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Coverage Report

  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.gui

File JDatabaseTree.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

78
191
26
2
558
472
71
0.37
7.35
13
2.73

Classes

Class Line # Actions
JDatabaseTree 61 173 62
0.00%
JDatabaseTree.DbTreeRenderer 255 18 9
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.gui;
22   
23    import java.util.Locale;
24   
25    import jalview.util.MessageManager;
26    import jalview.ws.seqfetcher.DbSourceProxy;
27   
28    import java.awt.BorderLayout;
29    import java.awt.Component;
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.awt.event.MouseAdapter;
38    import java.awt.event.MouseEvent;
39    import java.util.ArrayList;
40    import java.util.HashSet;
41    import java.util.Hashtable;
42    import java.util.List;
43    import java.util.Vector;
44   
45    import javax.swing.JButton;
46    import javax.swing.JLabel;
47    import javax.swing.JPanel;
48    import javax.swing.JScrollPane;
49    import javax.swing.JTree;
50    import javax.swing.ToolTipManager;
51    import javax.swing.event.TreeSelectionEvent;
52    import javax.swing.event.TreeSelectionListener;
53    import javax.swing.tree.DefaultMutableTreeNode;
54    import javax.swing.tree.DefaultTreeCellRenderer;
55    import javax.swing.tree.DefaultTreeModel;
56    import javax.swing.tree.TreeCellRenderer;
57    import javax.swing.tree.TreeNode;
58    import javax.swing.tree.TreePath;
59    import javax.swing.tree.TreeSelectionModel;
60   
 
61    public class JDatabaseTree extends JalviewDialog implements KeyListener
62    {
63    boolean allowMultiSelections = false;
64   
65    public int action;
66   
 
67  0 toggle JButton getDatabaseSelectorButton()
68    {
69  0 final JButton viewdbs = new JButton(
70    MessageManager.getString("action.select_ddbb"));
71  0 viewdbs.addActionListener(new ActionListener()
72    {
73   
 
74  0 toggle @Override
75    public void actionPerformed(ActionEvent arg0)
76    {
77  0 showDialog();
78    }
79    });
80  0 return viewdbs;
81    }
82   
83    JScrollPane svp;
84   
85    JTree dbviews;
86   
87    private jalview.ws.SequenceFetcher sfetcher;
88   
89    private JLabel dbstatus, dbstatex;
90   
91    private JPanel mainPanel = new JPanel(new BorderLayout());
92   
 
93  0 toggle public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
94    {
95  0 mainPanel.add(this);
96  0 initDialogFrame(mainPanel, true, false, MessageManager
97    .getString("label.select_database_retrieval_source"), 650, 490);
98    /*
99    * Dynamically generated database list will need a translation function from
100    * internal source to externally distinct names. UNIPROT and UP_NAME are
101    * identical DB sources, and should be collapsed.
102    */
103  0 DefaultMutableTreeNode tn = null, root = new DefaultMutableTreeNode();
104  0 Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<>();
105  0 sfetcher = sfetch;
106  0 String dbs[] = sfetch.getSupportedDb();
107  0 Hashtable<String, String> ht = new Hashtable<>();
108  0 for (int i = 0; i < dbs.length; i++)
109    {
110  0 tn = source.get(dbs[i]);
111  0 List<DbSourceProxy> srcs = sfetch.getSourceProxy(dbs[i]);
112  0 if (tn == null)
113    {
114  0 source.put(dbs[i], tn = new DefaultMutableTreeNode(dbs[i], true));
115    }
116  0 for (DbSourceProxy dbp : srcs)
117    {
118  0 if (ht.get(dbp.getDbName()) == null)
119    {
120  0 tn.add(new DefaultMutableTreeNode(dbp, false));
121  0 ht.put(dbp.getDbName(), dbp.getDbName());
122    }
123    else
124    {
125  0 jalview.bin.Console.errPrintln("dupe ig for : " + dbs[i] + " \t"
126    + dbp.getDbName() + " (" + dbp.getDbSource() + ")");
127  0 source.remove(tn);
128    }
129    }
130    }
131  0 for (int i = 0; i < dbs.length; i++)
132    {
133  0 tn = source.get(dbs[i]);
134  0 if (tn == null)
135    {
136  0 continue;
137    }
138  0 if (tn.getChildCount() == 1)
139    {
140  0 DefaultMutableTreeNode ttn = (DefaultMutableTreeNode) tn
141    .getChildAt(0);
142    // remove nodes with only one child
143  0 tn.setUserObject(ttn.getUserObject());
144  0 tn.removeAllChildren();
145  0 source.put(dbs[i], tn);
146  0 tn.setAllowsChildren(false);
147    }
148  0 root.add(tn);
149    }
150    // and sort the tree
151  0 sortTreeNodes(root);
152  0 dbviews = new JTree(new DefaultTreeModel(root, false));
153  0 dbviews.setCellRenderer(new DbTreeRenderer(this));
154   
155  0 dbviews.getSelectionModel()
156    .setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
157  0 svp = new JScrollPane(dbviews);
158  0 svp.setMinimumSize(new Dimension(100, 200));
159  0 svp.setPreferredSize(new Dimension(200, 400));
160  0 svp.setMaximumSize(new Dimension(300, 600));
161   
162  0 JPanel panel = new JPanel(new BorderLayout());
163  0 panel.setSize(new Dimension(350, 220));
164  0 panel.add(svp);
165  0 dbviews.addTreeSelectionListener(new TreeSelectionListener()
166    {
167   
 
168  0 toggle @Override
169    public void valueChanged(TreeSelectionEvent arg0)
170    {
171  0 _setSelectionState();
172    }
173    });
174  0 dbviews.addMouseListener(new MouseAdapter()
175    {
176   
 
177  0 toggle @Override
178    public void mousePressed(MouseEvent e)
179    {
180  0 if (e.getClickCount() == 2)
181    {
182  0 okPressed();
183  0 closeDialog();
184    }
185    }
186    });
187  0 JPanel jc = new JPanel(new BorderLayout()),
188    j = new JPanel(new FlowLayout());
189  0 jc.add(svp, BorderLayout.CENTER);
190   
191  0 java.awt.Font f;
192    // TODO: make the panel stay a fixed size for longest dbname+example set.
193  0 JPanel dbstat = new JPanel(new GridLayout(2, 1));
194  0 dbstatus = new JLabel(" "); // set the height correctly for layout
195  0 dbstatus.setFont(f = JvSwingUtils.getLabelFont(false, true));
196  0 dbstatus.setSize(new Dimension(290, 50));
197  0 dbstatex = new JLabel(" ");
198  0 dbstatex.setFont(f);
199  0 dbstatex.setSize(new Dimension(290, 50));
200  0 dbstat.add(dbstatus);
201  0 dbstat.add(dbstatex);
202  0 jc.add(dbstat, BorderLayout.SOUTH);
203  0 jc.validate();
204  0 add(jc, BorderLayout.CENTER);
205  0 ok.setEnabled(false);
206  0 j.add(ok);
207  0 j.add(cancel);
208  0 add(j, BorderLayout.SOUTH);
209  0 dbviews.addKeyListener(this);
210  0 validate();
211    }
212   
 
213  0 toggle private void sortTreeNodes(DefaultMutableTreeNode root)
214    {
215  0 if (root.getChildCount() == 0)
216    {
217  0 return;
218    }
219  0 int count = root.getChildCount();
220  0 String[] names = new String[count];
221  0 DefaultMutableTreeNode[] nodes = new DefaultMutableTreeNode[count];
222  0 for (int i = 0; i < count; i++)
223    {
224  0 TreeNode node = root.getChildAt(i);
225  0 if (node instanceof DefaultMutableTreeNode)
226    {
227  0 DefaultMutableTreeNode child = (DefaultMutableTreeNode) node;
228  0 nodes[i] = child;
229  0 if (child.getUserObject() instanceof DbSourceProxy)
230    {
231  0 names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
232    .toLowerCase(Locale.ROOT);
233    }
234    else
235    {
236  0 names[i] = ((String) child.getUserObject())
237    .toLowerCase(Locale.ROOT);
238  0 sortTreeNodes(child);
239    }
240    }
241    else
242    {
243  0 throw new Error(MessageManager
244    .getString("error.implementation_error_cant_reorder_tree"));
245    }
246    }
247  0 jalview.util.QuickSort.sort(names, nodes);
248  0 root.removeAllChildren();
249  0 for (int i = count - 1; i >= 0; i--)
250    {
251  0 root.add(nodes[i]);
252    }
253    }
254   
 
255    private class DbTreeRenderer extends DefaultTreeCellRenderer
256    implements TreeCellRenderer
257    {
258    JDatabaseTree us;
259   
 
260  0 toggle public DbTreeRenderer(JDatabaseTree me)
261    {
262  0 us = me;
263  0 ToolTipManager.sharedInstance().registerComponent(dbviews);
264    }
265   
 
266  0 toggle private Component returnLabel(String txt)
267    {
268  0 JLabel jl = new JLabel(txt);
269  0 jl.setFont(JvSwingUtils.getLabelFont());
270  0 return jl;
271    }
272   
 
273  0 toggle @Override
274    public Component getTreeCellRendererComponent(JTree tree, Object value,
275    boolean selected, boolean expanded, boolean leaf, int row,
276    boolean hasFocus)
277    {
278  0 String val = "";
279  0 if (value != null && value instanceof DefaultMutableTreeNode)
280    {
281  0 DefaultMutableTreeNode vl = (DefaultMutableTreeNode) value;
282  0 value = vl.getUserObject();
283  0 if (value instanceof DbSourceProxy)
284    {
285  0 val = ((DbSourceProxy) value).getDbName();
286  0 if (((DbSourceProxy) value).getDescription() != null)
287    { // getName()
288  0 this.setToolTipText(((DbSourceProxy) value).getDescription());
289    }
290    }
291    else
292    {
293  0 if (value instanceof String)
294    {
295  0 val = (String) value;
296    }
297    }
298    }
299  0 if (value == null)
300    {
301  0 val = "";
302    }
303  0 return super.getTreeCellRendererComponent(tree, val, selected,
304    expanded, leaf, row, hasFocus);
305   
306    }
307    }
308   
309    List<DbSourceProxy> oldselection, selection = null;
310   
311    TreePath[] tsel = null, oldtsel = null;
312   
 
313  0 toggle @Override
314    protected void raiseClosed()
315    {
316  0 for (ActionListener al : lstners)
317    {
318  0 al.actionPerformed(null);
319    }
320    }
321   
 
322  0 toggle @Override
323    protected void okPressed()
324    {
325  0 _setSelectionState();
326    }
327   
 
328  0 toggle @Override
329    protected void cancelPressed()
330    {
331  0 selection = oldselection;
332  0 tsel = oldtsel;
333  0 _revertSelectionState();
334  0 closeDialog();
335    }
336   
 
337  0 toggle void showDialog()
338    {
339  0 oldselection = selection;
340  0 oldtsel = tsel;
341  0 validate();
342  0 waitForInput();
343    }
344   
 
345  0 toggle public boolean hasSelection()
346    {
347  0 return selection == null ? false : selection.size() == 0 ? false : true;
348    }
349   
 
350  0 toggle public List<DbSourceProxy> getSelectedSources()
351    {
352  0 return selection;
353    }
354   
355    /**
356    * disable or enable selection handler
357    */
358    boolean handleSelections = true;
359   
 
360  0 toggle private void _setSelectionState()
361    {
362  0 if (!handleSelections)
363    {
364  0 return;
365    }
366  0 ok.setEnabled(false);
367  0 if (dbviews.getSelectionCount() == 0)
368    {
369  0 selection = null;
370    }
371   
372  0 tsel = dbviews.getSelectionPaths();
373  0 boolean forcedFirstChild = false;
374  0 List<DbSourceProxy> srcs = new ArrayList<>();
375  0 if (tsel != null)
376    {
377  0 for (TreePath tp : tsel)
378    {
379  0 DefaultMutableTreeNode admt,
380    dmt = (DefaultMutableTreeNode) tp.getLastPathComponent();
381  0 if (dmt.getUserObject() != null)
382    {
383    /*
384    * enable OK button once a selection has been made
385    */
386  0 ok.setEnabled(true);
387  0 if (dmt.getUserObject() instanceof DbSourceProxy)
388    {
389  0 srcs.add((DbSourceProxy) dmt.getUserObject());
390    }
391    else
392    {
393  0 if (allowMultiSelections)
394    {
395  0 srcs.addAll(sfetcher
396    .getSourceProxy((String) dmt.getUserObject()));
397    }
398    else
399    {
400  0 srcs.add(sfetcher.getSourceProxy((String) dmt.getUserObject())
401    .get(0));
402  0 forcedFirstChild = true;
403    }
404    }
405    }
406    }
407    }
408  0 updateDbStatus(srcs, forcedFirstChild);
409  0 selection = srcs;
410    }
411   
 
412  0 toggle private void _revertSelectionState()
413    {
414  0 handleSelections = false;
415  0 if (selection == null || selection.size() == 0)
416    {
417  0 dbviews.clearSelection();
418    }
419    else
420    {
421  0 dbviews.setSelectionPaths(tsel);
422    }
423  0 handleSelections = true;
424    }
425   
 
426  0 toggle private void updateDbStatus(List<DbSourceProxy> srcs,
427    boolean forcedFirstChild)
428    {
429  0 int x = 0;
430  0 String nm = "", qr = "";
431  0 for (DbSourceProxy dbs : srcs)
432    {
433  0 String tq = dbs.getTestQuery();
434  0 nm = dbs.getDbName();
435  0 if (tq != null && tq.trim().length() > 0 && dbs.isValidReference(tq))
436    {
437  0 qr = tq;
438  0 x++;
439    }
440    }
441   
442  0 dbstatex.setText(" ");
443  0 if (allowMultiSelections)
444    {
445  0 dbstatus.setText(MessageManager.formatMessage(
446    "label.selected_database_to_fetch_from", new String[]
447    { Integer.valueOf(srcs.size()).toString(),
448  0 (srcs.size() == 1 ? "" : "s"),
449  0 (srcs.size() > 0
450    ? " with " + x + " test quer"
451  0 + (x == 1 ? "y" : "ies")
452    : ".") }));
453    }
454    else
455    {
456  0 if (nm.length() > 0)
457    {
458  0 dbstatus.setText(MessageManager
459    .formatMessage("label.database_param", new String[]
460    { nm }));
461  0 if (qr.length() > 0)
462    {
463  0 dbstatex.setText(MessageManager
464    .formatMessage("label.example_param", new String[]
465    { qr }));
466    }
467    }
468    else
469    {
470  0 dbstatus.setText(" ");
471    }
472    }
473  0 dbstatus.invalidate();
474  0 dbstatex.invalidate();
475    }
476   
 
477  0 toggle public String getSelectedItem()
478    {
479  0 if (hasSelection())
480    {
481  0 return getSelectedSources().get(0).getDbName();
482    }
483  0 return null;
484    }
485   
 
486  0 toggle public String getExampleQueries()
487    {
488  0 if (!hasSelection())
489    {
490  0 return null;
491    }
492  0 StringBuffer sb = new StringBuffer();
493  0 HashSet<String> hs = new HashSet<>();
494  0 for (DbSourceProxy dbs : getSelectedSources())
495    {
496  0 String tq = dbs.getTestQuery();
497  0 ;
498  0 if (hs.add(tq))
499    {
500  0 if (sb.length() > 0)
501    {
502  0 sb.append(";");
503    }
504  0 sb.append(tq);
505    }
506    }
507  0 return sb.toString();
508    }
509   
510    List<ActionListener> lstners = new Vector<>();
511   
 
512  0 toggle public void addActionListener(ActionListener actionListener)
513    {
514  0 lstners.add(actionListener);
515    }
516   
 
517  0 toggle public void removeActionListener(ActionListener actionListener)
518    {
519  0 lstners.remove(actionListener);
520    }
521   
 
522  0 toggle @Override
523    public void keyPressed(KeyEvent arg0)
524    {
525  0 if (!arg0.isConsumed() && arg0.getKeyCode() == KeyEvent.VK_ENTER)
526    {
527  0 action = arg0.getKeyCode();
528  0 okPressed();
529  0 closeDialog();
530    }
531  0 if (!arg0.isConsumed() && arg0.getKeyChar() == KeyEvent.VK_ESCAPE)
532    {
533  0 action = arg0.getKeyCode();
534  0 cancelPressed();
535    }
536    }
537   
 
538  0 toggle @Override
539    public void keyReleased(KeyEvent arg0)
540    {
541    // TODO Auto-generated method stub
542   
543    }
544   
 
545  0 toggle @Override
546    public void keyTyped(KeyEvent arg0)
547    {
548    // TODO Auto-generated method stub
549   
550    }
551   
 
552  0 toggle @Override
553    public void setVisible(boolean arg0)
554    {
555  0 jalview.bin.Console.outPrintln("setVisible: " + arg0);
556  0 super.setVisible(arg0);
557    }
558    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.