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.Container;
30 import java.awt.Dimension;
31 import java.awt.FlowLayout;
32 import java.awt.GridLayout;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.KeyEvent;
36 import java.awt.event.KeyListener;
37 import java.util.ArrayList;
38 import java.util.HashSet;
39 import java.util.Hashtable;
40 import java.util.List;
41 import java.util.Vector;
43 import javax.swing.JButton;
44 import javax.swing.JFrame;
45 import javax.swing.JLabel;
46 import javax.swing.JPanel;
47 import javax.swing.JScrollPane;
48 import javax.swing.JTree;
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);
192 add(j, BorderLayout.SOUTH);
193 dbviews.addKeyListener(this);
197 private void sortTreeNodes(DefaultMutableTreeNode root)
199 if (root.getChildCount() == 0)
203 int count = root.getChildCount();
204 String[] names = new String[count];
205 DefaultMutableTreeNode[] nodes = new DefaultMutableTreeNode[count];
206 for (int i = 0; i < count; i++)
208 TreeNode node = root.getChildAt(i);
209 if (node instanceof DefaultMutableTreeNode)
211 DefaultMutableTreeNode child = (DefaultMutableTreeNode) node;
213 if (child.getUserObject() instanceof DbSourceProxy)
215 names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
220 names[i] = ((String) child.getUserObject()).toLowerCase();
221 sortTreeNodes(child);
228 .getString("error.implementation_error_cant_reorder_tree"));
231 jalview.util.QuickSort.sort(names, nodes);
232 root.removeAllChildren();
233 for (int i = count - 1; i >= 0; i--)
239 private class DbTreeRenderer extends DefaultTreeCellRenderer implements
244 public DbTreeRenderer(JDatabaseTree me)
249 private Component returnLabel(String txt)
251 JLabel jl = new JLabel(txt);
252 jl.setFont(JvSwingUtils.getLabelFont());
257 public Component getTreeCellRendererComponent(JTree tree, Object value,
258 boolean selected, boolean expanded, boolean leaf, int row,
262 if (value != null && value instanceof DefaultMutableTreeNode)
264 DefaultMutableTreeNode vl = (DefaultMutableTreeNode) value;
265 value = vl.getUserObject();
266 if (value instanceof DbSourceProxy)
268 val = (((DbSourceProxy) value).getDbName());
272 if (value instanceof String)
274 val = ((String) value);
282 return super.getTreeCellRendererComponent(tree, val, selected,
283 expanded, leaf, row, hasFocus);
288 List<DbSourceProxy> oldselection, selection = null;
290 TreePath[] tsel = null, oldtsel = null;
293 protected void raiseClosed()
295 for (ActionListener al : lstners)
297 al.actionPerformed(null);
302 protected void okPressed()
304 _setSelectionState();
309 protected void cancelPressed()
311 selection = oldselection;
313 _revertSelectionState();
317 private void showDialog(Container parent)
319 oldselection = selection;
325 public boolean hasSelection()
327 return selection == null ? false : selection.size() == 0 ? false : true;
330 public List<DbSourceProxy> getSelectedSources()
336 * disable or enable selection handler
338 boolean handleSelections = true;
340 private void _setSelectionState()
342 if (!handleSelections)
346 if (dbviews.getSelectionCount() == 0)
350 tsel = dbviews.getSelectionPaths();
351 boolean forcedFirstChild = false;
352 List<DbSourceProxy> srcs = new ArrayList<DbSourceProxy>();
355 for (TreePath tp : tsel)
357 DefaultMutableTreeNode admt, dmt = (DefaultMutableTreeNode) tp
358 .getLastPathComponent();
359 if (dmt.getUserObject() != null)
361 if (dmt.getUserObject() instanceof DbSourceProxy)
363 srcs.add((DbSourceProxy) dmt.getUserObject());
367 if (allowMultiSelections)
369 srcs.addAll(sfetcher.getSourceProxy((String) dmt
375 .getSourceProxy((String) dmt.getUserObject()).get(0));
376 forcedFirstChild = true;
382 updateDbStatus(srcs, forcedFirstChild);
386 private void _revertSelectionState()
388 handleSelections = false;
389 if (selection == null || selection.size() == 0)
391 dbviews.clearSelection();
395 dbviews.setSelectionPaths(tsel);
397 handleSelections = true;
400 private void updateDbStatus(List<DbSourceProxy> srcs,
401 boolean forcedFirstChild)
404 String nm = "", qr = "";
405 for (DbSourceProxy dbs : srcs)
407 String tq = dbs.getTestQuery();
408 nm = dbs.getDbName();
409 if (tq != null && tq.trim().length() > 0 && dbs.isValidReference(tq))
416 if (allowMultiSelections)
418 dbstatus.setText(MessageManager.formatMessage(
419 "label.selected_database_to_fetch_from", new String[] {
420 Integer.valueOf(srcs.size()).toString(),
421 (srcs.size() == 1 ? "" : "s"),
422 (srcs.size() > 0 ? " with " + x + " test quer"
423 + (x == 1 ? "y" : "ies") : ".") }));
424 dbstatex.setText(" ");
430 dbstatus.setText(MessageManager.formatMessage(
431 "label.database_param", new String[] { nm }));
434 dbstatex.setText(MessageManager.formatMessage(
435 "label.example_param", new String[] { qr }));
439 dbstatex.setText(" ");
444 dbstatus.setText(" ");
447 dbstatus.invalidate();
448 dbstatex.invalidate();
451 public String getSelectedItem()
455 return getSelectedSources().get(0).getDbName();
460 public String getExampleQueries()
466 StringBuffer sb = new StringBuffer();
467 HashSet<String> hs = new HashSet<String>();
468 for (DbSourceProxy dbs : getSelectedSources())
470 String tq = dbs.getTestQuery();
481 return sb.toString();
484 List<ActionListener> lstners = new Vector<ActionListener>();
486 public void addActionListener(ActionListener actionListener)
488 lstners.add(actionListener);
491 public void removeActionListener(ActionListener actionListener)
493 lstners.remove(actionListener);
496 public static void main(String args[])
498 Cache.getDasSourceRegistry();
499 JDatabaseTree jdt = new JDatabaseTree(new jalview.ws.SequenceFetcher());
500 JFrame foo = new JFrame();
501 foo.setLayout(new BorderLayout());
502 foo.add(jdt.getDatabaseSelectorButton(), BorderLayout.CENTER);
504 foo.setVisible(true);
506 final Thread us = Thread.currentThread();
507 jdt.addActionListener(new ActionListener()
511 public void actionPerformed(ActionEvent e)
521 } catch (InterruptedException x)
524 if (!jdt.hasSelection())
526 System.out.println("No Selection");
530 System.out.println("Selection: " + jdt.getSelectedItem());
532 for (DbSourceProxy pr : jdt.getSelectedSources())
534 System.out.println("Source " + s++ + ": " + pr.getDbName()
535 + " (" + pr.getDbSource() + ") Version "
536 + pr.getDbVersion() + ". Test:\t" + pr.getTestQuery());
538 System.out.println("Test queries: " + jdt.getExampleQueries());
541 } while (nultimes > 0 && foo.isVisible());
542 foo.setVisible(false);
546 public void keyPressed(KeyEvent arg0)
548 if (!arg0.isConsumed() && arg0.getKeyCode() == KeyEvent.VK_ENTER)
550 action = arg0.getKeyCode();
553 if (!arg0.isConsumed() && arg0.getKeyChar() == KeyEvent.VK_ESCAPE)
555 action = arg0.getKeyCode();
561 public void keyReleased(KeyEvent arg0)
563 // TODO Auto-generated method stub
568 public void keyTyped(KeyEvent arg0)
570 // TODO Auto-generated method stub