2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
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3 * Copyright (C) 2008 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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26 import javax.swing.event.*;
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27 import javax.swing.table.*;
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29 import org.biojava.dasobert.dasregistry.*;
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30 import jalview.jbgui.*;
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31 import jalview.util.*;
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33 public class DasSourceBrowser
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34 extends GDasSourceBrowser implements Runnable, ListSelectionListener
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36 static DasSource[] dasSources = null;
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38 Hashtable localSources = null;
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40 Vector selectedSources;
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42 public static String DEFAULT_REGISTRY =
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43 "http://www.dasregistry.org/das1/sources/";
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46 * true if thread is running and we are talking to DAS registry service
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48 public boolean loadingDasSources = false;
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49 protected static String getDasRegistryURL()
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51 String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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54 if (registry.indexOf("/registry/das1/sources/") > -1)
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56 jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);
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57 registry = DEFAULT_REGISTRY;
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61 public DasSourceBrowser()
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63 String registry = getDasRegistryURL();
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65 registryURL.setText(registry);
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67 setSelectedFromProperties();
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69 displayFullDetails(null);
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70 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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72 filter1.addListSelectionListener(this);
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73 filter2.addListSelectionListener(this);
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74 filter3.addListSelectionListener(this);
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76 //Ask to be notified of selection changes.
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77 ListSelectionModel rowSM = table.getSelectionModel();
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78 rowSM.addListSelectionListener(new ListSelectionListener()
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80 public void valueChanged(ListSelectionEvent e)
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82 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
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83 if (!lsm.isSelectionEmpty())
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85 int selectedRow = lsm.getMinSelectionIndex();
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86 displayFullDetails(table.getValueAt(selectedRow, 0).toString());
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91 table.addMouseListener(new MouseAdapter()
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93 public void mouseClicked(MouseEvent evt)
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95 if (evt.getClickCount() == 2
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96 || SwingUtilities.isRightMouseButton(evt))
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98 editRemoveLocalSource(evt);
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103 if (dasSources != null)
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109 public void paintComponent(java.awt.Graphics g)
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111 if (dasSources == null && !loadingDasSources)
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113 Thread worker = new Thread(this);
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120 int dSize = dasSources.length;
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121 Object[][] data = new Object[dSize][2];
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122 for (int i = 0; i < dSize; i++)
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124 data[i][0] = dasSources[i].getNickname();
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125 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
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129 refreshTableData(data);
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130 setCapabilities(dasSources);
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132 javax.swing.SwingUtilities.invokeLater(new Runnable()
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136 TableSorter sorter = (TableSorter) table.getModel();
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137 sorter.setSortingStatus(1, TableSorter.DESCENDING);
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138 sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
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142 progressBar.setIndeterminate(false);
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143 progressBar.setVisible(false);
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144 addLocal.setVisible(true);
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145 refresh.setVisible(true);
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148 public void refreshTableData(Object[][] data)
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150 TableSorter sorter = new TableSorter(new DASTableModel(data));
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151 sorter.setTableHeader(table.getTableHeader());
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152 table.setModel(sorter);
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155 void displayFullDetails(String nickName)
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158 StringBuffer text = new StringBuffer(
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159 "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
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161 if (nickName == null)
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163 fullDetails.setText(text +
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164 "Select a DAS service from the table"
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165 + " to read a full description here.</font></html>");
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169 int dSize = dasSources.length;
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170 for (int i = 0; i < dSize; i++)
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172 if (!dasSources[i].getNickname().equals(nickName))
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177 DasSource ds = dasSources[i];
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179 text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
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181 text.append("<font color=\"#0000FF\">Nickname:</font> " +
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182 dasSources[i].getNickname() + "<br>");
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183 text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
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187 "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
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188 + dasSources[i].getAdminemail()
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189 + "\">" + dasSources[i].getAdminemail() + "</a>" +
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192 text.append("<font color=\"#0000FF\">Registered at:</font> " +
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193 dasSources[i].getRegisterDate() +
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196 text.append("<font color=\"#0000FF\">Last successful test:</font> " +
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197 dasSources[i].getLeaseDate() +
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200 text.append("<font color=\"#0000FF\">Labels:</font> ");
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201 for (int s = 0; s < dasSources[i].getLabels().length; s++)
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203 text.append(dasSources[i].getLabels()[s]);
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204 if (s < dasSources[i].getLabels().length - 1)
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210 text.append("<br>");
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212 text.append("<font color=\"#0000FF\">Capabilities:</font> ");
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213 String[] scap = dasSources[i].getCapabilities();
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214 for (int j = 0; j < scap.length; j++)
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216 text.append(scap[j]);
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217 if (j < scap.length - 1)
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222 text.append("<br>");
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224 text.append("<font color=\"#0000FF\">Coordinates:</font> ");
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225 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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226 for (int j = 0; j < dcs.length; j++)
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228 text.append("(" + dcs[j].getUniqueId() + ") "
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229 + dcs[j].getCategory() + ", " + dcs[j].getName());
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230 if (dcs[j].getNCBITaxId() != 0)
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232 text.append(", " + dcs[j].getNCBITaxId());
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234 if (dcs[j].getOrganismName().length() > 0)
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236 text.append(", " + dcs[j].getOrganismName());
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239 text.append("<br>");
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242 text.append("<font color=\"#0000FF\">Description:</font> " +
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243 dasSources[i].getDescription() + "<br>");
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245 if (dasSources[i].getHelperurl() != null
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246 && dasSources[i].getHelperurl().length() > 0)
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248 text.append("<font color=\"#0000FF\"><a href=\"" +
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249 dasSources[i].getHelperurl()
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250 + "\">Go to site</a></font<br>");
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253 text.append("</font></html>");
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258 fullDetails.setText(text.toString());
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259 javax.swing.SwingUtilities.invokeLater(new Runnable()
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263 fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
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270 loadingDasSources = true;
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272 addLocal.setVisible(false);
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273 refresh.setVisible(false);
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274 progressBar.setVisible(true);
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275 progressBar.setIndeterminate(true);
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276 // Refresh the source list.
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282 loadingDasSources = false;
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286 public Vector getSelectedSources()
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288 Vector selected = new Vector();
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289 for (int r = 0; r < selectedSources.size(); r++)
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291 for (int i = 0; i < dasSources.length; i++)
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293 if (dasSources[i].getNickname().equals(
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294 selectedSources.elementAt(r)))
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296 selected.addElement(dasSources[i]);
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305 * retrieve das sources from registry and add local source list
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308 public DasSource[] getDASSource()
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310 if (dasSources == null)
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312 dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
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313 appendLocalSources();
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319 public void refresh_actionPerformed(ActionEvent e)
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321 saveProperties(jalview.bin.Cache.applicationProperties);
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323 Thread worker = new Thread(this);
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327 private void setCapabilities(DasSource[] sources)
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329 Vector authority = new Vector();
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330 Vector type = new Vector();
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331 Vector label = new Vector();
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333 authority.addElement("Any");
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334 type.addElement("Any");
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335 label.addElement("Any");
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337 for (int i = 0; i < sources.length; i++)
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339 DasSource ds = sources[i];
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341 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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343 for (int j = 0; j < dcs.length; j++)
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345 if (!type.contains(dcs[j].getCategory()))
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347 type.addElement(dcs[j].getCategory());
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350 if (!authority.contains(dcs[j].getName()))
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352 authority.addElement(dcs[j].getName());
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356 String[] slabels = ds.getLabels();
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357 for (int s = 0; s < slabels.length; s++)
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359 if (!label.contains(slabels[s]))
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361 label.addElement(slabels[s]);
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367 filter1.setListData(authority);
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368 filter2.setListData(type);
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369 filter3.setListData(label);
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371 javax.swing.SwingUtilities.invokeLater(new Runnable()
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375 filter1.setSelectedIndex(0);
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376 filter2.setSelectedIndex(0);
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377 filter3.setSelectedIndex(0);
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382 public void amendLocal(boolean newSource)
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384 String url = "http://localhost:8080/", nickname = "";
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388 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
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389 nickname = table.getValueAt(selectedRow, 0).toString();
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390 url = ( (DasSource) localSources.get(nickname)).getUrl();
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393 JTextField nametf = new JTextField(nickname, 40);
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394 JTextField urltf = new JTextField(url, 40);
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396 JPanel panel = new JPanel(new BorderLayout());
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397 JPanel pane12 = new JPanel(new BorderLayout());
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398 pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
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399 pane12.add(nametf, BorderLayout.EAST);
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400 panel.add(pane12, BorderLayout.NORTH);
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401 pane12 = new JPanel(new BorderLayout());
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402 pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
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403 pane12.add(urltf, BorderLayout.EAST);
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404 panel.add(pane12, BorderLayout.SOUTH);
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406 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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407 panel, "Enter Nickname & URL of Local DAS Source",
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408 JOptionPane.OK_CANCEL_OPTION);
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410 if (reply != JOptionPane.OK_OPTION)
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415 if (!urltf.getText().endsWith("/"))
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417 urltf.setText(urltf.getText() + "/");
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420 Das1Source local = new Das1Source();
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422 local.setUrl(urltf.getText());
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423 local.setNickname(nametf.getText());
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425 if (localSources == null)
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427 localSources = new Hashtable();
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430 localSources.put(local.getNickname(), local);
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432 if (!newSource && !nickname.equals(nametf.getText()))
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434 localSources.remove(nickname);
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437 int size = dasSources.length;
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438 int adjust = newSource ? 1 : 0;
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440 Object[][] data = new Object[size + adjust][2];
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441 for (int i = 0; i < size; i++)
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443 if (!newSource && dasSources[i].getNickname().equals(nickname))
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445 ( (DasSource) dasSources[i]).setNickname(local.getNickname());
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446 ( (DasSource) dasSources[i]).setUrl(local.getUrl());
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447 data[i][0] = local.getNickname();
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448 data[i][1] = new Boolean(true);
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452 data[i][0] = dasSources[i].getNickname();
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453 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
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460 data[size][0] = local.getNickname();
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461 data[size][1] = new Boolean(true);
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462 selectedSources.add(local.getNickname());
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465 DasSource[] tmp = new DasSource[size + adjust];
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467 System.arraycopy(dasSources, 0, tmp, 0, size);
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476 refreshTableData(data);
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478 SwingUtilities.invokeLater(new Runnable()
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482 scrollPane.getVerticalScrollBar().setValue(
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483 scrollPane.getVerticalScrollBar().getMaximum()
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488 displayFullDetails(local.getNickname());
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491 public void editRemoveLocalSource(MouseEvent evt)
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493 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
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494 if (selectedRow == -1)
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499 String nickname = table.getValueAt(selectedRow, 0).toString();
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501 if (!localSources.containsKey(nickname))
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503 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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504 "You can only edit or remove local DAS Sources!",
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505 "Public DAS source - not editable",
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506 JOptionPane.WARNING_MESSAGE);
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512 "Edit", "Remove", "Cancel"};
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513 int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
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514 "Do you want to edit or remove " + nickname + "?",
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515 "Edit / Remove Local DAS Source",
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516 JOptionPane.YES_NO_CANCEL_OPTION,
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517 JOptionPane.QUESTION_MESSAGE,
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528 localSources.remove(nickname);
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529 selectedSources.remove(nickname);
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530 Object[][] data = new Object[dasSources.length - 1][2];
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531 DasSource[] tmp = new DasSource[dasSources.length - 1];
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533 for (int i = 0; i < dasSources.length; i++)
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535 if (dasSources[i].getNickname().equals(nickname))
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541 tmp[index] = dasSources[i];
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542 data[index][0] = dasSources[i].getNickname();
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543 data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
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549 refreshTableData(data);
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550 SwingUtilities.invokeLater(new Runnable()
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554 scrollPane.getVerticalScrollBar().setValue(
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555 scrollPane.getVerticalScrollBar().getMaximum()
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564 void appendLocalSources()
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566 if (localSources == null)
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571 int size = dasSources != null ? dasSources.length : 0;
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572 int lsize = localSources.size();
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574 Object[][] data = new Object[size + lsize][2];
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575 for (int i = 0; i < size; i++)
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577 data[i][0] = dasSources[i].getNickname();
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578 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
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582 DasSource[] tmp = new DasSource[size + lsize];
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583 if (dasSources != null)
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585 System.arraycopy(dasSources, 0, tmp, 0, size);
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588 Enumeration en = localSources.keys();
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590 while (en.hasMoreElements())
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592 String key = en.nextElement().toString();
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593 data[index][0] = key;
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594 data[index][1] = new Boolean(false);
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595 tmp[index] = new Das1Source();
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596 tmp[index].setNickname(key);
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597 tmp[index].setUrl( ( (DasSource) localSources.get(key)).getUrl());
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604 refreshTableData(data);
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607 public void valueChanged(ListSelectionEvent evt)
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609 //Called when the MainTable selection changes
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610 if (evt.getValueIsAdjusting())
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615 displayFullDetails(null);
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617 // Filter the displayed data sources
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618 int dSize = dasSources.length;
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620 ArrayList names = new ArrayList();
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621 ArrayList selected = new ArrayList();
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624 //The features filter is not visible, but we must still
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625 //filter the das source list here.
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626 //July 2006 - only 6 sources fo not serve features
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627 Object[] dummyFeatureList = new Object[]
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631 for (int i = 0; i < dSize; i++)
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633 ds = dasSources[i];
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634 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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636 if (dcs.length == 0 && ds.getCapabilities().length == 0
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637 && filter1.getSelectedIndex() == 0
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638 && filter2.getSelectedIndex() == 0
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639 && filter3.getSelectedIndex() == 0)
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641 //THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
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642 //HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
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643 //IS ADDED FROM THE REGISTRY
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644 names.add(ds.getNickname());
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645 selected.add(new Boolean(
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646 selectedSources.contains(ds.getNickname())));
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650 if (!selectedInList(dummyFeatureList, ds.getCapabilities())
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651 || !selectedInList(filter3.getSelectedValues(),
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657 for (int j = 0; j < dcs.length; j++)
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659 if (selectedInList(filter1.getSelectedValues(),
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661 {dcs[j].getName()})
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662 && selectedInList(filter2.getSelectedValues(),
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664 {dcs[j].getCategory()}))
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666 names.add(ds.getNickname());
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667 selected.add(new Boolean(
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668 selectedSources.contains(ds.getNickname())));
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674 dSize = names.size();
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675 Object[][] data = new Object[dSize][2];
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676 for (int d = 0; d < dSize; d++)
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678 data[d][0] = names.get(d);
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679 data[d][1] = selected.get(d);
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682 refreshTableData(data);
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685 boolean selectedInList(Object[] selection, String[] items)
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687 for (int i = 0; i < selection.length; i++)
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689 if (selection[i].equals("Any"))
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694 for (int j = 0; j < items.length; j++)
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696 if (selection[i].equals(items[j]))
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706 void setSelectedFromProperties()
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708 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
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709 StringTokenizer st = new StringTokenizer(active, "\t");
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710 selectedSources = new Vector();
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711 while (st.hasMoreTokens())
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713 selectedSources.addElement(st.nextToken());
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716 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
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719 if (localSources == null)
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721 localSources = new Hashtable();
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724 st = new StringTokenizer(local, "\t");
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725 while (st.hasMoreTokens())
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727 String token = st.nextToken();
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728 int bar = token.indexOf("|");
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729 Das1Source source = new Das1Source();
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731 source.setUrl(token.substring(bar + 1));
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732 source.setNickname(token.substring(0, bar));
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734 localSources.put(source.getNickname(), source);
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739 public void reset_actionPerformed(ActionEvent e)
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741 registryURL.setText(DEFAULT_REGISTRY);
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744 public void saveProperties(Properties properties)
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746 if (registryURL.getText() == null || registryURL.getText().length() < 1)
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748 properties.remove("DAS_REGISTRY_URL");
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752 properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
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755 StringBuffer sb = new StringBuffer();
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756 for (int r = 0; r < table.getModel().getRowCount(); r++)
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758 if ( ( (Boolean) table.getValueAt(r, 1)).booleanValue())
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760 sb.append(table.getValueAt(r, 0) + "\t");
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764 properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString());
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766 if (localSources != null)
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768 sb = new StringBuffer();
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769 Enumeration en = localSources.keys();
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770 while (en.hasMoreElements())
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772 String token = en.nextElement().toString();
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773 sb.append(token + "|"
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774 + ( (DasSource) localSources.get(token)).getUrl()
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778 properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
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783 class DASTableModel
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784 extends AbstractTableModel
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787 public DASTableModel(Object[][] data)
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792 private String[] columnNames = new String[]
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794 "Nickname", "Use Source"};
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796 private Object[][] data;
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798 public int getColumnCount()
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800 return columnNames.length;
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803 public int getRowCount()
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805 return data.length;
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808 public String getColumnName(int col)
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810 return columnNames[col];
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813 public Object getValueAt(int row, int col)
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815 return data[row][col];
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819 * JTable uses this method to determine the default renderer/
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820 * editor for each cell. If we didn't implement this method,
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821 * then the last column would contain text ("true"/"false"),
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822 * rather than a check box.
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824 public Class getColumnClass(int c)
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826 return getValueAt(0, c).getClass();
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830 * Don't need to implement this method unless your table's
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833 public boolean isCellEditable(int row, int col)
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835 //Note that the data/cell address is constant,
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836 //no matter where the cell appears onscreen.
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842 * Don't need to implement this method unless your table's
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845 public void setValueAt(Object value, int row, int col)
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847 data[row][col] = value;
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848 fireTableCellUpdated(row, col);
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850 String name = getValueAt(row, 0).toString();
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851 boolean selected = ( (Boolean) value).booleanValue();
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853 if (selectedSources.contains(name) && !selected)
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855 selectedSources.remove(name);
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858 if (!selectedSources.contains(name) && selected)
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860 selectedSources.add(name);
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