2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.gui;
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23 import java.awt.event.*;
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24 import javax.swing.*;
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25 import javax.swing.event.*;
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26 import javax.swing.table.*;
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28 import org.biojava.dasobert.dasregistry.*;
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29 import jalview.jbgui.*;
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30 import jalview.util.*;
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32 public class DasSourceBrowser extends GDasSourceBrowser implements
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33 Runnable, ListSelectionListener
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35 static DasSource[] dasSources = null;
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37 Hashtable localSources = null;
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39 Vector selectedSources;
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41 public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
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44 * true if thread is running and we are talking to DAS registry service
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46 public boolean loadingDasSources = false;
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48 protected static String getDasRegistryURL()
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50 String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
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53 if (registry.indexOf("/registry/das1/sources/") > -1)
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55 jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
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57 registry = DEFAULT_REGISTRY;
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62 public DasSourceBrowser()
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64 String registry = getDasRegistryURL();
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66 registryURL.setText(registry);
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68 setSelectedFromProperties();
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70 displayFullDetails(null);
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71 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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73 filter1.addListSelectionListener(this);
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74 filter2.addListSelectionListener(this);
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75 filter3.addListSelectionListener(this);
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77 // Ask to be notified of selection changes.
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78 ListSelectionModel rowSM = table.getSelectionModel();
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79 rowSM.addListSelectionListener(new ListSelectionListener()
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81 public void valueChanged(ListSelectionEvent e)
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83 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
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84 if (!lsm.isSelectionEmpty())
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86 int selectedRow = lsm.getMinSelectionIndex();
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87 displayFullDetails(table.getValueAt(selectedRow, 0).toString());
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92 table.addMouseListener(new MouseAdapter()
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94 public void mouseClicked(MouseEvent evt)
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96 if (evt.getClickCount() == 2
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97 || SwingUtilities.isRightMouseButton(evt))
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99 editRemoveLocalSource(evt);
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104 if (dasSources != null)
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110 public void paintComponent(java.awt.Graphics g)
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112 if (dasSources == null && !loadingDasSources)
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114 Thread worker = new Thread(this);
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121 int dSize = dasSources.length;
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122 Object[][] data = new Object[dSize][2];
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123 for (int i = 0; i < dSize; i++)
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125 data[i][0] = dasSources[i].getNickname();
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126 data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
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130 refreshTableData(data);
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131 setCapabilities(dasSources);
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133 javax.swing.SwingUtilities.invokeLater(new Runnable()
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137 TableSorter sorter = (TableSorter) table.getModel();
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138 sorter.setSortingStatus(1, TableSorter.DESCENDING);
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139 sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
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143 progressBar.setIndeterminate(false);
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144 progressBar.setVisible(false);
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145 addLocal.setVisible(true);
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146 refresh.setVisible(true);
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149 public void refreshTableData(Object[][] data)
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151 TableSorter sorter = new TableSorter(new DASTableModel(data));
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152 sorter.setTableHeader(table.getTableHeader());
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153 table.setModel(sorter);
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156 void displayFullDetails(String nickName)
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159 StringBuffer text = new StringBuffer(
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160 "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
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162 if (nickName == null)
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164 fullDetails.setText(text + "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> "
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180 + dasSources[i].getId() + "<br>");
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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> "
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184 + dasSources[i].getUrl() + "<br>");
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187 .append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
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188 + dasSources[i].getAdminemail()
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190 + dasSources[i].getAdminemail() + "</a>" + "<br>");
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192 text.append("<font color=\"#0000FF\">Registered at:</font> "
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193 + dasSources[i].getRegisterDate() + "<br>");
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195 text.append("<font color=\"#0000FF\">Last successful test:</font> "
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196 + dasSources[i].getLeaseDate() + "<br>");
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198 text.append("<font color=\"#0000FF\">Labels:</font> ");
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199 for (int s = 0; s < dasSources[i].getLabels().length; s++)
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201 text.append(dasSources[i].getLabels()[s]);
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202 if (s < dasSources[i].getLabels().length - 1)
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208 text.append("<br>");
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210 text.append("<font color=\"#0000FF\">Capabilities:</font> ");
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211 String[] scap = dasSources[i].getCapabilities();
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212 for (int j = 0; j < scap.length; j++)
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214 text.append(scap[j]);
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215 if (j < scap.length - 1)
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220 text.append("<br>");
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222 text.append("<font color=\"#0000FF\">Coordinates:</font> ");
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223 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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224 for (int j = 0; j < dcs.length; j++)
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226 text.append("(" + dcs[j].getUniqueId() + ") "
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227 + dcs[j].getCategory() + ", " + dcs[j].getName());
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228 if (dcs[j].getNCBITaxId() != 0)
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230 text.append(", " + dcs[j].getNCBITaxId());
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232 if (dcs[j].getOrganismName().length() > 0)
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234 text.append(", " + dcs[j].getOrganismName());
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237 text.append("<br>");
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240 text.append("<font color=\"#0000FF\">Description:</font> "
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241 + dasSources[i].getDescription() + "<br>");
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243 if (dasSources[i].getHelperurl() != null
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244 && dasSources[i].getHelperurl().length() > 0)
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246 text.append("<font color=\"#0000FF\"><a href=\""
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247 + dasSources[i].getHelperurl()
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248 + "\">Go to site</a></font<br>");
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251 text.append("</font></html>");
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256 fullDetails.setText(text.toString());
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257 javax.swing.SwingUtilities.invokeLater(new Runnable()
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261 fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
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268 loadingDasSources = true;
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270 addLocal.setVisible(false);
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271 refresh.setVisible(false);
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272 progressBar.setVisible(true);
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273 progressBar.setIndeterminate(true);
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274 // Refresh the source list.
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280 loadingDasSources = false;
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284 public Vector getSelectedSources()
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286 // wait around if we're still loading.
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287 while (dasSources == null)
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289 if (!loadingDasSources)
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291 new Thread(this).start();
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295 } catch (Exception e)
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299 while (loadingDasSources)
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304 } catch (Exception e)
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313 Vector selected = new Vector();
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314 for (int r = 0; r < selectedSources.size(); r++)
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316 for (int i = 0; i < dasSources.length; i++)
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318 if (dasSources[i].getNickname()
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319 .equals(selectedSources.elementAt(r)))
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321 selected.addElement(dasSources[i]);
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331 * retrieve das sources from registry and add local source list
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335 public DasSource[] getDASSource()
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337 if (dasSources == null)
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339 dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
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340 appendLocalSources();
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346 public void refresh_actionPerformed(ActionEvent e)
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348 saveProperties(jalview.bin.Cache.applicationProperties);
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350 Thread worker = new Thread(this);
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354 private void setCapabilities(DasSource[] sources)
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356 Vector authority = new Vector();
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357 Vector type = new Vector();
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358 Vector label = new Vector();
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360 authority.addElement("Any");
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361 type.addElement("Any");
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362 label.addElement("Any");
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364 for (int i = 0; i < sources.length; i++)
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366 DasSource ds = sources[i];
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368 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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370 for (int j = 0; j < dcs.length; j++)
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372 if (!type.contains(dcs[j].getCategory()))
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374 type.addElement(dcs[j].getCategory());
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377 if (!authority.contains(dcs[j].getName()))
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379 authority.addElement(dcs[j].getName());
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383 String[] slabels = ds.getLabels();
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384 for (int s = 0; s < slabels.length; s++)
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386 if (!label.contains(slabels[s]))
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388 label.addElement(slabels[s]);
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394 filter1.setListData(authority);
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395 filter2.setListData(type);
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396 filter3.setListData(label);
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398 javax.swing.SwingUtilities.invokeLater(new Runnable()
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402 filter1.setSelectedIndex(0);
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403 filter2.setSelectedIndex(0);
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404 filter3.setSelectedIndex(0);
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409 public void amendLocal(boolean newSource)
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411 String url = "http://localhost:8080/", nickname = "";
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412 boolean seqsrc = false;
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415 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
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416 nickname = table.getValueAt(selectedRow, 0).toString();
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417 url = ((DasSource) localSources.get(nickname)).getUrl();
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418 seqsrc = ((DasSource) localSources.get(nickname))
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419 .hasCapability("sequence");
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422 JTextField nametf = new JTextField(nickname, 40);
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423 JTextField urltf = new JTextField(url, 40);
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424 JCheckBox seqs = new JCheckBox("Sequence Source");
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425 seqs.setSelected(seqsrc);
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426 JPanel panel = new JPanel(new BorderLayout());
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427 JPanel pane12 = new JPanel(new BorderLayout());
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428 pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
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429 pane12.add(nametf, BorderLayout.EAST);
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430 panel.add(pane12, BorderLayout.NORTH);
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431 pane12 = new JPanel(new BorderLayout());
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432 pane12.add(new JLabel("URL: "), BorderLayout.NORTH);
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433 pane12.add(seqs, BorderLayout.SOUTH);
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434 pane12.add(urltf, BorderLayout.EAST);
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435 panel.add(pane12, BorderLayout.SOUTH);
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437 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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438 panel, "Enter Nickname & URL of Local DAS Source",
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439 JOptionPane.OK_CANCEL_OPTION);
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441 if (reply != JOptionPane.OK_OPTION)
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446 if (!urltf.getText().endsWith("/"))
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448 urltf.setText(urltf.getText() + "/");
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451 Das1Source local = new Das1Source();
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453 local.setUrl(urltf.getText());
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454 local.setNickname(nametf.getText());
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455 if (seqs.isSelected())
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457 local.setCapabilities(new String[]
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458 { "features", "sequence" });
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460 if (localSources == null)
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462 localSources = new Hashtable();
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465 localSources.put(local.getNickname(), local);
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467 if (!newSource && !nickname.equals(nametf.getText()))
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469 localSources.remove(nickname);
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472 int size = dasSources.length;
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473 int adjust = newSource ? 1 : 0;
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475 Object[][] data = new Object[size + adjust][2];
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476 for (int i = 0; i < size; i++)
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478 if (!newSource && dasSources[i].getNickname().equals(nickname))
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480 ((DasSource) dasSources[i]).setNickname(local.getNickname());
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481 ((DasSource) dasSources[i]).setUrl(local.getUrl());
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482 data[i][0] = local.getNickname();
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483 data[i][1] = new Boolean(true);
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487 data[i][0] = dasSources[i].getNickname();
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488 data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
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495 data[size][0] = local.getNickname();
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496 data[size][1] = new Boolean(true);
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497 selectedSources.add(local.getNickname());
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500 DasSource[] tmp = new DasSource[size + adjust];
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502 System.arraycopy(dasSources, 0, tmp, 0, size);
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511 refreshTableData(data);
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513 SwingUtilities.invokeLater(new Runnable()
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517 scrollPane.getVerticalScrollBar().setValue(
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518 scrollPane.getVerticalScrollBar().getMaximum());
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522 displayFullDetails(local.getNickname());
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525 public void editRemoveLocalSource(MouseEvent evt)
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527 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
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528 if (selectedRow == -1)
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533 String nickname = table.getValueAt(selectedRow, 0).toString();
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535 if (!localSources.containsKey(nickname))
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537 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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538 "You can only edit or remove local DAS Sources!",
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539 "Public DAS source - not editable",
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540 JOptionPane.WARNING_MESSAGE);
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545 { "Edit", "Remove", "Cancel" };
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546 int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
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547 "Do you want to edit or remove " + nickname + "?",
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548 "Edit / Remove Local DAS Source",
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549 JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
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550 null, options, options[2]);
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558 localSources.remove(nickname);
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559 selectedSources.remove(nickname);
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560 Object[][] data = new Object[dasSources.length - 1][2];
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561 DasSource[] tmp = new DasSource[dasSources.length - 1];
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563 for (int i = 0; i < dasSources.length; i++)
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565 if (dasSources[i].getNickname().equals(nickname))
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571 tmp[index] = dasSources[i];
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572 data[index][0] = dasSources[i].getNickname();
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573 data[index][1] = new Boolean(selectedSources
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574 .contains(dasSources[i].getNickname()));
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579 refreshTableData(data);
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580 SwingUtilities.invokeLater(new Runnable()
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584 scrollPane.getVerticalScrollBar().setValue(
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585 scrollPane.getVerticalScrollBar().getMaximum());
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593 void appendLocalSources()
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595 if (localSources == null)
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599 // note - we add all das sources to list so they can be filtered for the
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600 // standard fetchDbRefs function
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601 int size = dasSources != null ? dasSources.length : 0;
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602 int lsize = localSources.size();
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604 Object[][] data = new Object[size + lsize][2];
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605 for (int i = 0; i < size; i++)
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607 data[i][0] = dasSources[i].getNickname();
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608 data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
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612 DasSource[] tmp = new DasSource[size + lsize];
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613 if (dasSources != null)
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615 System.arraycopy(dasSources, 0, tmp, 0, size);
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618 Enumeration en = localSources.keys();
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620 while (en.hasMoreElements())
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622 String key = en.nextElement().toString();
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623 data[index][0] = key;
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624 data[index][1] = new Boolean(false);
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625 tmp[index] = new Das1Source();
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626 tmp[index].setNickname(key);
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627 tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl());
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634 refreshTableData(data);
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637 public void valueChanged(ListSelectionEvent evt)
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639 // Called when the MainTable selection changes
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640 if (evt.getValueIsAdjusting())
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645 displayFullDetails(null);
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647 // Filter the displayed data sources
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648 int dSize = dasSources.length;
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650 ArrayList names = new ArrayList();
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651 ArrayList selected = new ArrayList();
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654 // The features filter is not visible, but we must still
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655 // filter the das source list here.
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656 // July 2006 - only 6 sources fo not serve features
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657 Object[] dummyFeatureList = new Object[]
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660 for (int i = 0; i < dSize; i++)
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662 ds = dasSources[i];
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663 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
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665 if (dcs.length == 0 && ds.getCapabilities().length == 0
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666 && filter1.getSelectedIndex() == 0
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667 && filter2.getSelectedIndex() == 0
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668 && filter3.getSelectedIndex() == 0)
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670 // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
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671 // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
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672 // IS ADDED FROM THE REGISTRY
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673 names.add(ds.getNickname());
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675 .add(new Boolean(selectedSources.contains(ds.getNickname())));
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679 if (!selectedInList(dummyFeatureList, ds.getCapabilities())
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680 || !selectedInList(filter3.getSelectedValues(), ds
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686 for (int j = 0; j < dcs.length; j++)
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688 if (selectedInList(filter1.getSelectedValues(), new String[]
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689 { dcs[j].getName() })
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690 && selectedInList(filter2.getSelectedValues(), new String[]
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691 { dcs[j].getCategory() }))
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693 names.add(ds.getNickname());
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694 selected.add(new Boolean(selectedSources.contains(ds
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701 dSize = names.size();
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702 Object[][] data = new Object[dSize][2];
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703 for (int d = 0; d < dSize; d++)
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705 data[d][0] = names.get(d);
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706 data[d][1] = selected.get(d);
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709 refreshTableData(data);
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712 boolean selectedInList(Object[] selection, String[] items)
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714 for (int i = 0; i < selection.length; i++)
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716 if (selection[i].equals("Any"))
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721 for (int j = 0; j < items.length; j++)
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723 if (selection[i].equals(items[j]))
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733 void setSelectedFromProperties()
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735 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
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737 StringTokenizer st = new StringTokenizer(active, "\t");
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738 selectedSources = new Vector();
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739 while (st.hasMoreTokens())
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741 selectedSources.addElement(st.nextToken());
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744 Vector _localSources = jalview.bin.Cache.getLocalDasSources();
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745 if (_localSources != null)
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747 if (localSources == null)
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749 localSources = new Hashtable();
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751 Enumeration sources = _localSources.elements();
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752 while (sources.hasMoreElements())
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754 Das1Source source = (Das1Source) sources.nextElement();
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755 localSources.put(source.getNickname(), source);
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760 public void reset_actionPerformed(ActionEvent e)
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762 registryURL.setText(DEFAULT_REGISTRY);
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766 * set the DAS source settings in the given jalview properties.
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768 * @param properties
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770 public void saveProperties(Properties properties)
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772 if (registryURL.getText() == null || registryURL.getText().length() < 1)
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774 properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);
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778 properties.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
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779 registryURL.getText());
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782 StringBuffer sb = new StringBuffer();
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783 for (int r = 0; r < table.getModel().getRowCount(); r++)
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785 if (((Boolean) table.getValueAt(r, 1)).booleanValue())
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787 sb.append(table.getValueAt(r, 0) + "\t");
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791 properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE, sb
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794 if (localSources != null)
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796 sb = new StringBuffer();
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797 Enumeration en = localSources.keys();
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798 while (en.hasMoreElements())
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800 String token = en.nextElement().toString();
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803 + (((DasSource) localSources.get(token))
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804 .hasCapability("sequence") ? "sequence:" : "")
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805 + ((DasSource) localSources.get(token)).getUrl() + "\t");
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808 properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE, sb
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814 class DASTableModel extends AbstractTableModel
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817 public DASTableModel(Object[][] data)
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822 private String[] columnNames = new String[]
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823 { "Nickname", "Use Source" };
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825 private Object[][] data;
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827 public int getColumnCount()
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829 return columnNames.length;
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832 public int getRowCount()
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834 return data.length;
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837 public String getColumnName(int col)
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839 return columnNames[col];
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842 public Object getValueAt(int row, int col)
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844 return data[row][col];
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848 * JTable uses this method to determine the default renderer/ editor for
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849 * each cell. If we didn't implement this method, then the last column would
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850 * contain text ("true"/"false"), rather than a check box.
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852 public Class getColumnClass(int c)
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854 return getValueAt(0, c).getClass();
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858 * Don't need to implement this method unless your table's editable.
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860 public boolean isCellEditable(int row, int col)
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862 // Note that the data/cell address is constant,
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863 // no matter where the cell appears onscreen.
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869 * Don't need to implement this method unless your table's data can change.
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871 public void setValueAt(Object value, int row, int col)
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873 data[row][col] = value;
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874 fireTableCellUpdated(row, col);
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876 String name = getValueAt(row, 0).toString();
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877 boolean selected = ((Boolean) value).booleanValue();
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879 if (selectedSources.contains(name) && !selected)
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881 selectedSources.remove(name);
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884 if (!selectedSources.contains(name) && selected)
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886 selectedSources.add(name);
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891 public void initDasSources()
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894 Thread thr = new Thread(new Runnable()
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898 // this actually initialises the das source list
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899 paintComponent(null); // yuk
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903 while (loadingDasSources || dasSources == null)
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908 } catch (Exception e)
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915 public Vector resolveSourceNicknames(Vector sources)
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918 Vector resolved = new Vector();
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919 if (sources != null)
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921 for (int i = 0; i < dasSources.length; i++)
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923 if (sources.contains(dasSources[i].getNickname()))
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925 if (!resolved.contains(dasSources[i]))
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927 resolved.addElement(dasSources[i]);
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