2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 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
21 import jalview.jbgui.*;
\r
22 import javax.swing.table.AbstractTableModel;
\r
23 import javax.swing.event.*;
\r
24 import jalview.util.TableSorter;
\r
25 import java.awt.event.*;
\r
26 import javax.swing.*;
\r
30 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
\r
31 import org.biojava.dasobert.dasregistry.DasSource;
\r
32 import org.biojava.dasobert.dasregistry.Das1Source;
\r
33 import java.awt.BorderLayout;
\r
35 public class DasSourceBrowser extends GDasSourceBrowser
\r
36 implements Runnable, ListSelectionListener
\r
38 static DasSource[] dasSources = null;
\r
40 Hashtable localSources = null;
\r
42 Vector selectedSources;
\r
44 public DasSourceBrowser()
\r
46 registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
\r
47 "http://www.spice-3d.org/dasregistry/das1/sources") );
\r
49 setSelectedFromProperties();
\r
51 displayFullDetails(null);
\r
52 table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
\r
54 capabilities.addListSelectionListener(this);
\r
55 coords1.addListSelectionListener(this);
\r
56 coords2.addListSelectionListener(this);
\r
58 //Ask to be notified of selection changes.
\r
59 ListSelectionModel rowSM = table.getSelectionModel();
\r
60 rowSM.addListSelectionListener(new ListSelectionListener()
\r
62 public void valueChanged(ListSelectionEvent e)
\r
64 //Ignore extra messages.
\r
65 if (e.getValueIsAdjusting())
\r
68 ListSelectionModel lsm = (ListSelectionModel) e.getSource();
\r
69 if (!lsm.isSelectionEmpty())
\r
71 int selectedRow = lsm.getMinSelectionIndex();
\r
72 displayFullDetails(table.getValueAt(selectedRow, 0).toString());
\r
77 table.addMouseListener(new MouseAdapter()
\r
79 public void mouseClicked(MouseEvent evt)
\r
81 if(evt.getClickCount()==2
\r
82 || SwingUtilities.isRightMouseButton(evt))
\r
83 editRemoveLocalSource(evt);
\r
87 if(dasSources==null)
\r
89 Thread worker = new Thread(this);
\r
100 int dSize = dasSources.length;
\r
101 Object[][] data = new Object[dSize][2];
\r
102 for (int i = 0; i < dSize; i++)
\r
104 data[i][0] = dasSources[i].getNickname();
\r
105 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
\r
109 refreshTableData(data);
\r
110 setCapabilities(dasSources);
\r
112 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
116 TableSorter sorter = (TableSorter)table.getModel();
\r
117 sorter.setSortingStatus(1, TableSorter.DESCENDING);
\r
118 sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
\r
122 progressBar.setIndeterminate(false);
\r
123 progressBar.setVisible(false);
\r
124 addLocal.setVisible(true);
\r
125 refresh.setVisible(true);
\r
129 public void refreshTableData(Object[][] data)
\r
131 TableSorter sorter = new TableSorter(new DASTableModel(data));
\r
132 sorter.setTableHeader(table.getTableHeader());
\r
133 table.setModel(sorter);
\r
136 void displayFullDetails(String nickName)
\r
139 StringBuffer text = new StringBuffer(
\r
140 "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
\r
142 if (nickName == null)
\r
144 fullDetails.setText(text +
\r
145 "Select a DAS service from the table"
\r
146 + " to read a full description here.</font></html>");
\r
150 int dSize = dasSources.length;
\r
151 for (int i = 0; i < dSize; i++)
\r
153 if (!dasSources[i].getNickname().equals(nickName))
\r
156 DasSource ds = dasSources[i];
\r
158 text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
\r
160 text.append("<font color=\"#0000FF\">Nickname:</font> " +
\r
161 dasSources[i].getNickname() + "<br>");
\r
162 text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
\r
165 text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
\r
166 +dasSources[i].getAdminemail()
\r
167 +"\">"+dasSources[i].getAdminemail()+"</a>" +
\r
171 text.append("<font color=\"#0000FF\">Registered at:</font> " + dasSources[i].getRegisterDate() +
\r
174 text.append("<font color=\"#0000FF\">Last successful test:</font> " + dasSources[i].getLeaseDate() +
\r
177 text.append("<font color=\"#0000FF\">Labels:</font> ");
\r
178 for(int s=0; s<dasSources[i].getLabels().length; s++)
\r
180 text.append( dasSources[i].getLabels()[s]);
\r
181 if(s<dasSources[i].getLabels().length-1)
\r
185 text.append("<br>");
\r
189 text.append("<font color=\"#0000FF\">Capabilities:</font> ");
\r
190 String[] scap = dasSources[i].getCapabilities();
\r
191 for (int j = 0; j < scap.length; j++)
\r
193 text.append(scap[j]);
\r
194 if (j < scap.length - 1)
\r
197 text.append("<br>");
\r
199 text.append("<font color=\"#0000FF\">Coordinates:</font> ");
\r
200 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
\r
201 for (int j = 0; j < dcs.length; j++)
\r
203 text.append("(" + dcs[j].getUniqueId() + ") "
\r
204 + dcs[j].getCategory() + ", " + dcs[j].getName());
\r
205 if (dcs[j].getNCBITaxId() != 0)
\r
206 text.append(", " + dcs[j].getNCBITaxId());
\r
207 if (dcs[j].getOrganismName().length() > 0)
\r
208 text.append(", " + dcs[j].getOrganismName());
\r
210 text.append("<br>");
\r
213 text.append("<font color=\"#0000FF\">Description:</font> " +
\r
214 dasSources[i].getDescription() + "<br>");
\r
217 if (dasSources[i].getHelperurl()!=null
\r
218 && dasSources[i].getHelperurl().length() > 0)
\r
220 text.append("<font color=\"#0000FF\"><a href=\"" +
\r
221 dasSources[i].getHelperurl()
\r
222 + "\">Go to site</a></font<br>");
\r
225 text.append("</font></html>");
\r
230 fullDetails.setText(text.toString());
\r
231 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
235 fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
\r
243 addLocal.setVisible(false);
\r
244 refresh.setVisible(false);
\r
245 progressBar.setVisible(true);
\r
246 progressBar.setIndeterminate(true);
\r
248 dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
\r
250 appendLocalSources();
\r
255 public DasSource[] getDASSource()
\r
257 if(dasSources==null)
\r
259 dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
\r
260 appendLocalSources();
\r
266 public void refresh_actionPerformed(ActionEvent e)
\r
268 saveProperties(jalview.bin.Cache.applicationProperties);
\r
270 Thread worker = new Thread(this);
\r
274 private void setCapabilities(DasSource[] sources)
\r
276 Vector vcapabilities = new Vector();
\r
277 Vector vcoords = new Vector();
\r
278 Vector vcoords2 = new Vector();
\r
280 vcapabilities.addElement("All");
\r
281 vcoords.addElement("All");
\r
282 vcoords2.addElement("All");
\r
284 for (int i = 0; i < sources.length; i++)
\r
286 DasSource ds = sources[i];
\r
287 String[] scap = ds.getCapabilities();
\r
288 for (int s = 0; s < scap.length; s++)
\r
290 if (!vcapabilities.contains(scap[s]))
\r
292 vcapabilities.addElement(scap[s]);
\r
296 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
\r
298 for (int j = 0; j < dcs.length; j++)
\r
300 if (!vcoords.contains(dcs[j].getCategory()))
\r
301 vcoords.addElement(dcs[j].getCategory());
\r
303 if (!vcoords2.contains(dcs[j].getName()))
\r
304 vcoords2.addElement(dcs[j].getName());
\r
308 capabilities.setListData(vcapabilities);
\r
309 coords1.setListData(vcoords);
\r
310 coords2.setListData(vcoords2);
\r
312 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
316 capabilities.setSelectedIndex(0);
\r
317 coords1.setSelectedIndex(0);
\r
318 coords2.setSelectedIndex(0);
\r
323 public void amendLocal(boolean newSource)
\r
325 String url = "http://localhost:8080/", nickname = "";
\r
329 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
\r
330 nickname = table.getValueAt(selectedRow, 0).toString();
\r
331 url = ((DasSource)localSources.get(nickname)).getUrl();
\r
334 JTextField nametf = new JTextField(nickname, 40);
\r
335 JTextField urltf = new JTextField(url, 40);
\r
337 JPanel panel = new JPanel(new BorderLayout());
\r
338 JPanel pane12 = new JPanel(new BorderLayout());
\r
339 pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
\r
340 pane12.add(nametf, BorderLayout.EAST);
\r
341 panel.add(pane12, BorderLayout.NORTH);
\r
342 pane12 = new JPanel(new BorderLayout());
\r
343 pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
\r
344 pane12.add(urltf, BorderLayout.EAST);
\r
345 panel.add(pane12, BorderLayout.SOUTH);
\r
348 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
349 panel, "Enter Nickname & URL of Local DAS Source",
\r
350 JOptionPane.OK_CANCEL_OPTION);
\r
352 if (reply != JOptionPane.OK_OPTION )
\r
357 if(!urltf.getText().endsWith("/"))
\r
358 urltf.setText(urltf.getText()+"/");
\r
360 Das1Source local = new Das1Source();
\r
362 local.setUrl(urltf.getText());
\r
363 local.setNickname(nametf.getText());
\r
366 if(localSources==null)
\r
367 localSources = new Hashtable();
\r
369 localSources.put(local.getNickname(), local);
\r
371 if(!newSource && !nickname.equals(nametf.getText()))
\r
373 localSources.remove(nickname);
\r
376 int size = dasSources.length;
\r
377 int adjust = newSource ? 1 : 0;
\r
379 Object[][] data = new Object[size+adjust][2];
\r
380 for (int i = 0; i < size; i++)
\r
382 if(!newSource && dasSources[i].getNickname().equals(nickname))
\r
384 ((DasSource)dasSources[i]).setNickname(local.getNickname());
\r
385 ((DasSource)dasSources[i]).setUrl(local.getUrl());
\r
386 data[i][0] = local.getNickname();
\r
387 data[i][1] = new Boolean(true);
\r
391 data[i][0] = dasSources[i].getNickname();
\r
392 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
\r
399 data[size][0] = local.getNickname();
\r
400 data[size][1] = new Boolean(true);
\r
401 selectedSources.add(local.getNickname());
\r
404 DasSource [] tmp = new DasSource[size+adjust];
\r
406 System.arraycopy(dasSources, 0, tmp, 0, size);
\r
413 refreshTableData(data);
\r
415 SwingUtilities.invokeLater(new Runnable()
\r
419 scrollPane.getVerticalScrollBar().setValue(
\r
420 scrollPane.getVerticalScrollBar().getMaximum()
\r
425 displayFullDetails(local.getNickname());
\r
428 public void editRemoveLocalSource(MouseEvent evt)
\r
430 int selectedRow = table.getSelectionModel().getMinSelectionIndex();
\r
431 if(selectedRow==-1)
\r
434 String nickname = table.getValueAt(selectedRow, 0).toString();
\r
436 if (!localSources.containsKey(nickname))
\r
438 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
439 "You can only edit or remove local DAS Sources!",
\r
440 "Public DAS source - not editable",
\r
441 JOptionPane.WARNING_MESSAGE);
\r
446 Object[] options = {"Edit", "Remove", "Cancel"};
\r
447 int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
\r
448 "Do you want to edit or remove "+nickname+"?",
\r
449 "Edit / Remove Local DAS Source",
\r
450 JOptionPane.YES_NO_CANCEL_OPTION,
\r
451 JOptionPane.QUESTION_MESSAGE,
\r
458 case 0: amendLocal(false); break;
\r
460 localSources.remove(nickname);
\r
461 selectedSources.remove(nickname);
\r
462 Object[][] data = new Object[dasSources.length-1][2];
\r
463 DasSource [] tmp = new DasSource[dasSources.length-1];
\r
465 for (int i = 0; i < dasSources.length; i++)
\r
467 if (dasSources[i].getNickname().equals(nickname))
\r
473 tmp[index] = dasSources[i];
\r
474 data[index][0] = dasSources[i].getNickname();
\r
475 data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
\r
481 refreshTableData(data);
\r
482 SwingUtilities.invokeLater(new Runnable()
\r
486 scrollPane.getVerticalScrollBar().setValue(
\r
487 scrollPane.getVerticalScrollBar().getMaximum()
\r
496 void appendLocalSources()
\r
498 if(localSources==null)
\r
501 int size = dasSources!=null ? dasSources.length : 0;
\r
502 int lsize = localSources.size();
\r
504 Object[][] data = new Object[size+lsize][2];
\r
505 for (int i = 0; i < size; i++)
\r
507 data[i][0] = dasSources[i].getNickname();
\r
508 data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
\r
512 DasSource [] tmp = new DasSource[size+lsize];
\r
513 if(dasSources!=null)
\r
514 System.arraycopy(dasSources, 0, tmp, 0, size);
\r
516 Enumeration en = localSources.keys();
\r
518 while(en.hasMoreElements())
\r
520 String key = en.nextElement().toString();
\r
521 data[index][0] = key;
\r
522 data[index][1] = new Boolean(false);
\r
523 tmp[index] = new Das1Source();
\r
524 tmp[index].setNickname(key);
\r
525 tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );
\r
532 refreshTableData(data);
\r
535 public void valueChanged(ListSelectionEvent evt)
\r
537 //Called when the MainTable selection changes
\r
538 if (evt.getValueIsAdjusting())
\r
543 displayFullDetails(null);
\r
545 // Filter the displayed data sources
\r
546 int dSize = dasSources.length;
\r
547 ArrayList names = new ArrayList();
\r
548 ArrayList selected = new ArrayList();
\r
551 // capabilities.get
\r
552 for (int i = 0; i < dSize; i++)
\r
554 ds = dasSources[i];
\r
556 if (!selectedInList(capabilities, ds.getCapabilities()))
\r
561 DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
\r
562 for (int j = 0; j < dcs.length; j++)
\r
564 if (selectedInList(coords1, new String[]
\r
565 {dcs[j].getCategory()})
\r
566 && selectedInList(coords2, new String[]
\r
567 {dcs[j].getName()}))
\r
569 names.add(ds.getNickname());
\r
570 selected.add(new Boolean(
\r
571 selectedSources.contains(ds.getNickname())));
\r
577 dSize = names.size();
\r
578 Object[][] data = new Object[dSize][2];
\r
579 for (int d = 0; d < dSize; d++)
\r
581 data[d][0] = names.get(d);
\r
582 data[d][1] = selected.get(d);
\r
585 refreshTableData(data);
\r
588 boolean selectedInList(JList list, String[] items)
\r
590 Object[] selection = list.getSelectedValues();
\r
591 for (int i = 0; i < selection.length; i++)
\r
593 if (selection[i].equals("All"))
\r
596 for (int j = 0; j < items.length; j++)
\r
598 if (selection[i].equals(items[j]))
\r
606 void setSelectedFromProperties()
\r
608 String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
\r
609 StringTokenizer st = new StringTokenizer(active, "\t");
\r
610 selectedSources = new Vector();
\r
611 while(st.hasMoreTokens())
\r
613 selectedSources.addElement(st.nextToken());
\r
616 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
\r
619 if(localSources == null)
\r
620 localSources = new Hashtable();
\r
622 st = new StringTokenizer(local, "\t");
\r
623 while(st.hasMoreTokens())
\r
625 String token = st.nextToken();
\r
626 int bar = token.indexOf("|");
\r
627 Das1Source source = new Das1Source();
\r
629 source.setUrl(token.substring(bar + 1));
\r
630 source.setNickname(token.substring(0, bar));
\r
632 localSources.put(source.getNickname(), source);
\r
637 void saveProperties(Properties properties)
\r
639 properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());
\r
641 StringBuffer sb = new StringBuffer();
\r
642 for(int r=0; r<table.getModel().getRowCount(); r++)
\r
644 if( ((Boolean)table.getValueAt(r,1)).booleanValue())
\r
646 sb.append(table.getValueAt(r,0)+"\t");
\r
650 properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );
\r
652 if(localSources!=null)
\r
654 sb = new StringBuffer();
\r
655 Enumeration en = localSources.keys();
\r
656 while(en.hasMoreElements())
\r
658 String token = en.nextElement().toString();
\r
659 sb.append(token+"|"
\r
660 + ((DasSource)localSources.get(token)).getUrl()
\r
664 properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
\r
669 class DASTableModel
\r
670 extends AbstractTableModel
\r
673 public DASTableModel(Object[][] data)
\r
678 private String[] columnNames = new String[] {"Nickname", "Use Source"};
\r
680 private Object[][] data;
\r
682 public int getColumnCount()
\r
684 return columnNames.length;
\r
687 public int getRowCount()
\r
689 return data.length;
\r
692 public String getColumnName(int col)
\r
694 return columnNames[col];
\r
697 public Object getValueAt(int row, int col)
\r
699 return data[row][col];
\r
703 * JTable uses this method to determine the default renderer/
\r
704 * editor for each cell. If we didn't implement this method,
\r
705 * then the last column would contain text ("true"/"false"),
\r
706 * rather than a check box.
\r
708 public Class getColumnClass(int c)
\r
710 return getValueAt(0, c).getClass();
\r
714 * Don't need to implement this method unless your table's
\r
717 public boolean isCellEditable(int row, int col)
\r
719 //Note that the data/cell address is constant,
\r
720 //no matter where the cell appears onscreen.
\r
726 * Don't need to implement this method unless your table's
\r
729 public void setValueAt(Object value, int row, int col)
\r
731 data[row][col] = value;
\r
732 fireTableCellUpdated(row, col);
\r
734 String name = getValueAt(row,0).toString();
\r
735 boolean selected = ((Boolean)value).booleanValue();
\r
737 if(selectedSources.contains(name) && !selected)
\r
738 selectedSources.remove(name);
\r
740 if(!selectedSources.contains(name) && selected)
\r
741 selectedSources.add(name);
\r