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.util.MessageManager;
25 import jalview.ws.seqfetcher.DbSourceProxy;
27 import java.awt.BorderLayout;
28 import java.awt.Component;
29 import java.awt.Dimension;
30 import java.awt.FlowLayout;
31 import java.awt.GridLayout;
32 import java.awt.event.ActionEvent;
33 import java.awt.event.ActionListener;
34 import java.awt.event.KeyEvent;
35 import java.awt.event.KeyListener;
36 import java.util.ArrayList;
37 import java.util.HashSet;
38 import java.util.Hashtable;
39 import java.util.List;
40 import java.util.Vector;
42 import javax.swing.JButton;
43 import javax.swing.JFrame;
44 import javax.swing.JLabel;
45 import javax.swing.JPanel;
46 import javax.swing.JScrollPane;
47 import javax.swing.JTree;
48 import javax.swing.ToolTipManager;
49 import javax.swing.event.TreeSelectionEvent;
50 import javax.swing.event.TreeSelectionListener;
51 import javax.swing.tree.DefaultMutableTreeNode;
52 import javax.swing.tree.DefaultTreeCellRenderer;
53 import javax.swing.tree.DefaultTreeModel;
54 import javax.swing.tree.TreeCellRenderer;
55 import javax.swing.tree.TreeNode;
56 import javax.swing.tree.TreePath;
57 import javax.swing.tree.TreeSelectionModel;
59 public class JDatabaseTree extends JalviewDialog implements KeyListener
61 boolean allowMultiSelections = false;
65 JButton getDatabaseSelectorButton()
67 final JButton viewdbs = new JButton(
68 MessageManager.getString("action.select_ddbb"));
69 viewdbs.addActionListener(new ActionListener()
73 public void actionPerformed(ActionEvent arg0)
85 private jalview.ws.SequenceFetcher sfetcher;
87 private JLabel dbstatus, dbstatex;
89 public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
91 initDialogFrame(this, true, false,
93 .getString("label.select_database_retrieval_source"),
96 * Dynamically generated database list will need a translation function from
97 * internal source to externally distinct names. UNIPROT and UP_NAME are
98 * identical DB sources, and should be collapsed.
100 DefaultMutableTreeNode tn = null, root = new DefaultMutableTreeNode();
101 Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<String, DefaultMutableTreeNode>();
103 String dbs[] = sfetch.getSupportedDb();
104 Hashtable<String, String> ht = new Hashtable<String, String>();
105 for (int i = 0; i < dbs.length; i++)
107 tn = source.get(dbs[i]);
108 List<DbSourceProxy> srcs = sfetch.getSourceProxy(dbs[i]);
111 source.put(dbs[i], tn = new DefaultMutableTreeNode(dbs[i], true));
113 for (DbSourceProxy dbp : srcs)
115 if (ht.get(dbp.getDbName()) == null)
117 tn.add(new DefaultMutableTreeNode(dbp, false));
118 ht.put(dbp.getDbName(), dbp.getDbName());
122 System.err.println("dupe ig for : " + dbs[i] + " \t"
123 + dbp.getDbName() + " (" + dbp.getDbSource() + ")");
128 for (int i = 0; i < dbs.length; i++)
130 tn = source.get(dbs[i]);
135 if (tn.getChildCount() == 1)
137 DefaultMutableTreeNode ttn = (DefaultMutableTreeNode) tn
139 // remove nodes with only one child
140 tn.setUserObject(ttn.getUserObject());
141 tn.removeAllChildren();
142 source.put(dbs[i], tn);
143 tn.setAllowsChildren(false);
149 svp = new JScrollPane();
150 // svp.setAutoscrolls(true);
151 dbviews = new JTree(new DefaultTreeModel(root, false));
152 dbviews.setCellRenderer(new DbTreeRenderer(this));
154 dbviews.getSelectionModel().setSelectionMode(
155 TreeSelectionModel.SINGLE_TREE_SELECTION);
156 svp.getViewport().setView(dbviews);
157 // svp.getViewport().setMinimumSize(new Dimension(300,200));
158 // svp.setSize(300,250);
159 // JPanel panel=new JPanel();
160 // panel.setSize(new Dimension(350,220));
162 dbviews.addTreeSelectionListener(new TreeSelectionListener()
166 public void valueChanged(TreeSelectionEvent arg0)
168 _setSelectionState();
171 JPanel jc = new JPanel(new BorderLayout()), j = new JPanel(
173 jc.add(svp, BorderLayout.CENTER);
176 // TODO: make the panel stay a fixed size for longest dbname+example set.
177 JPanel dbstat = new JPanel(new GridLayout(2, 1));
178 dbstatus = new JLabel(" "); // set the height correctly for layout
179 dbstatus.setFont(f = JvSwingUtils.getLabelFont(false, true));
180 dbstatus.setSize(new Dimension(290, 50));
181 dbstatex = new JLabel(" ");
183 dbstatex.setSize(new Dimension(290, 50));
184 dbstat.add(dbstatus);
185 dbstat.add(dbstatex);
186 jc.add(dbstat, BorderLayout.SOUTH);
188 // j.setPreferredSize(new Dimension(300,50));
189 add(jc, BorderLayout.CENTER);
190 ok.setEnabled(false);
193 add(j, BorderLayout.SOUTH);
194 dbviews.addKeyListener(this);
198 private void sortTreeNodes(DefaultMutableTreeNode root)
200 if (root.getChildCount() == 0)
204 int count = root.getChildCount();
205 String[] names = new String[count];
206 DefaultMutableTreeNode[] nodes = new DefaultMutableTreeNode[count];
207 for (int i = 0; i < count; i++)
209 TreeNode node = root.getChildAt(i);
210 if (node instanceof DefaultMutableTreeNode)
212 DefaultMutableTreeNode child = (DefaultMutableTreeNode) node;
214 if (child.getUserObject() instanceof DbSourceProxy)
216 names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
221 names[i] = ((String) child.getUserObject()).toLowerCase();
222 sortTreeNodes(child);
229 .getString("error.implementation_error_cant_reorder_tree"));
232 jalview.util.QuickSort.sort(names, nodes);
233 root.removeAllChildren();
234 for (int i = count - 1; i >= 0; i--)
240 private class DbTreeRenderer extends DefaultTreeCellRenderer implements
245 public DbTreeRenderer(JDatabaseTree me)
248 ToolTipManager.sharedInstance().registerComponent(dbviews);
251 private Component returnLabel(String txt)
253 JLabel jl = new JLabel(txt);
254 jl.setFont(JvSwingUtils.getLabelFont());
259 public Component getTreeCellRendererComponent(JTree tree, Object value,
260 boolean selected, boolean expanded, boolean leaf, int row,
264 if (value != null && value instanceof DefaultMutableTreeNode)
266 DefaultMutableTreeNode vl = (DefaultMutableTreeNode) value;
267 value = vl.getUserObject();
268 if (value instanceof DbSourceProxy)
270 val = ((DbSourceProxy) value).getDbName();
271 if (((DbSourceProxy) value).getDescription() != null)
273 this.setToolTipText(((DbSourceProxy) value).getDescription());
278 if (value instanceof String)
280 val = (String) value;
288 return super.getTreeCellRendererComponent(tree, val, selected,
289 expanded, leaf, row, hasFocus);
294 List<DbSourceProxy> oldselection, selection = null;
296 TreePath[] tsel = null, oldtsel = null;
299 protected void raiseClosed()
301 for (ActionListener al : lstners)
303 al.actionPerformed(null);
308 protected void okPressed()
310 _setSelectionState();
315 protected void cancelPressed()
317 selection = oldselection;
319 _revertSelectionState();
325 oldselection = selection;
331 public boolean hasSelection()
333 return selection == null ? false : selection.size() == 0 ? false : true;
336 public List<DbSourceProxy> getSelectedSources()
342 * disable or enable selection handler
344 boolean handleSelections = true;
346 private void _setSelectionState()
348 if (!handleSelections)
352 ok.setEnabled(false);
353 if (dbviews.getSelectionCount() == 0)
358 tsel = dbviews.getSelectionPaths();
359 boolean forcedFirstChild = false;
360 List<DbSourceProxy> srcs = new ArrayList<DbSourceProxy>();
363 for (TreePath tp : tsel)
365 DefaultMutableTreeNode admt, dmt = (DefaultMutableTreeNode) tp
366 .getLastPathComponent();
367 if (dmt.getUserObject() != null)
370 * enable OK button once a selection has been made
373 if (dmt.getUserObject() instanceof DbSourceProxy)
375 srcs.add((DbSourceProxy) dmt.getUserObject());
379 if (allowMultiSelections)
381 srcs.addAll(sfetcher.getSourceProxy((String) dmt
387 .getSourceProxy((String) dmt.getUserObject()).get(0));
388 forcedFirstChild = true;
394 updateDbStatus(srcs, forcedFirstChild);
398 private void _revertSelectionState()
400 handleSelections = false;
401 if (selection == null || selection.size() == 0)
403 dbviews.clearSelection();
407 dbviews.setSelectionPaths(tsel);
409 handleSelections = true;
412 private void updateDbStatus(List<DbSourceProxy> srcs,
413 boolean forcedFirstChild)
416 String nm = "", qr = "";
417 for (DbSourceProxy dbs : srcs)
419 String tq = dbs.getTestQuery();
420 nm = dbs.getDbName();
421 if (tq != null && tq.trim().length() > 0 && dbs.isValidReference(tq))
428 dbstatex.setText(" ");
429 if (allowMultiSelections)
431 dbstatus.setText(MessageManager.formatMessage(
432 "label.selected_database_to_fetch_from", new String[] {
433 Integer.valueOf(srcs.size()).toString(),
434 (srcs.size() == 1 ? "" : "s"),
435 (srcs.size() > 0 ? " with " + x + " test quer"
436 + (x == 1 ? "y" : "ies") : ".") }));
442 dbstatus.setText(MessageManager.formatMessage(
443 "label.database_param", new String[] { nm }));
446 dbstatex.setText(MessageManager.formatMessage(
447 "label.example_param", new String[] { qr }));
452 dbstatus.setText(" ");
455 dbstatus.invalidate();
456 dbstatex.invalidate();
459 public String getSelectedItem()
463 return getSelectedSources().get(0).getDbName();
468 public String getExampleQueries()
474 StringBuffer sb = new StringBuffer();
475 HashSet<String> hs = new HashSet<String>();
476 for (DbSourceProxy dbs : getSelectedSources())
478 String tq = dbs.getTestQuery();
489 return sb.toString();
492 List<ActionListener> lstners = new Vector<ActionListener>();
494 public void addActionListener(ActionListener actionListener)
496 lstners.add(actionListener);
499 public void removeActionListener(ActionListener actionListener)
501 lstners.remove(actionListener);
504 public static void main(String args[])
506 Cache.getDasSourceRegistry();
507 JDatabaseTree jdt = new JDatabaseTree(new jalview.ws.SequenceFetcher());
508 JFrame foo = new JFrame();
509 foo.setLayout(new BorderLayout());
510 foo.add(jdt.getDatabaseSelectorButton(), BorderLayout.CENTER);
512 foo.setVisible(true);
514 final Thread us = Thread.currentThread();
515 jdt.addActionListener(new ActionListener()
519 public void actionPerformed(ActionEvent e)
529 } catch (InterruptedException x)
532 if (!jdt.hasSelection())
534 System.out.println("No Selection");
538 System.out.println("Selection: " + jdt.getSelectedItem());
540 for (DbSourceProxy pr : jdt.getSelectedSources())
542 System.out.println("Source " + s++ + ": " + pr.getDbName()
543 + " (" + pr.getDbSource() + ") Version "
544 + pr.getDbVersion() + ". Test:\t" + pr.getTestQuery());
546 System.out.println("Test queries: " + jdt.getExampleQueries());
549 } while (nultimes > 0 && foo.isVisible());
550 foo.setVisible(false);
554 public void keyPressed(KeyEvent arg0)
556 if (!arg0.isConsumed() && arg0.getKeyCode() == KeyEvent.VK_ENTER)
558 action = arg0.getKeyCode();
561 if (!arg0.isConsumed() && arg0.getKeyChar() == KeyEvent.VK_ESCAPE)
563 action = arg0.getKeyCode();
569 public void keyReleased(KeyEvent arg0)
571 // TODO Auto-generated method stub
576 public void keyTyped(KeyEvent arg0)
578 // TODO Auto-generated method stub