2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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;
63 JButton getDatabaseSelectorButton()
65 final JButton viewdbs = new JButton(MessageManager.getString("action.select_ddbb"));
66 viewdbs.addActionListener(new ActionListener()
70 public void actionPerformed(ActionEvent arg0)
82 private jalview.ws.SequenceFetcher sfetcher;
84 private JLabel dbstatus, dbstatex;
86 public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
88 initDialogFrame(this, true, false, "Select Database Retrieval Source",
91 * Dynamically generated database list will need a translation function from
92 * internal source to externally distinct names. UNIPROT and UP_NAME are
93 * identical DB sources, and should be collapsed.
95 DefaultMutableTreeNode tn = null, root = new DefaultMutableTreeNode();
96 Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<String, DefaultMutableTreeNode>();
98 String dbs[] = sfetch.getSupportedDb();
99 Hashtable<String, String> ht = new Hashtable<String, String>();
100 for (int i = 0; i < dbs.length; i++)
102 tn = source.get(dbs[i]);
103 List<DbSourceProxy> srcs = sfetch.getSourceProxy(dbs[i]);
106 source.put(dbs[i], tn = new DefaultMutableTreeNode(dbs[i], true));
108 for (DbSourceProxy dbp : srcs)
110 if (ht.get(dbp.getDbName()) == null)
112 tn.add(new DefaultMutableTreeNode(dbp, false));
113 ht.put(dbp.getDbName(), dbp.getDbName());
117 System.err.println("dupe ig for : " + dbs[i] + " \t"
118 + dbp.getDbName() + " (" + dbp.getDbSource() + ")");
123 for (int i = 0; i < dbs.length; i++)
125 tn = source.get(dbs[i]);
130 if (tn.getChildCount() == 1)
132 DefaultMutableTreeNode ttn = (DefaultMutableTreeNode) tn
134 // remove nodes with only one child
135 tn.setUserObject(ttn.getUserObject());
136 tn.removeAllChildren();
137 source.put(dbs[i], tn);
138 tn.setAllowsChildren(false);
144 svp = new JScrollPane();
145 // svp.setAutoscrolls(true);
146 dbviews = new JTree(new DefaultTreeModel(root, false));
147 dbviews.setCellRenderer(new DbTreeRenderer(this));
149 dbviews.getSelectionModel().setSelectionMode(
150 TreeSelectionModel.SINGLE_TREE_SELECTION);
151 svp.getViewport().setView(dbviews);
152 // svp.getViewport().setMinimumSize(new Dimension(300,200));
153 // svp.setSize(300,250);
154 // JPanel panel=new JPanel();
155 // panel.setSize(new Dimension(350,220));
157 dbviews.addTreeSelectionListener(new TreeSelectionListener()
161 public void valueChanged(TreeSelectionEvent arg0)
163 _setSelectionState();
166 JPanel jc = new JPanel(new BorderLayout()), j = new JPanel(
168 jc.add(svp, BorderLayout.CENTER);
171 // TODO: make the panel stay a fixed size for longest dbname+example set.
172 JPanel dbstat = new JPanel(new GridLayout(2, 1));
173 dbstatus = new JLabel(" "); // set the height correctly for layout
174 dbstatus.setFont(f = JvSwingUtils.getLabelFont(false, true));
175 dbstatus.setSize(new Dimension(290, 50));
176 dbstatex = new JLabel(" ");
178 dbstatex.setSize(new Dimension(290, 50));
179 dbstat.add(dbstatus);
180 dbstat.add(dbstatex);
181 jc.add(dbstat, BorderLayout.SOUTH);
183 // j.setPreferredSize(new Dimension(300,50));
184 add(jc, BorderLayout.CENTER);
187 add(j, BorderLayout.SOUTH);
188 dbviews.addKeyListener(this);
192 private void sortTreeNodes(DefaultMutableTreeNode root)
194 if (root.getChildCount() == 0)
198 int count = root.getChildCount();
199 String[] names = new String[count];
200 DefaultMutableTreeNode[] nodes = new DefaultMutableTreeNode[count];
201 for (int i = 0; i < count; i++)
203 TreeNode node = root.getChildAt(i);
204 if (node instanceof DefaultMutableTreeNode)
206 DefaultMutableTreeNode child = (DefaultMutableTreeNode) node;
208 if (child.getUserObject() instanceof DbSourceProxy)
210 names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
215 names[i] = ((String) child.getUserObject()).toLowerCase();
216 sortTreeNodes(child);
222 "Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.");
225 jalview.util.QuickSort.sort(names, nodes);
226 root.removeAllChildren();
227 for (int i = count - 1; i >= 0; i--)
233 private class DbTreeRenderer extends DefaultTreeCellRenderer implements
238 public DbTreeRenderer(JDatabaseTree me)
243 private Component returnLabel(String txt)
245 JLabel jl = new JLabel(txt);
246 jl.setFont(JvSwingUtils.getLabelFont());
251 public Component getTreeCellRendererComponent(JTree tree, Object value,
252 boolean selected, boolean expanded, boolean leaf, int row,
256 if (value != null && value instanceof DefaultMutableTreeNode)
258 DefaultMutableTreeNode vl = (DefaultMutableTreeNode) value;
259 value = vl.getUserObject();
260 if (value instanceof DbSourceProxy)
262 val = (((DbSourceProxy) value).getDbName());
266 if (value instanceof String)
268 val = ((String) value);
276 return super.getTreeCellRendererComponent(tree, val, selected,
277 expanded, leaf, row, hasFocus);
282 List<DbSourceProxy> oldselection, selection = null;
284 TreePath[] tsel = null, oldtsel = null;
287 protected void raiseClosed()
289 for (ActionListener al : lstners)
291 al.actionPerformed(null);
296 protected void okPressed()
298 _setSelectionState();
303 protected void cancelPressed()
305 selection = oldselection;
307 _revertSelectionState();
311 private void showDialog(Container parent)
313 oldselection = selection;
319 public boolean hasSelection()
321 return selection == null ? false : selection.size() == 0 ? false : true;
324 public List<DbSourceProxy> getSelectedSources()
330 * disable or enable selection handler
332 boolean handleSelections = true;
334 private void _setSelectionState()
336 if (!handleSelections)
340 if (dbviews.getSelectionCount() == 0)
344 tsel = dbviews.getSelectionPaths();
345 boolean forcedFirstChild = false;
346 List<DbSourceProxy> srcs = new ArrayList<DbSourceProxy>();
349 for (TreePath tp : tsel)
351 DefaultMutableTreeNode admt, dmt = (DefaultMutableTreeNode) tp
352 .getLastPathComponent();
353 if (dmt.getUserObject() != null)
355 if (dmt.getUserObject() instanceof DbSourceProxy)
357 srcs.add((DbSourceProxy) dmt.getUserObject());
361 if (allowMultiSelections)
363 srcs.addAll(sfetcher.getSourceProxy((String) dmt
368 srcs.add(sfetcher.getSourceProxy((String) dmt
369 .getUserObject()).get(0));
370 forcedFirstChild = true;
376 updateDbStatus(srcs, forcedFirstChild);
380 private void _revertSelectionState()
382 handleSelections = false;
383 if (selection == null || selection.size() == 0)
385 dbviews.clearSelection();
389 dbviews.setSelectionPaths(tsel);
391 handleSelections = true;
394 private void updateDbStatus(List<DbSourceProxy> srcs,
395 boolean forcedFirstChild)
398 String nm = "", qr = "";
399 for (DbSourceProxy dbs : srcs)
401 String tq = dbs.getTestQuery();
402 nm = dbs.getDbName();
403 if (tq != null && tq.trim().length() > 0 && dbs.isValidReference(tq))
410 if (allowMultiSelections)
412 dbstatus.setText(MessageManager.formatMessage("label.selected_database_to_fetch_from", new String[]{Integer.valueOf(srcs.size()).toString(),(srcs.size() == 1 ? "" : "s"),(srcs.size() > 0 ? " with " + x + " test quer" + (x == 1 ? "y" : "ies") : ".")}));
413 dbstatex.setText(" ");
419 dbstatus.setText(MessageManager.formatMessage("label.database_param",new String[]{nm}));
422 dbstatex.setText(MessageManager.formatMessage("label.example_param", new String[]{qr}));
426 dbstatex.setText(" ");
431 dbstatus.setText(" ");
434 dbstatus.invalidate();
435 dbstatex.invalidate();
438 public String getSelectedItem()
442 return getSelectedSources().get(0).getDbName();
447 public String getExampleQueries()
453 StringBuffer sb = new StringBuffer();
454 HashSet<String> hs = new HashSet<String>();
455 for (DbSourceProxy dbs : getSelectedSources())
457 String tq = dbs.getTestQuery();
468 return sb.toString();
471 List<ActionListener> lstners = new Vector<ActionListener>();
473 public void addActionListener(ActionListener actionListener)
475 lstners.add(actionListener);
478 public void removeActionListener(ActionListener actionListener)
480 lstners.remove(actionListener);
483 public static void main(String args[])
485 Cache.getDasSourceRegistry();
486 JDatabaseTree jdt = new JDatabaseTree(new jalview.ws.SequenceFetcher());
487 JFrame foo = new JFrame();
488 foo.setLayout(new BorderLayout());
489 foo.add(jdt.getDatabaseSelectorButton(), BorderLayout.CENTER);
491 foo.setVisible(true);
493 final Thread us = Thread.currentThread();
494 jdt.addActionListener(new ActionListener()
498 public void actionPerformed(ActionEvent e)
508 } catch (InterruptedException x)
511 if (!jdt.hasSelection())
513 System.out.println("No Selection");
517 System.out.println("Selection: " + jdt.getSelectedItem());
519 for (DbSourceProxy pr : jdt.getSelectedSources())
521 System.out.println("Source " + s++ + ": " + pr.getDbName()
522 + " (" + pr.getDbSource() + ") Version "
523 + pr.getDbVersion() + ". Test:\t" + pr.getTestQuery());
525 System.out.println("Test queries: " + jdt.getExampleQueries());
528 } while (nultimes > 0 && foo.isVisible());
529 foo.setVisible(false);
533 public void keyPressed(KeyEvent arg0)
535 if (!arg0.isConsumed() && arg0.getKeyCode() == KeyEvent.VK_ENTER)
539 if (!arg0.isConsumed() && arg0.getKeyChar() == KeyEvent.VK_ESCAPE)
546 public void keyReleased(KeyEvent arg0)
548 // TODO Auto-generated method stub
553 public void keyTyped(KeyEvent arg0)
555 // TODO Auto-generated method stub