2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.jbgui.GDasSourceBrowser;
25 import jalview.util.MessageManager;
26 import jalview.util.TableSorter;
27 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
28 import jalview.ws.dbsources.das.api.jalviewSourceI;
30 import java.awt.BorderLayout;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.MouseAdapter;
33 import java.awt.event.MouseEvent;
34 import java.util.ArrayList;
35 import java.util.List;
36 import java.util.Properties;
37 import java.util.StringTokenizer;
38 import java.util.Vector;
40 import javax.swing.JCheckBox;
41 import javax.swing.JLabel;
42 import javax.swing.JOptionPane;
43 import javax.swing.JPanel;
44 import javax.swing.JTextField;
45 import javax.swing.ListSelectionModel;
46 import javax.swing.SwingUtilities;
47 import javax.swing.event.ListSelectionEvent;
48 import javax.swing.event.ListSelectionListener;
49 import javax.swing.table.AbstractTableModel;
51 import org.biodas.jdas.schema.sources.CAPABILITY;
52 import org.biodas.jdas.schema.sources.COORDINATES;
53 import org.biodas.jdas.schema.sources.PROP;
54 import org.biodas.jdas.schema.sources.VERSION;
56 public class DasSourceBrowser extends GDasSourceBrowser implements
57 Runnable, ListSelectionListener
59 DasSourceRegistryI sourceRegistry = null;
61 Vector<String> selectedSources;
63 public DasSourceBrowser(FeatureSettings featureSettings)
66 // TODO DasSourceRegistryProvider API
67 sourceRegistry = Cache.getDasSourceRegistry();
68 String registry = sourceRegistry.getDasRegistryURL();
70 registryURL.setText(registry);
72 setSelectedFromProperties();
74 displayFullDetails(null);
75 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
77 filter1.addListSelectionListener(this);
78 filter2.addListSelectionListener(this);
79 filter3.addListSelectionListener(this);
81 // Ask to be notified of selection changes.
82 ListSelectionModel rowSM = table.getSelectionModel();
83 rowSM.addListSelectionListener(new ListSelectionListener()
85 public void valueChanged(ListSelectionEvent e)
87 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
88 if (!lsm.isSelectionEmpty())
90 int selectedRow = lsm.getMinSelectionIndex();
91 displayFullDetails(table.getValueAt(selectedRow, 0).toString());
96 table.addMouseListener(new MouseAdapter()
98 public void mouseClicked(MouseEvent evt)
100 if (evt.getClickCount() == 2
101 || SwingUtilities.isRightMouseButton(evt))
103 editRemoveLocalSource(evt);
108 if (sourceRegistry.getSources() != null)
114 FeatureSettings fs = null;
116 private boolean loadingDasSources;
118 public DasSourceBrowser()
123 public void paintComponent(java.awt.Graphics g)
125 if (sourceRegistry == null)
127 Thread worker = new Thread(this);
134 List<jalviewSourceI> sources = sourceRegistry.getSources();
135 int dSize = sources.size();
136 Object[][] data = new Object[dSize][2];
137 for (int i = 0; i < dSize; i++)
139 data[i][0] = sources.get(i).getTitle(); // what's equivalent of nickname
140 data[i][1] = new Boolean(selectedSources.contains(sources.get(i)
144 refreshTableData(data);
145 setCapabilities(sourceRegistry);
147 javax.swing.SwingUtilities.invokeLater(new Runnable()
151 TableSorter sorter = (TableSorter) table.getModel();
152 sorter.setSortingStatus(1, TableSorter.DESCENDING);
153 sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
157 progressBar.setIndeterminate(false);
158 progressBar.setVisible(false);
159 addLocal.setVisible(true);
160 refresh.setVisible(true);
163 public void refreshTableData(Object[][] data)
165 TableSorter sorter = new TableSorter(new DASTableModel(data));
166 sorter.setTableHeader(table.getTableHeader());
167 table.setModel(sorter);
170 void displayFullDetails(String nickName)
173 StringBuffer text = new StringBuffer(
174 "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
176 if (nickName == null)
178 fullDetails.setText(text
180 .getString("label.select_das_service_from_table"));
184 int dSize = sourceRegistry.getSources().size();
185 for (jalviewSourceI ds : sourceRegistry.getSources())
187 if (!ds.getTitle().equals(nickName))
192 VERSION latest = ds.getVersion();
193 text.append("<font color=\"#0000FF\">Id:</font> " + ds.getUri()
195 text.append("<font color=\"#0000FF\">Nickname:</font> "
196 + ds.getTitle() + "<br>");
198 text.append("<font color=\"#0000FF\">URL:</font> <a href=\""
199 + ds.getSourceURL() + "\">" + ds.getSourceURL() + "</a>"
203 if (ds.getDocHref() != null && ds.getDocHref().length() > 0)
205 text.append("<font color=\"#0000FF\">Site:</font> <a href=\""
206 + ds.getDocHref() + "\">" + ds.getDocHref() + "</a>"
210 text.append("<font color=\"#0000FF\">Description:</font> "
211 + ds.getDescription() + "<br>");
213 text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
214 + ds.getEmail() + "\">" + ds.getEmail() + "</a>" + "<br>");
216 text.append("<font color=\"#0000FF\">Registered at:</font> "
217 + latest.getCreated() + "<br>");
219 // TODO: Identify last successful test date
220 // text.append("<font color=\"#0000FF\">Last successful test:</font> "
221 // + latest.dasSources[i].getLeaseDate() + "<br>");
225 text.append("Source was added manually.<br/>");
227 text.append("<font color=\"#0000FF\">Labels:</font> ");
229 for (PROP labl : latest.getPROP())
231 if (labl.getName().equalsIgnoreCase("LABEL"))
239 text.append(labl.getValue());
246 text.append("<font color=\"#0000FF\">Capabilities:</font> ");
247 CAPABILITY[] scap = latest.getCAPABILITY().toArray(new CAPABILITY[0]);
248 for (int j = 0; j < scap.length; j++)
250 text.append(scap[j].getType());
251 if (j < scap.length - 1)
258 text.append("<font color=\"#0000FF\">Coordinates:</font>");
260 for (COORDINATES dcs : latest.getCOORDINATES())
262 text.append("<br/>" + i++ + ". ");
263 text.append(dcs.getAuthority() + " : " + dcs.getSource());
264 if (dcs.getTaxid() != null && dcs.getTaxid().trim().length() > 0)
266 text.append(" [TaxId:" + dcs.getTaxid() + "]");
268 if (dcs.getVersion() != null
269 && dcs.getVersion().trim().length() > 0)
272 text.append(" {v. " + dcs.getVersion() + "}");
275 text.append(" (<a href=\"" + dcs.getUri() + "\">" + dcs.getUri()
278 text.append("</font></html>");
283 fullDetails.setText(text.toString());
284 javax.swing.SwingUtilities.invokeLater(new Runnable()
288 fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
295 loadingDasSources = true;
297 addLocal.setVisible(false);
298 refresh.setVisible(false);
299 progressBar.setVisible(true);
300 progressBar.setIndeterminate(true);
301 setParentGuiEnabled(false);
302 // Refresh the source list.
303 sourceRegistry.refreshSources();
307 setParentGuiEnabled(true);
308 loadingDasSources = false;
312 private void setParentGuiEnabled(boolean b)
316 fs.fetchDAS.setEnabled(b);
317 fs.saveDAS.setEnabled(b);
321 public Vector<jalviewSourceI> getSelectedSources()
323 // wait around if we're still loading.
324 while (sourceRegistry == null)
326 if (!loadingDasSources)
328 new Thread(this).start();
332 } catch (Exception e)
336 while (loadingDasSources)
341 } catch (Exception e)
350 Vector<jalviewSourceI> selected = new Vector<jalviewSourceI>();
351 for (String source : selectedSources)
353 jalviewSourceI srce = sourceRegistry.getSource(source);
356 selected.addElement(srce);
362 public void refresh_actionPerformed(ActionEvent e)
364 saveProperties(Cache.applicationProperties);
366 Thread worker = new Thread(this);
370 private void setCapabilities(DasSourceRegistryI sourceRegistry2)
372 Vector<String> authority = new Vector<String>();
373 Vector<String> type = new Vector<String>();
374 Vector<String> label = new Vector<String>();
375 Vector<String> taxIds = new Vector<String>();
376 authority.add("Any");
380 for (jalviewSourceI ds : sourceRegistry2.getSources())
382 VERSION latest = ds.getVersion();
384 for (COORDINATES cs : latest.getCOORDINATES())
386 if (!type.contains(cs.getSource()))
388 type.add(cs.getSource()); // source==category
391 if (!authority.contains(cs.getAuthority()))
393 authority.add(cs.getAuthority());
397 for (PROP slabel : latest.getPROP())
399 if (slabel.getName().equalsIgnoreCase("LABEL")
400 && !label.contains(slabel.getValue()))
402 label.add(slabel.getValue());
408 filter1.setListData(authority);
409 filter2.setListData(type);
410 filter3.setListData(label);
413 javax.swing.SwingUtilities.invokeLater(new Runnable()
417 filter1.setSelectedIndex(0);
418 filter2.setSelectedIndex(0);
419 filter3.setSelectedIndex(0);
424 public void amendLocal(boolean newSource)
426 String url = "http://localhost:8080/", nickname = "";
427 boolean seqsrc = false;
430 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
431 nickname = table.getValueAt(selectedRow, 0).toString();
432 jalviewSourceI source = sourceRegistry.getSource(nickname);
433 url = source.getUri();
434 seqsrc = source.isSequenceSource();
437 JTextField nametf = new JTextField(nickname, 40);
438 JTextField urltf = new JTextField(url, 40);
439 JCheckBox seqs = new JCheckBox(
440 MessageManager.getString("label.sequence_source"));
441 seqs.setSelected(seqsrc);
442 JPanel panel = new JPanel(new BorderLayout());
443 JPanel pane12 = new JPanel(new BorderLayout());
444 pane12.add(new JLabel(MessageManager.getString("label.name")),
445 BorderLayout.CENTER);
446 pane12.add(nametf, BorderLayout.EAST);
447 panel.add(pane12, BorderLayout.NORTH);
448 pane12 = new JPanel(new BorderLayout());
449 pane12.add(new JLabel(MessageManager.getString("label.url")),
451 pane12.add(seqs, BorderLayout.SOUTH);
452 pane12.add(urltf, BorderLayout.EAST);
453 panel.add(pane12, BorderLayout.SOUTH);
455 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
457 MessageManager.getString("label.enter_local_das_source"),
458 JOptionPane.OK_CANCEL_OPTION);
460 if (reply != JOptionPane.OK_OPTION)
465 if (!urltf.getText().endsWith("/"))
467 urltf.setText(urltf.getText() + "/");
470 jalviewSourceI local = sourceRegistry.createLocalSource(
471 urltf.getText(), nametf.getText(), seqs.isSelected(), true);
472 List sources = sourceRegistry.getSources();
473 int osize = sources.size();
474 int size = osize + (newSource ? 1 : 0);
476 Object[][] data = new Object[size][2];
477 DASTableModel dtm = (table != null) ? (DASTableModel) ((TableSorter) table
478 .getModel()).getTableModel() : null;
479 for (int i = 0; i < osize; i++)
481 String osrc = (dtm == null || i >= osize) ? null : (String) dtm
483 if (!newSource && osrc != null
484 && dtm.getValueAt(i, 0).equals(nickname))
486 data[i][0] = local.getTitle();
487 data[i][1] = new Boolean(true);
492 data[i][1] = new Boolean(selectedSources.contains(osrc));
495 // Always add a new source at the end
498 data[osize][0] = local.getTitle();
499 data[osize][1] = new Boolean(true);
500 selectedSources.add(local.getTitle());
503 refreshTableData(data);
505 SwingUtilities.invokeLater(new Runnable()
509 scrollPane.getVerticalScrollBar().setValue(
510 scrollPane.getVerticalScrollBar().getMaximum());
514 displayFullDetails(local.getTitle());
517 public void editRemoveLocalSource(MouseEvent evt)
519 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
520 if (selectedRow == -1)
525 String nickname = table.getValueAt(selectedRow, 0).toString();
527 if (!sourceRegistry.getSource(nickname).isLocal())
530 .showInternalMessageDialog(
533 .getString("label.you_can_only_edit_or_remove_local_das_sources"),
534 MessageManager.getString("label.public_das_source"),
535 JOptionPane.WARNING_MESSAGE);
540 { "Edit", "Remove", "Cancel" };
541 int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
542 "Do you want to edit or remove " + nickname + "?",
543 "Edit / Remove Local DAS Source",
544 JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
545 null, options, options[2]);
553 sourceRegistry.removeLocalSource(sourceRegistry.getSource(nickname));
554 selectedSources.remove(nickname);
555 Object[][] data = new Object[sourceRegistry.getSources().size()][2];
557 l = table.getRowCount();
559 for (int i = 0; i < l; i++)
562 if ((nm = (String) table.getValueAt(i, 0)).equals(nickname))
569 data[index][1] = new Boolean(selectedSources.contains(nm));
573 refreshTableData(data);
574 SwingUtilities.invokeLater(new Runnable()
578 scrollPane.getVerticalScrollBar().setValue(
579 scrollPane.getVerticalScrollBar().getMaximum());
587 public void valueChanged(ListSelectionEvent evt)
589 // Called when the MainTable selection changes
590 if (evt.getValueIsAdjusting())
595 displayFullDetails(null);
597 // Filter the displayed data sources
599 ArrayList names = new ArrayList();
600 ArrayList selected = new ArrayList();
602 // The features filter is not visible, but we must still
603 // filter the das source list here.
604 // July 2006 - only 6 sources fo not serve features
605 Object[] dummyFeatureList = new Object[]
607 List<jalviewSourceI> srcs = sourceRegistry.getSources();
608 for (jalviewSourceI ds : srcs)
611 VERSION v = ds.getVersion();
612 List<COORDINATES> coords = v.getCOORDINATES();
614 || ((coords == null || coords.size() == 0)
615 && filter1.getSelectedIndex() == 0
616 && filter2.getSelectedIndex() == 0 && filter3
617 .getSelectedIndex() == 0))
619 // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
620 // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
621 // IS ADDED FROM THE REGISTRY
622 names.add(ds.getTitle());
623 selected.add(new Boolean(selectedSources.contains(ds.getTitle())));
627 if (!selectedInList(dummyFeatureList, ds.getCapabilityList(v))
628 || !selectedInList(filter3.getSelectedValues(),
634 for (int j = 0; j < coords.size(); j++)
636 if (selectedInList(filter1.getSelectedValues(), new String[]
637 { coords.get(j).getAuthority() })
638 && selectedInList(filter2.getSelectedValues(), new String[]
639 { coords.get(j).getSource() }))
641 names.add(ds.getTitle());
642 selected.add(new Boolean(selectedSources.contains(ds.getTitle())));
648 int dSize = names.size();
649 Object[][] data = new Object[dSize][2];
650 for (int d = 0; d < dSize; d++)
652 data[d][0] = names.get(d);
653 data[d][1] = selected.get(d);
656 refreshTableData(data);
659 private boolean selectedInList(Object[] selection, String[] items)
661 for (int i = 0; i < selection.length; i++)
663 if (selection[i].equals("Any"))
667 if (items == null || items.length == 0)
671 String sel = (items[0].startsWith("das1:") ? "das1:" : "")
673 for (int j = 0; j < items.length; j++)
675 if (sel.equals(items[j]))
685 void setSelectedFromProperties()
687 String active = Cache.getDefault("DAS_ACTIVE_SOURCE",
689 StringTokenizer st = new StringTokenizer(active, "\t");
690 selectedSources = new Vector();
691 while (st.hasMoreTokens())
693 selectedSources.addElement(st.nextToken());
697 public void reset_actionPerformed(ActionEvent e)
699 registryURL.setText(sourceRegistry.getDasRegistryURL());
703 * set the DAS source settings in the given jalview properties.
707 public void saveProperties(Properties properties)
709 if (registryURL.getText() == null || registryURL.getText().length() < 1)
711 properties.remove(Cache.DAS_REGISTRY_URL);
715 properties.setProperty(Cache.DAS_REGISTRY_URL,
716 registryURL.getText());
719 StringBuffer sb = new StringBuffer();
720 for (int r = 0; r < table.getModel().getRowCount(); r++)
722 if (((Boolean) table.getValueAt(r, 1)).booleanValue())
724 sb.append(table.getValueAt(r, 0) + "\t");
728 properties.setProperty(Cache.DAS_ACTIVE_SOURCE,
731 String sourceprop = sourceRegistry.getLocalSourceString();
732 properties.setProperty(Cache.DAS_LOCAL_SOURCE, sourceprop);
735 class DASTableModel extends AbstractTableModel
738 public DASTableModel(Object[][] data)
743 private String[] columnNames = new String[]
744 { MessageManager.getString("label.nickname"), MessageManager.getString("label.use_source") };
746 private Object[][] data;
748 public int getColumnCount()
750 return columnNames.length;
753 public int getRowCount()
758 public String getColumnName(int col)
760 return columnNames[col];
763 public Object getValueAt(int row, int col)
765 return data[row][col];
769 * JTable uses this method to determine the default renderer/ editor for
770 * each cell. If we didn't implement this method, then the last column would
771 * contain text ("true"/"false"), rather than a check box.
773 public Class getColumnClass(int c)
775 return getValueAt(0, c).getClass();
779 * Don't need to implement this method unless your table's editable.
781 public boolean isCellEditable(int row, int col)
783 // Note that the data/cell address is constant,
784 // no matter where the cell appears onscreen.
790 * Don't need to implement this method unless your table's data can change.
792 public void setValueAt(Object value, int row, int col)
794 data[row][col] = value;
795 fireTableCellUpdated(row, col);
797 String name = getValueAt(row, 0).toString();
798 boolean selected = ((Boolean) value).booleanValue();
800 if (selectedSources.contains(name) && !selected)
802 selectedSources.remove(name);
805 if (!selectedSources.contains(name) && selected)
807 selectedSources.add(name);
812 public void initDasSources()
815 Thread thr = new Thread(new Runnable()
819 // this actually initialises the das source list
820 paintComponent(null); // yuk
824 while (loadingDasSources || sourceRegistry == null)
829 } catch (Exception e)
837 * disable or enable the buttons on the source browser
841 public void setGuiEnabled(boolean b)
843 refresh.setEnabled(b);
844 addLocal.setEnabled(b);