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(
66 MessageManager.getString("action.select_ddbb"));
67 viewdbs.addActionListener(new ActionListener()
71 public void actionPerformed(ActionEvent arg0)
83 private jalview.ws.SequenceFetcher sfetcher;
85 private JLabel dbstatus, dbstatex;
87 public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
89 initDialogFrame(this, true, false, "Select Database Retrieval Source",
92 * Dynamically generated database list will need a translation function from
93 * internal source to externally distinct names. UNIPROT and UP_NAME are
94 * identical DB sources, and should be collapsed.
96 DefaultMutableTreeNode tn = null, root = new DefaultMutableTreeNode();
97 Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<String, DefaultMutableTreeNode>();
99 String dbs[] = sfetch.getSupportedDb();
100 Hashtable<String, String> ht = new Hashtable<String, String>();
101 for (int i = 0; i < dbs.length; i++)
103 tn = source.get(dbs[i]);
104 List<DbSourceProxy> srcs = sfetch.getSourceProxy(dbs[i]);
107 source.put(dbs[i], tn = new DefaultMutableTreeNode(dbs[i], true));
109 for (DbSourceProxy dbp : srcs)
111 if (ht.get(dbp.getDbName()) == null)
113 tn.add(new DefaultMutableTreeNode(dbp, false));
114 ht.put(dbp.getDbName(), dbp.getDbName());
118 System.err.println("dupe ig for : " + dbs[i] + " \t"
119 + dbp.getDbName() + " (" + dbp.getDbSource() + ")");
124 for (int i = 0; i < dbs.length; i++)
126 tn = source.get(dbs[i]);
131 if (tn.getChildCount() == 1)
133 DefaultMutableTreeNode ttn = (DefaultMutableTreeNode) tn
135 // remove nodes with only one child
136 tn.setUserObject(ttn.getUserObject());
137 tn.removeAllChildren();
138 source.put(dbs[i], tn);
139 tn.setAllowsChildren(false);
145 svp = new JScrollPane();
146 // svp.setAutoscrolls(true);
147 dbviews = new JTree(new DefaultTreeModel(root, false));
148 dbviews.setCellRenderer(new DbTreeRenderer(this));
150 dbviews.getSelectionModel().setSelectionMode(
151 TreeSelectionModel.SINGLE_TREE_SELECTION);
152 svp.getViewport().setView(dbviews);
153 // svp.getViewport().setMinimumSize(new Dimension(300,200));
154 // svp.setSize(300,250);
155 // JPanel panel=new JPanel();
156 // panel.setSize(new Dimension(350,220));
158 dbviews.addTreeSelectionListener(new TreeSelectionListener()
162 public void valueChanged(TreeSelectionEvent arg0)
164 _setSelectionState();
167 JPanel jc = new JPanel(new BorderLayout()), j = new JPanel(
169 jc.add(svp, BorderLayout.CENTER);
172 // TODO: make the panel stay a fixed size for longest dbname+example set.
173 JPanel dbstat = new JPanel(new GridLayout(2, 1));
174 dbstatus = new JLabel(" "); // set the height correctly for layout
175 dbstatus.setFont(f = JvSwingUtils.getLabelFont(false, true));
176 dbstatus.setSize(new Dimension(290, 50));
177 dbstatex = new JLabel(" ");
179 dbstatex.setSize(new Dimension(290, 50));
180 dbstat.add(dbstatus);
181 dbstat.add(dbstatex);
182 jc.add(dbstat, BorderLayout.SOUTH);
184 // j.setPreferredSize(new Dimension(300,50));
185 add(jc, BorderLayout.CENTER);
188 add(j, BorderLayout.SOUTH);
189 dbviews.addKeyListener(this);
193 private void sortTreeNodes(DefaultMutableTreeNode root)
195 if (root.getChildCount() == 0)
199 int count = root.getChildCount();
200 String[] names = new String[count];
201 DefaultMutableTreeNode[] nodes = new DefaultMutableTreeNode[count];
202 for (int i = 0; i < count; i++)
204 TreeNode node = root.getChildAt(i);
205 if (node instanceof DefaultMutableTreeNode)
207 DefaultMutableTreeNode child = (DefaultMutableTreeNode) node;
209 if (child.getUserObject() instanceof DbSourceProxy)
211 names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
216 names[i] = ((String) child.getUserObject()).toLowerCase();
217 sortTreeNodes(child);
223 "Implementation Error: Can't reorder this tree. Not DefaultMutableTreeNode.");
226 jalview.util.QuickSort.sort(names, nodes);
227 root.removeAllChildren();
228 for (int i = count - 1; i >= 0; i--)
234 private class DbTreeRenderer extends DefaultTreeCellRenderer implements
239 public DbTreeRenderer(JDatabaseTree me)
244 private Component returnLabel(String txt)
246 JLabel jl = new JLabel(txt);
247 jl.setFont(JvSwingUtils.getLabelFont());
252 public Component getTreeCellRendererComponent(JTree tree, Object value,
253 boolean selected, boolean expanded, boolean leaf, int row,
257 if (value != null && value instanceof DefaultMutableTreeNode)
259 DefaultMutableTreeNode vl = (DefaultMutableTreeNode) value;
260 value = vl.getUserObject();
261 if (value instanceof DbSourceProxy)
263 val = (((DbSourceProxy) value).getDbName());
267 if (value instanceof String)
269 val = ((String) value);
277 return super.getTreeCellRendererComponent(tree, val, selected,
278 expanded, leaf, row, hasFocus);
283 List<DbSourceProxy> oldselection, selection = null;
285 TreePath[] tsel = null, oldtsel = null;
288 protected void raiseClosed()
290 for (ActionListener al : lstners)
292 al.actionPerformed(null);
297 protected void okPressed()
299 _setSelectionState();
304 protected void cancelPressed()
306 selection = oldselection;
308 _revertSelectionState();
312 private void showDialog(Container parent)
314 oldselection = selection;
320 public boolean hasSelection()
322 return selection == null ? false : selection.size() == 0 ? false : true;
325 public List<DbSourceProxy> getSelectedSources()
331 * disable or enable selection handler
333 boolean handleSelections = true;
335 private void _setSelectionState()
337 if (!handleSelections)
341 if (dbviews.getSelectionCount() == 0)
345 tsel = dbviews.getSelectionPaths();
346 boolean forcedFirstChild = false;
347 List<DbSourceProxy> srcs = new ArrayList<DbSourceProxy>();
350 for (TreePath tp : tsel)
352 DefaultMutableTreeNode admt, dmt = (DefaultMutableTreeNode) tp
353 .getLastPathComponent();
354 if (dmt.getUserObject() != null)
356 if (dmt.getUserObject() instanceof DbSourceProxy)
358 srcs.add((DbSourceProxy) dmt.getUserObject());
362 if (allowMultiSelections)
364 srcs.addAll(sfetcher.getSourceProxy((String) dmt
370 .getSourceProxy((String) dmt.getUserObject()).get(0));
371 forcedFirstChild = true;
377 updateDbStatus(srcs, forcedFirstChild);
381 private void _revertSelectionState()
383 handleSelections = false;
384 if (selection == null || selection.size() == 0)
386 dbviews.clearSelection();
390 dbviews.setSelectionPaths(tsel);
392 handleSelections = true;
395 private void updateDbStatus(List<DbSourceProxy> srcs,
396 boolean forcedFirstChild)
399 String nm = "", qr = "";
400 for (DbSourceProxy dbs : srcs)
402 String tq = dbs.getTestQuery();
403 nm = dbs.getDbName();
404 if (tq != null && tq.trim().length() > 0 && dbs.isValidReference(tq))
411 if (allowMultiSelections)
413 dbstatus.setText(MessageManager.formatMessage(
414 "label.selected_database_to_fetch_from", new String[]
416 Integer.valueOf(srcs.size()).toString(),
417 (srcs.size() == 1 ? "" : "s"),
418 (srcs.size() > 0 ? " with " + x + " test quer"
419 + (x == 1 ? "y" : "ies") : ".") }));
420 dbstatex.setText(" ");
426 dbstatus.setText(MessageManager.formatMessage(
427 "label.database_param", new String[]
431 dbstatex.setText(MessageManager.formatMessage(
432 "label.example_param", new String[]
437 dbstatex.setText(" ");
442 dbstatus.setText(" ");
445 dbstatus.invalidate();
446 dbstatex.invalidate();
449 public String getSelectedItem()
453 return getSelectedSources().get(0).getDbName();
458 public String getExampleQueries()
464 StringBuffer sb = new StringBuffer();
465 HashSet<String> hs = new HashSet<String>();
466 for (DbSourceProxy dbs : getSelectedSources())
468 String tq = dbs.getTestQuery();
479 return sb.toString();
482 List<ActionListener> lstners = new Vector<ActionListener>();
484 public void addActionListener(ActionListener actionListener)
486 lstners.add(actionListener);
489 public void removeActionListener(ActionListener actionListener)
491 lstners.remove(actionListener);
494 public static void main(String args[])
496 Cache.getDasSourceRegistry();
497 JDatabaseTree jdt = new JDatabaseTree(new jalview.ws.SequenceFetcher());
498 JFrame foo = new JFrame();
499 foo.setLayout(new BorderLayout());
500 foo.add(jdt.getDatabaseSelectorButton(), BorderLayout.CENTER);
502 foo.setVisible(true);
504 final Thread us = Thread.currentThread();
505 jdt.addActionListener(new ActionListener()
509 public void actionPerformed(ActionEvent e)
519 } catch (InterruptedException x)
522 if (!jdt.hasSelection())
524 System.out.println("No Selection");
528 System.out.println("Selection: " + jdt.getSelectedItem());
530 for (DbSourceProxy pr : jdt.getSelectedSources())
532 System.out.println("Source " + s++ + ": " + pr.getDbName()
533 + " (" + pr.getDbSource() + ") Version "
534 + pr.getDbVersion() + ". Test:\t" + pr.getTestQuery());
536 System.out.println("Test queries: " + jdt.getExampleQueries());
539 } while (nultimes > 0 && foo.isVisible());
540 foo.setVisible(false);
544 public void keyPressed(KeyEvent arg0)
546 if (!arg0.isConsumed() && arg0.getKeyCode() == KeyEvent.VK_ENTER)
550 if (!arg0.isConsumed() && arg0.getKeyChar() == KeyEvent.VK_ESCAPE)
557 public void keyReleased(KeyEvent arg0)
559 // TODO Auto-generated method stub
564 public void keyTyped(KeyEvent arg0)
566 // TODO Auto-generated method stub