * then the last column would contain text ("true"/"false"),
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740 * rather than a check box.
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742 public Class getColumnClass(int c)
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744 return getValueAt(0, c).getClass();
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748 * Don't need to implement this method unless your table's
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751 public boolean isCellEditable(int row, int col)
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753 //Note that the data/cell address is constant,
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754 //no matter where the cell appears onscreen.
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760 * Don't need to implement this method unless your table's
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763 public void setValueAt(Object value, int row, int col)
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765 data[row][col] = value;
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766 fireTableCellUpdated(row, col);
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768 String name = getValueAt(row,0).toString();
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769 boolean selected = ((Boolean)value).booleanValue();
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771 if(selectedSources.contains(name) && !selected)
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772 selectedSources.remove(name);
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774 if(!selectedSources.contains(name) && selected)
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775 selectedSources.add(name);
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