2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
\r
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
24 import java.awt.event.*;
\r
25 import javax.swing.*;
\r
26 import javax.swing.event.*;
\r
27 import javax.swing.table.*;
\r
29 import org.biojava.dasobert.dasregistry.*;
\r
30 import jalview.jbgui.*;
\r
31 import jalview.util.*;
\r
33 public class DasSourceBrowser extends GDasSourceBrowser implements
\r
34 Runnable, ListSelectionListener
\r
36 static DasSource[] dasSources = null;
\r
38 Hashtable localSources = null;
\r
40 Vector selectedSources;
\r
42 public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";
\r
45 * true if thread is running and we are talking to DAS registry service
\r
47 public boolean loadingDasSources = false;
\r
49 protected static String getDasRegistryURL()
\r
51 String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
\r
54 if (registry.indexOf("/registry/das1/sources/") > -1)
\r
56 jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL, DEFAULT_REGISTRY);
\r
57 registry = DEFAULT_REGISTRY;
\r
62 public DasSourceBrowser()
\r
64 String registry = getDasRegistryURL();
\r
66 registryURL.setText(registry);
\r
68 setSelectedFromProperties();
\r
70 displayFullDetails(null);
\r
71 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
\r
73 filter1.addListSelectionListener(this);
\r
74 filter2.addListSelectionListener(this);
\r
75 filter3.addListSelectionListener(this);
\r
77 // Ask to be notified of selection changes.
\r
78 ListSelectionModel rowSM = table.getSelectionModel();
\r
79 rowSM.addListSelectionListener(new ListSelectionListener()
\r
81 public void valueChanged(ListSelectionEvent e)
\r
83 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
\r
84 if (!lsm.isSelectionEmpty())
\r
86 int selectedRow = lsm.getMinSelectionIndex();
\r
87 displayFullDetails(table.getValueAt(selectedRow, 0).toString());
\r
92 table.addMouseListener(new MouseAdapter()
\r
94 public void mouseClicked(MouseEvent evt)
\r
96 if (evt.getClickCount() == 2
\r
97 || SwingUtilities.isRightMouseButton(evt))
\r
99 editRemoveLocalSource(evt);
\r
104 if (dasSources != null)
\r
110 public void paintComponent(java.awt.Graphics g)
\r
112 if (dasSources == null && !loadingDasSources)
\r
114 Thread worker = new Thread(this);
\r
121 int dSize = dasSources.length;
\r
122 Object[][] data = new Object[dSize][2];
\r
123 for (int i = 0; i < dSize; i++)
\r
125 data[i][0] = dasSources[i].getNickname();
\r
126 data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
\r
130 refreshTableData(data);
\r
131 setCapabilities(dasSources);
\r
133 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
137 TableSorter sorter = (TableSorter) table.getModel();
\r
138 sorter.setSortingStatus(1, TableSorter.DESCENDING);
\r
139 sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
\r
143 progressBar.setIndeterminate(false);
\r
144 progressBar.setVisible(false);
\r
145 addLocal.setVisible(true);
\r
146 refresh.setVisible(true);
\r
149 public void refreshTableData(Object[][] data)
\r
151 TableSorter sorter = new TableSorter(new DASTableModel(data));
\r
152 sorter.setTableHeader(table.getTableHeader());
\r
153 table.setModel(sorter);
\r
156 void displayFullDetails(String nickName)
\r
159 StringBuffer text = new StringBuffer(
\r
160 "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
\r
162 if (nickName == null)
\r
164 fullDetails.setText(text + "Select a DAS service from the table"
\r
165 + " to read a full description here.</font></html>");
\r
169 int dSize = dasSources.length;
\r
170 for (int i = 0; i < dSize; i++)
\r
172 if (!dasSources[i].getNickname().equals(nickName))
\r
177 DasSource ds = dasSources[i];
\r
179 text.append("<font color=\"#0000FF\">Id:</font> "
\r
180 + dasSources[i].getId() + "<br>");
\r
181 text.append("<font color=\"#0000FF\">Nickname:</font> "
\r
182 + dasSources[i].getNickname() + "<br>");
\r
183 text.append("<font color=\"#0000FF\">URL:</font> "
\r
184 + dasSources[i].getUrl() + "<br>");
\r
187 .append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
\r
188 + dasSources[i].getAdminemail()
\r
190 + dasSources[i].getAdminemail() + "</a>" + "<br>");
\r
192 text.append("<font color=\"#0000FF\">Registered at:</font> "
\r
193 + dasSources[i].getRegisterDate() + "<br>");
\r
195 text.append("<font color=\"#0000FF\">Last successful test:</font> "
\r
196 + dasSources[i].getLeaseDate() + "<br>");
\r
198 text.append("<font color=\"#0000FF\">Labels:</font> ");
\r
199 for (int s = 0; s < dasSources[i].getLabels().length; s++)
\r
201 text.append(dasSources[i].getLabels()[s]);
\r
202 if (s < dasSources[i].getLabels().length - 1)
\r
208 text.append("<br>");
\r
210 text.append("<font color=\"#0000FF\">Capabilities:</font> ");
\r
211 String[] scap = dasSources[i].getCapabilities();
\r
212 for (int j = 0; j < scap.length; j++)
\r
214 text.append(scap[j]);
\r
215 if (j < scap.length - 1)
\r
220 text.append("<br>");
\r
222 text.append("<font color=\"#0000FF\">Coordinates:</font> ");
\r
223 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
\r
224 for (int j = 0; j < dcs.length; j++)
\r
226 text.append("(" + dcs[j].getUniqueId() + ") "
\r
227 + dcs[j].getCategory() + ", " + dcs[j].getName());
\r
228 if (dcs[j].getNCBITaxId() != 0)
\r
230 text.append(", " + dcs[j].getNCBITaxId());
\r
232 if (dcs[j].getOrganismName().length() > 0)
\r
234 text.append(", " + dcs[j].getOrganismName());
\r
237 text.append("<br>");
\r
240 text.append("<font color=\"#0000FF\">Description:</font> "
\r
241 + dasSources[i].getDescription() + "<br>");
\r
243 if (dasSources[i].getHelperurl() != null
\r
244 && dasSources[i].getHelperurl().length() > 0)
\r
246 text.append("<font color=\"#0000FF\"><a href=\""
\r
247 + dasSources[i].getHelperurl()
\r
248 + "\">Go to site</a></font<br>");
\r
251 text.append("</font></html>");
\r
256 fullDetails.setText(text.toString());
\r
257 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
261 fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
\r
268 loadingDasSources = true;
\r
270 addLocal.setVisible(false);
\r
271 refresh.setVisible(false);
\r
272 progressBar.setVisible(true);
\r
273 progressBar.setIndeterminate(true);
\r
274 // Refresh the source list.
\r
280 loadingDasSources = false;
\r
284 public Vector getSelectedSources()
\r
286 // wait around if we're still loading.
\r
287 while (dasSources ==null) {
\r
288 if (!loadingDasSources)
\r
290 new Thread(this).start();
\r
291 try { Thread.sleep(5); } catch (Exception e) {};
\r
292 while (loadingDasSources)
\r
294 try { Thread.sleep(5); } catch (Exception e) {};
\r
299 Vector selected = new Vector();
\r
300 for (int r = 0; r < selectedSources.size(); r++)
\r
302 for (int i = 0; i < dasSources.length; i++)
\r
304 if (dasSources[i].getNickname()
\r
305 .equals(selectedSources.elementAt(r)))
\r
307 selected.addElement(dasSources[i]);
\r
317 * retrieve das sources from registry and add local source list
\r
321 public DasSource[] getDASSource()
\r
323 if (dasSources == null)
\r
325 dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
\r
326 appendLocalSources();
\r
332 public void refresh_actionPerformed(ActionEvent e)
\r
334 saveProperties(jalview.bin.Cache.applicationProperties);
\r
336 Thread worker = new Thread(this);
\r
340 private void setCapabilities(DasSource[] sources)
\r
342 Vector authority = new Vector();
\r
343 Vector type = new Vector();
\r
344 Vector label = new Vector();
\r
346 authority.addElement("Any");
\r
347 type.addElement("Any");
\r
348 label.addElement("Any");
\r
350 for (int i = 0; i < sources.length; i++)
\r
352 DasSource ds = sources[i];
\r
354 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
\r
356 for (int j = 0; j < dcs.length; j++)
\r
358 if (!type.contains(dcs[j].getCategory()))
\r
360 type.addElement(dcs[j].getCategory());
\r
363 if (!authority.contains(dcs[j].getName()))
\r
365 authority.addElement(dcs[j].getName());
\r
369 String[] slabels = ds.getLabels();
\r
370 for (int s = 0; s < slabels.length; s++)
\r
372 if (!label.contains(slabels[s]))
\r
374 label.addElement(slabels[s]);
\r
380 filter1.setListData(authority);
\r
381 filter2.setListData(type);
\r
382 filter3.setListData(label);
\r
384 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
388 filter1.setSelectedIndex(0);
\r
389 filter2.setSelectedIndex(0);
\r
390 filter3.setSelectedIndex(0);
\r
395 public void amendLocal(boolean newSource)
\r
397 String url = "http://localhost:8080/", nickname = "";
\r
401 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
\r
402 nickname = table.getValueAt(selectedRow, 0).toString();
\r
403 url = ((DasSource) localSources.get(nickname)).getUrl();
\r
406 JTextField nametf = new JTextField(nickname, 40);
\r
407 JTextField urltf = new JTextField(url, 40);
\r
408 JCheckBox seqs = new JCheckBox("Sequence Source");
\r
410 JPanel panel = new JPanel(new BorderLayout());
\r
411 JPanel pane12 = new JPanel(new BorderLayout());
\r
412 pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
\r
413 pane12.add(nametf, BorderLayout.EAST);
\r
414 panel.add(pane12, BorderLayout.NORTH);
\r
415 pane12 = new JPanel(new BorderLayout());
\r
416 pane12.add(new JLabel("URL: "), BorderLayout.NORTH);
\r
417 pane12.add(seqs, BorderLayout.SOUTH);
\r
418 pane12.add(urltf, BorderLayout.EAST);
\r
419 panel.add(pane12, BorderLayout.SOUTH);
\r
421 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
422 panel, "Enter Nickname & URL of Local DAS Source",
\r
423 JOptionPane.OK_CANCEL_OPTION);
\r
425 if (reply != JOptionPane.OK_OPTION)
\r
430 if (!urltf.getText().endsWith("/"))
\r
432 urltf.setText(urltf.getText() + "/");
\r
435 Das1Source local = new Das1Source();
\r
437 local.setUrl(urltf.getText());
\r
438 local.setNickname(nametf.getText());
\r
439 if (seqs.isSelected())
\r
441 local.setCapabilities(new String[] {"sequence"});
\r
443 if (localSources == null)
\r
445 localSources = new Hashtable();
\r
448 localSources.put(local.getNickname(), local);
\r
450 if (!newSource && !nickname.equals(nametf.getText()))
\r
452 localSources.remove(nickname);
\r
455 int size = dasSources.length;
\r
456 int adjust = newSource ? 1 : 0;
\r
458 Object[][] data = new Object[size + adjust][2];
\r
459 for (int i = 0; i < size; i++)
\r
461 if (!newSource && dasSources[i].getNickname().equals(nickname))
\r
463 ((DasSource) dasSources[i]).setNickname(local.getNickname());
\r
464 ((DasSource) dasSources[i]).setUrl(local.getUrl());
\r
465 data[i][0] = local.getNickname();
\r
466 data[i][1] = new Boolean(true);
\r
470 data[i][0] = dasSources[i].getNickname();
\r
471 data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
\r
478 data[size][0] = local.getNickname();
\r
479 data[size][1] = new Boolean(true);
\r
480 selectedSources.add(local.getNickname());
\r
483 DasSource[] tmp = new DasSource[size + adjust];
\r
485 System.arraycopy(dasSources, 0, tmp, 0, size);
\r
494 refreshTableData(data);
\r
496 SwingUtilities.invokeLater(new Runnable()
\r
500 scrollPane.getVerticalScrollBar().setValue(
\r
501 scrollPane.getVerticalScrollBar().getMaximum());
\r
505 displayFullDetails(local.getNickname());
\r
508 public void editRemoveLocalSource(MouseEvent evt)
\r
510 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
\r
511 if (selectedRow == -1)
\r
516 String nickname = table.getValueAt(selectedRow, 0).toString();
\r
518 if (!localSources.containsKey(nickname))
\r
520 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
521 "You can only edit or remove local DAS Sources!",
\r
522 "Public DAS source - not editable",
\r
523 JOptionPane.WARNING_MESSAGE);
\r
528 { "Edit", "Remove", "Cancel" };
\r
529 int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
\r
530 "Do you want to edit or remove " + nickname + "?",
\r
531 "Edit / Remove Local DAS Source",
\r
532 JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
\r
533 null, options, options[2]);
\r
541 localSources.remove(nickname);
\r
542 selectedSources.remove(nickname);
\r
543 Object[][] data = new Object[dasSources.length - 1][2];
\r
544 DasSource[] tmp = new DasSource[dasSources.length - 1];
\r
546 for (int i = 0; i < dasSources.length; i++)
\r
548 if (dasSources[i].getNickname().equals(nickname))
\r
554 tmp[index] = dasSources[i];
\r
555 data[index][0] = dasSources[i].getNickname();
\r
556 data[index][1] = new Boolean(selectedSources
\r
557 .contains(dasSources[i].getNickname()));
\r
562 refreshTableData(data);
\r
563 SwingUtilities.invokeLater(new Runnable()
\r
567 scrollPane.getVerticalScrollBar().setValue(
\r
568 scrollPane.getVerticalScrollBar().getMaximum());
\r
576 void appendLocalSources()
\r
578 if (localSources == null)
\r
582 // note - we add all das sources to list so they can be filtered for the standard fetchDbRefs function
\r
583 int size = dasSources != null ? dasSources.length : 0;
\r
584 int lsize = localSources.size();
\r
586 Object[][] data = new Object[size + lsize][2];
\r
587 for (int i = 0; i < size; i++)
\r
589 data[i][0] = dasSources[i].getNickname();
\r
590 data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
\r
594 DasSource[] tmp = new DasSource[size + lsize];
\r
595 if (dasSources != null)
\r
597 System.arraycopy(dasSources, 0, tmp, 0, size);
\r
600 Enumeration en = localSources.keys();
\r
602 while (en.hasMoreElements())
\r
604 String key = en.nextElement().toString();
\r
605 data[index][0] = key;
\r
606 data[index][1] = new Boolean(false);
\r
607 tmp[index] = new Das1Source();
\r
608 tmp[index].setNickname(key);
\r
609 tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl());
\r
616 refreshTableData(data);
\r
619 public void valueChanged(ListSelectionEvent evt)
\r
621 // Called when the MainTable selection changes
\r
622 if (evt.getValueIsAdjusting())
\r
627 displayFullDetails(null);
\r
629 // Filter the displayed data sources
\r
630 int dSize = dasSources.length;
\r
632 ArrayList names = new ArrayList();
\r
633 ArrayList selected = new ArrayList();
\r
636 // The features filter is not visible, but we must still
\r
637 // filter the das source list here.
\r
638 // July 2006 - only 6 sources fo not serve features
\r
639 Object[] dummyFeatureList = new Object[]
\r
642 for (int i = 0; i < dSize; i++)
\r
644 ds = dasSources[i];
\r
645 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
\r
647 if (dcs.length == 0 && ds.getCapabilities().length == 0
\r
648 && filter1.getSelectedIndex() == 0
\r
649 && filter2.getSelectedIndex() == 0
\r
650 && filter3.getSelectedIndex() == 0)
\r
652 // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
\r
653 // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
\r
654 // IS ADDED FROM THE REGISTRY
\r
655 names.add(ds.getNickname());
\r
657 .add(new Boolean(selectedSources.contains(ds.getNickname())));
\r
661 if (!selectedInList(dummyFeatureList, ds.getCapabilities())
\r
662 || !selectedInList(filter3.getSelectedValues(), ds
\r
668 for (int j = 0; j < dcs.length; j++)
\r
670 if (selectedInList(filter1.getSelectedValues(), new String[]
\r
671 { dcs[j].getName() })
\r
672 && selectedInList(filter2.getSelectedValues(), new String[]
\r
673 { dcs[j].getCategory() }))
\r
675 names.add(ds.getNickname());
\r
676 selected.add(new Boolean(selectedSources.contains(ds
\r
683 dSize = names.size();
\r
684 Object[][] data = new Object[dSize][2];
\r
685 for (int d = 0; d < dSize; d++)
\r
687 data[d][0] = names.get(d);
\r
688 data[d][1] = selected.get(d);
\r
691 refreshTableData(data);
\r
694 boolean selectedInList(Object[] selection, String[] items)
\r
696 for (int i = 0; i < selection.length; i++)
\r
698 if (selection[i].equals("Any"))
\r
703 for (int j = 0; j < items.length; j++)
\r
705 if (selection[i].equals(items[j]))
\r
715 void setSelectedFromProperties()
\r
717 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
\r
719 StringTokenizer st = new StringTokenizer(active, "\t");
\r
720 selectedSources = new Vector();
\r
721 while (st.hasMoreTokens())
\r
723 selectedSources.addElement(st.nextToken());
\r
726 Vector _localSources = jalview.bin.Cache.getLocalDasSources();
\r
727 if (_localSources!=null)
\r
729 if (localSources==null)
\r
731 localSources = new Hashtable();
\r
733 Enumeration sources = _localSources.elements();
\r
734 while (sources.hasMoreElements())
\r
736 Das1Source source = (Das1Source) sources.nextElement();
\r
737 localSources.put(source.getNickname(), source);
\r
742 public void reset_actionPerformed(ActionEvent e)
\r
744 registryURL.setText(DEFAULT_REGISTRY);
\r
748 * set the DAS source settings in the given jalview properties.
\r
749 * @param properties
\r
751 public void saveProperties(Properties properties)
\r
753 if (registryURL.getText() == null || registryURL.getText().length() < 1)
\r
755 properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);
\r
759 properties.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL, registryURL.getText());
\r
762 StringBuffer sb = new StringBuffer();
\r
763 for (int r = 0; r < table.getModel().getRowCount(); r++)
\r
765 if (((Boolean) table.getValueAt(r, 1)).booleanValue())
\r
767 sb.append(table.getValueAt(r, 0) + "\t");
\r
771 properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE, sb.toString());
\r
773 if (localSources != null)
\r
775 sb = new StringBuffer();
\r
776 Enumeration en = localSources.keys();
\r
777 while (en.hasMoreElements())
\r
779 String token = en.nextElement().toString();
\r
780 sb.append(token + "|"
\r
781 +(((DasSource) localSources.get(token)).hasCapability("sequence") ? "sequence:" : "")
\r
782 + ((DasSource) localSources.get(token)).getUrl() + "\t");
\r
785 properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE, sb.toString());
\r
790 class DASTableModel extends AbstractTableModel
\r
793 public DASTableModel(Object[][] data)
\r
798 private String[] columnNames = new String[]
\r
799 { "Nickname", "Use Source" };
\r
801 private Object[][] data;
\r
803 public int getColumnCount()
\r
805 return columnNames.length;
\r
808 public int getRowCount()
\r
810 return data.length;
\r
813 public String getColumnName(int col)
\r
815 return columnNames[col];
\r
818 public Object getValueAt(int row, int col)
\r
820 return data[row][col];
\r
824 * JTable uses this method to determine the default renderer/ editor for
\r
825 * each cell. If we didn't implement this method, then the last column would
\r
826 * contain text ("true"/"false"), rather than a check box.
\r
828 public Class getColumnClass(int c)
\r
830 return getValueAt(0, c).getClass();
\r
834 * Don't need to implement this method unless your table's editable.
\r
836 public boolean isCellEditable(int row, int col)
\r
838 // Note that the data/cell address is constant,
\r
839 // no matter where the cell appears onscreen.
\r
845 * Don't need to implement this method unless your table's data can change.
\r
847 public void setValueAt(Object value, int row, int col)
\r
849 data[row][col] = value;
\r
850 fireTableCellUpdated(row, col);
\r
852 String name = getValueAt(row, 0).toString();
\r
853 boolean selected = ((Boolean) value).booleanValue();
\r
855 if (selectedSources.contains(name) && !selected)
\r
857 selectedSources.remove(name);
\r
860 if (!selectedSources.contains(name) && selected)
\r
862 selectedSources.add(name);
\r
867 public void initDasSources()
\r
870 Thread thr = new Thread(new Runnable()
\r
874 // this actually initialises the das source list
\r
875 paintComponent(null); // yuk
\r
879 while (loadingDasSources
\r
880 || dasSources == null)
\r
885 } catch (Exception e)
\r
892 public Vector resolveSourceNicknames(Vector sources)
\r
895 Vector resolved = new Vector();
\r
896 if (sources != null)
\r
898 for (int i = 0; i < dasSources.length; i++)
\r
900 if (sources.contains(dasSources[i].getNickname()))
\r
902 if (!resolved.contains(dasSources[i]))
\r
904 resolved.addElement(dasSources[i]);
\r