Clover icon

Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.jbgui

File GStructureChooser.java

 

Coverage histogram

../../img/srcFileCovDistChart5.png
39% of files have more coverage

Code metrics

54
260
58
5
967
739
97
0.37
4.48
11.6
1.67

Classes

Class Line # Actions
GStructureChooser 86 220 69
0.4569536445.7%
GStructureChooser.FilterOption 708 13 10
0.6521739465.2%
GStructureChooser.AssociateSeqOptions 794 9 8
0.277777827.8%
GStructureChooser.AssociateSeqPanel 850 10 6
0.823529482.4%
GStructureChooser.CustomComboSeparatorsRenderer 908 8 4
1.0100%
 

Contributing tests

This file is covered by 1 test. .

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   
22    package jalview.jbgui;
23   
24    import jalview.datamodel.SequenceI;
25    import jalview.fts.api.FTSDataColumnI;
26    import jalview.fts.core.FTSDataColumnPreferences;
27    import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
28    import jalview.fts.service.pdb.PDBFTSRestClient;
29    import jalview.gui.AlignmentPanel;
30    import jalview.gui.Desktop;
31    import jalview.gui.JvSwingUtils;
32    import jalview.gui.StructureViewer;
33    import jalview.util.MessageManager;
34   
35    import java.awt.BorderLayout;
36    import java.awt.CardLayout;
37    import java.awt.Component;
38    import java.awt.Dimension;
39    import java.awt.FlowLayout;
40    import java.awt.Font;
41    import java.awt.GridLayout;
42    import java.awt.event.ActionEvent;
43    import java.awt.event.ActionListener;
44    import java.awt.event.ItemEvent;
45    import java.awt.event.ItemListener;
46    import java.awt.event.KeyAdapter;
47    import java.awt.event.KeyEvent;
48    import java.awt.event.MouseAdapter;
49    import java.awt.event.MouseEvent;
50    import java.util.Arrays;
51    import java.util.HashMap;
52    import java.util.Map;
53   
54    import javax.swing.ImageIcon;
55    import javax.swing.JButton;
56    import javax.swing.JCheckBox;
57    import javax.swing.JComboBox;
58    import javax.swing.JFrame;
59    import javax.swing.JInternalFrame;
60    import javax.swing.JLabel;
61    import javax.swing.JList;
62    import javax.swing.JPanel;
63    import javax.swing.JScrollPane;
64    import javax.swing.JSeparator;
65    import javax.swing.JTabbedPane;
66    import javax.swing.JTable;
67    import javax.swing.JTextField;
68    import javax.swing.ListCellRenderer;
69    import javax.swing.Timer;
70    import javax.swing.event.ChangeEvent;
71    import javax.swing.event.ChangeListener;
72    import javax.swing.event.DocumentEvent;
73    import javax.swing.event.DocumentListener;
74    import javax.swing.event.InternalFrameEvent;
75    import javax.swing.table.TableColumn;
76   
77    import net.miginfocom.swing.MigLayout;
78   
79    @SuppressWarnings("serial")
80    /**
81    * GUI layout for structure chooser
82    *
83    * @author tcnofoegbu
84    *
85    */
 
86    public abstract class GStructureChooser extends JPanel
87    implements ItemListener
88    {
89    private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
90   
91    protected static final String VIEWS_FILTER = "VIEWS_FILTER";
92   
93    protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
94   
95    protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
96   
97    /*
98    * 'cached' structure view
99    */
100    protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
101   
102    protected JPanel statusPanel = new JPanel();
103   
104    public JLabel statusBar = new JLabel();
105   
106    protected String frameTitle = MessageManager
107    .getString("label.structure_chooser");
108   
109    protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
110   
111    protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
112   
113    protected AlignmentPanel ap;
114   
115    protected StringBuilder errorWarning = new StringBuilder();
116   
117    protected JButton btn_add;
118   
119    protected JButton btn_newView;
120   
121    protected JButton btn_pdbFromFile = new JButton();
122   
123    protected JCheckBox chk_superpose = new JCheckBox(
124    MessageManager.getString("label.superpose_structures"));
125   
126    protected JTextField txt_search = new JTextField(14);
127   
128    protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
129   
130    protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
131    .getLayout());
132   
133    protected JCheckBox chk_invertFilter = new JCheckBox(
134    MessageManager.getString("label.invert"));
135   
136    protected ImageIcon loadingImage = new ImageIcon(
137    getClass().getResource("/images/loading.gif"));
138   
139    protected ImageIcon goodImage = new ImageIcon(
140    getClass().getResource("/images/good.png"));
141   
142    protected ImageIcon errorImage = new ImageIcon(
143    getClass().getResource("/images/error.png"));
144   
145    protected ImageIcon warningImage = new ImageIcon(
146    getClass().getResource("/images/warning.gif"));
147   
148    protected JLabel lbl_loading = new JLabel(loadingImage);
149   
150    protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
151   
152    protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
153   
154    protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel();
155   
156    protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel();
157   
158    protected JComboBox<StructureViewer> targetView = new JComboBox<>();
159   
160    protected JTable tbl_local_pdb = new JTable();
161   
162    protected JTabbedPane pnl_filter = new JTabbedPane();
163   
164    protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
165    PreferenceSource.STRUCTURE_CHOOSER,
166    PDBFTSRestClient.getInstance());
167   
168    protected FTSDataColumnI[] previousWantedFields;
169   
170    protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
171   
172    private JTable tbl_summary = new JTable()
173    {
174    private boolean inLayout;
175   
 
176  11 toggle @Override
177    public boolean getScrollableTracksViewportWidth()
178    {
179  11 return hasExcessWidth();
180   
181    }
182   
 
183  2 toggle @Override
184    public void doLayout()
185    {
186  2 if (hasExcessWidth())
187    {
188  2 autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
189    }
190  2 inLayout = true;
191  2 super.doLayout();
192  2 inLayout = false;
193  2 autoResizeMode = AUTO_RESIZE_OFF;
194    }
195   
 
196  13 toggle protected boolean hasExcessWidth()
197    {
198  13 return getPreferredSize().width < getParent().getWidth();
199    }
200   
 
201  0 toggle @Override
202    public void columnMarginChanged(ChangeEvent e)
203    {
204  0 if (isEditing())
205    {
206  0 removeEditor();
207    }
208  0 TableColumn resizingColumn = getTableHeader().getResizingColumn();
209    // Need to do this here, before the parent's
210    // layout manager calls getPreferredSize().
211  0 if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
212    && !inLayout)
213    {
214  0 resizingColumn.setPreferredWidth(resizingColumn.getWidth());
215  0 String colHeader = resizingColumn.getHeaderValue().toString();
216  0 tempUserPrefs.put(colHeader, resizingColumn.getWidth());
217    }
218  0 resizeAndRepaint();
219    }
220   
 
221  0 toggle @Override
222    public String getToolTipText(MouseEvent evt)
223    {
224  0 String toolTipText = null;
225  0 java.awt.Point pnt = evt.getPoint();
226  0 int rowIndex = rowAtPoint(pnt);
227  0 int colIndex = columnAtPoint(pnt);
228   
229  0 try
230    {
231  0 if (getValueAt(rowIndex, colIndex) == null)
232    {
233  0 return null;
234    }
235  0 toolTipText = getValueAt(rowIndex, colIndex).toString();
236    } catch (Exception e)
237    {
238    // e.printStackTrace();
239    }
240  0 toolTipText = (toolTipText == null ? null
241  0 : (toolTipText.length() > 500
242    ? JvSwingUtils.wrapTooltip(true,
243    "\"" + toolTipText.subSequence(0, 500)
244    + "...\"")
245    : JvSwingUtils.wrapTooltip(true, toolTipText)));
246  0 return toolTipText;
247    }
248    };
249   
 
250  1 toggle public GStructureChooser()
251    {
252  1 try
253    {
254  1 jbInit();
255  1 mainFrame.setVisible(false);
256  1 mainFrame.invalidate();
257  1 mainFrame.pack();
258    } catch (Exception e)
259    {
260  0 System.out.println(e); // for JavaScript TypeError
261  0 e.printStackTrace();
262    }
263    }
264   
265    // BH SwingJS optimization
266    // (a) 100-ms interruptable timer for text entry -- BH 1/10/2019
267    // (b) two-character minimum, at least for JavaScript.
268   
269    private Timer timer;
270   
 
271  0 toggle protected void txt_search_ActionPerformedDelayed() {
272  0 if (timer != null) {
273  0 timer.stop();
274    }
275  0 timer = new Timer(300, new ActionListener() {
276   
 
277  0 toggle @Override
278    public void actionPerformed(ActionEvent e) {
279  0 txt_search_ActionPerformed();
280    }
281    });
282  0 timer.setRepeats(false);
283  0 timer.start();
284    }
285    //
286   
287    /**
288    * Initializes the GUI default properties
289    *
290    * @throws Exception
291    */
 
292  1 toggle private void jbInit() throws Exception
293    {
294  1 Integer width = tempUserPrefs.get("structureChooser.width") == null
295    ? 800
296    : tempUserPrefs.get("structureChooser.width");
297  1 Integer height = tempUserPrefs.get("structureChooser.height") == null
298    ? 400
299    : tempUserPrefs.get("structureChooser.height");
300  1 tbl_summary.setAutoCreateRowSorter(true);
301  1 tbl_summary.getTableHeader().setReorderingAllowed(false);
302  1 tbl_summary.addMouseListener(new MouseAdapter()
303    {
 
304  0 toggle @Override
305    public void mouseClicked(MouseEvent e)
306    {
307  0 validateSelections();
308    }
309   
 
310  0 toggle @Override
311    public void mouseReleased(MouseEvent e)
312    {
313  0 validateSelections();
314    }
315    });
316  1 tbl_summary.addKeyListener(new KeyAdapter()
317    {
 
318  0 toggle @Override
319    public void keyPressed(KeyEvent evt)
320    {
321  0 validateSelections();
322  0 switch (evt.getKeyCode())
323    {
324  0 case KeyEvent.VK_ESCAPE: // escape key
325  0 mainFrame.dispose();
326  0 break;
327  0 case KeyEvent.VK_ENTER: // enter key
328  0 if (btn_add.isEnabled())
329    {
330  0 add_ActionPerformed();
331    }
332  0 break;
333  0 case KeyEvent.VK_TAB: // tab key
334  0 if (evt.isShiftDown())
335    {
336  0 pnl_filter.requestFocus();
337    }
338    else
339    {
340  0 btn_add.requestFocus();
341    }
342  0 evt.consume();
343  0 break;
344  0 default:
345  0 return;
346    }
347    }
348    });
349   
350  1 JButton btn_cancel = new JButton(
351    MessageManager.getString("action.cancel"));
352  1 btn_cancel.setFont(VERDANA_12);
353  1 btn_cancel.addActionListener(new java.awt.event.ActionListener()
354    {
 
355  0 toggle @Override
356    public void actionPerformed(ActionEvent e)
357    {
358  0 closeAction(pnl_filter.getHeight());
359    }
360    });
361  1 btn_cancel.addKeyListener(new KeyAdapter()
362    {
 
363  0 toggle @Override
364    public void keyPressed(KeyEvent evt)
365    {
366  0 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
367    {
368  0 closeAction(pnl_filter.getHeight());
369    }
370    }
371    });
372   
373  1 tbl_local_pdb.setAutoCreateRowSorter(true);
374  1 tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
375  1 tbl_local_pdb.addMouseListener(new MouseAdapter()
376    {
 
377  0 toggle @Override
378    public void mouseClicked(MouseEvent e)
379    {
380  0 validateSelections();
381    }
382   
 
383  0 toggle @Override
384    public void mouseReleased(MouseEvent e)
385    {
386  0 validateSelections();
387    }
388    });
389  1 tbl_local_pdb.addKeyListener(new KeyAdapter()
390    {
 
391  0 toggle @Override
392    public void keyPressed(KeyEvent evt)
393    {
394  0 validateSelections();
395  0 switch (evt.getKeyCode())
396    {
397  0 case KeyEvent.VK_ESCAPE: // escape key
398  0 mainFrame.dispose();
399  0 break;
400  0 case KeyEvent.VK_ENTER: // enter key
401  0 if (btn_add.isEnabled())
402    {
403  0 add_ActionPerformed();
404    }
405  0 break;
406  0 case KeyEvent.VK_TAB: // tab key
407  0 if (evt.isShiftDown())
408    {
409  0 cmb_filterOption.requestFocus();
410    }
411    else
412    {
413  0 if (btn_add.isEnabled())
414    {
415  0 btn_add.requestFocus();
416    }
417    else
418    {
419  0 btn_cancel.requestFocus();
420    }
421    }
422  0 evt.consume();
423  0 break;
424  0 default:
425  0 return;
426    }
427    }
428    });
429   
430  1 btn_newView = new JButton(MessageManager.getString("action.new_view"));
431  1 btn_newView.setFont(VERDANA_12);
432  1 btn_newView.addActionListener(new java.awt.event.ActionListener()
433    {
 
434  0 toggle @Override
435    public void actionPerformed(ActionEvent e)
436    {
437  0 newView_ActionPerformed();
438    }
439    });
440  1 btn_newView.addKeyListener(new KeyAdapter()
441    {
 
442  0 toggle @Override
443    public void keyPressed(KeyEvent evt)
444    {
445  0 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
446    {
447  0 newView_ActionPerformed();
448    }
449    }
450    });
451   
452  1 btn_add = new JButton(MessageManager.getString("action.add"));
453  1 btn_add.setFont(VERDANA_12);
454  1 btn_add.addActionListener(new java.awt.event.ActionListener()
455    {
 
456  0 toggle @Override
457    public void actionPerformed(ActionEvent e)
458    {
459  0 add_ActionPerformed();
460    }
461    });
462  1 btn_add.addKeyListener(new KeyAdapter()
463    {
 
464  0 toggle @Override
465    public void keyPressed(KeyEvent evt)
466    {
467  0 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
468    {
469  0 add_ActionPerformed();
470    }
471    }
472    });
473   
474  1 btn_pdbFromFile.setFont(VERDANA_12);
475  1 String btn_title = MessageManager.getString("label.select_pdb_file");
476  1 btn_pdbFromFile.setText(btn_title + " ");
477  1 btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
478    {
 
479  0 toggle @Override
480    public void actionPerformed(ActionEvent e)
481    {
482  0 pdbFromFile_actionPerformed();
483    }
484    });
485  1 btn_pdbFromFile.addKeyListener(new KeyAdapter()
486    {
 
487  0 toggle @Override
488    public void keyPressed(KeyEvent evt)
489    {
490  0 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
491    {
492  0 pdbFromFile_actionPerformed();
493    }
494    }
495    });
496   
497  1 JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
498  1 scrl_foundStructures.setPreferredSize(new Dimension(width, height));
499   
500  1 JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
501  1 scrl_localPDB.setPreferredSize(new Dimension(width, height));
502  1 scrl_localPDB.setHorizontalScrollBarPolicy(
503    JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
504   
505  1 chk_invertFilter.setFont(VERDANA_12);
506  1 txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
507    MessageManager.getString("label.enter_pdb_id_tip")));
508  1 txt_search.getDocument().addDocumentListener(new DocumentListener()
509    {
 
510  0 toggle @Override
511    public void insertUpdate(DocumentEvent e)
512    {
513  0 txt_search_ActionPerformedDelayed();
514    }
515   
 
516  0 toggle @Override
517    public void removeUpdate(DocumentEvent e)
518    {
519  0 txt_search_ActionPerformedDelayed();
520    }
521   
 
522  0 toggle @Override
523    public void changedUpdate(DocumentEvent e)
524    {
525  0 txt_search_ActionPerformedDelayed();
526    }
527    });
528   
529  1 cmb_filterOption.setFont(VERDANA_12);
530  1 cmb_filterOption.setToolTipText(
531    MessageManager.getString("info.select_filter_option"));
532  1 cmb_filterOption.addItemListener(this);
533    // add CustomComboSeparatorsRenderer to filter option combo-box
534  1 cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
535    (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
536    {
 
537  16 toggle @Override
538    protected boolean addSeparatorAfter(JList list, FilterOption value,
539    int index)
540    {
541  16 return value.isAddSeparatorAfter();
542    }
543    });
544   
545  1 chk_invertFilter.addItemListener(this);
546   
547  1 targetView.setVisible(false);
548   
549  1 JPanel actionsPanel = new JPanel(new MigLayout());
550  1 actionsPanel.add(targetView, "left");
551  1 actionsPanel.add(btn_add, "wrap");
552  1 actionsPanel.add(chk_superpose, "left");
553  1 actionsPanel.add(btn_newView);
554  1 actionsPanel.add(btn_cancel, "right");
555   
556  1 JPanel pnl_main = new JPanel();
557  1 pnl_main.add(cmb_filterOption);
558  1 pnl_main.add(lbl_loading);
559  1 pnl_main.add(chk_invertFilter);
560  1 lbl_loading.setVisible(false);
561   
562  1 JPanel pnl_fileChooser = new JPanel(new FlowLayout());
563  1 pnl_fileChooser.add(btn_pdbFromFile);
564  1 pnl_fileChooser.add(lbl_fromFileStatus);
565  1 JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
566  1 pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
567  1 pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
568   
569  1 JPanel pnl_idInput = new JPanel(new FlowLayout());
570  1 pnl_idInput.add(txt_search);
571  1 pnl_idInput.add(lbl_pdbManualFetchStatus);
572   
573  1 JPanel pnl_idInputBL = new JPanel(new BorderLayout());
574  1 pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
575  1 pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
576   
577  1 final String foundStructureSummary = MessageManager
578    .getString("label.found_structures_summary");
579  1 final String configureCols = MessageManager
580    .getString("label.configure_displayed_columns");
581  1 ChangeListener changeListener = new ChangeListener()
582    {
 
583  1 toggle @Override
584    public void stateChanged(ChangeEvent changeEvent)
585    {
586  1 JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
587    .getSource();
588  1 int index = sourceTabbedPane.getSelectedIndex();
589  1 btn_add.setVisible(targetView.isVisible());
590  1 btn_newView.setVisible(true);
591  1 btn_cancel.setVisible(true);
592  1 if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
593    {
594  0 btn_add.setEnabled(false);
595  0 btn_cancel.setEnabled(false);
596  0 btn_add.setVisible(false);
597  0 btn_newView.setEnabled(false);
598  0 btn_cancel.setVisible(false);
599  0 previousWantedFields = pdbDocFieldPrefs
600    .getStructureSummaryFields()
601    .toArray(new FTSDataColumnI[0]);
602    }
603  1 if (sourceTabbedPane.getTitleAt(index)
604    .equals(foundStructureSummary))
605    {
606  1 btn_cancel.setEnabled(true);
607  1 if (wantedFieldsUpdated())
608    {
609  1 tabRefresh();
610    }
611    else
612    {
613  0 validateSelections();
614    }
615    }
616    }
617    };
618  1 pnl_filter.addChangeListener(changeListener);
619  1 pnl_filter.setPreferredSize(new Dimension(width, height));
620  1 pnl_filter.add(foundStructureSummary, scrl_foundStructures);
621  1 pnl_filter.add(configureCols, pdbDocFieldPrefs);
622   
623  1 JPanel pnl_locPDB = new JPanel(new BorderLayout());
624  1 pnl_locPDB.add(scrl_localPDB);
625   
626  1 pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
627  1 pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
628  1 pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
629  1 pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
630   
631  1 this.setLayout(new BorderLayout());
632  1 this.add(pnl_main, java.awt.BorderLayout.NORTH);
633  1 this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
634    // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
635  1 statusPanel.setLayout(new GridLayout());
636   
637  1 JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
638  1 pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER);
639  1 pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
640  1 statusPanel.add(statusBar, null);
641  1 this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
642   
643  1 mainFrame.addInternalFrameListener(
644    new javax.swing.event.InternalFrameAdapter()
645    {
 
646  0 toggle @Override
647    public void internalFrameClosing(InternalFrameEvent e)
648    {
649  0 closeAction(pnl_filter.getHeight());
650    }
651    });
652  1 mainFrame.setVisible(true);
653  1 mainFrame.setContentPane(this);
654  1 mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
655  1 Integer x = tempUserPrefs.get("structureChooser.x");
656  1 Integer y = tempUserPrefs.get("structureChooser.y");
657  1 if (x != null && y != null)
658    {
659  0 mainFrame.setLocation(x, y);
660    }
661  1 Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
662    }
663   
664   
 
665  0 toggleprotected void closeAction(int preferredHeight)
666    {
667    // System.out.println(">>>>>>>>>> closing internal frame!!!");
668    // System.out.println("width : " + mainFrame.getWidth());
669    // System.out.println("heigh : " + mainFrame.getHeight());
670    // System.out.println("x : " + mainFrame.getX());
671    // System.out.println("y : " + mainFrame.getY());
672  0 tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
673  0 tempUserPrefs.put("structureChooser.height", preferredHeight);
674  0 tempUserPrefs.put("structureChooser.x", mainFrame.getX());
675  0 tempUserPrefs.put("structureChooser.y", mainFrame.getY());
676  0 mainFrame.dispose();
677    }
678   
 
679  1 toggle public boolean wantedFieldsUpdated()
680    {
681  1 if (previousWantedFields == null)
682    {
683  1 return true;
684    }
685   
686  0 FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
687    .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
688  0 return Arrays.equals(currentWantedFields, previousWantedFields) ? false
689    : true;
690   
691    }
692   
 
693  0 toggle @Override
694    /**
695    * Event listener for the 'filter' combo-box and 'invert' check-box
696    */
697    public void itemStateChanged(ItemEvent e)
698    {
699  0 stateChanged(e);
700    }
701   
702    /**
703    * This inner class provides the data model for the structure filter combo-box
704    *
705    * @author tcnofoegbu
706    *
707    */
 
708    public class FilterOption
709    {
710    private String name;
711   
712    private String value;
713   
714    private String view;
715   
716    private boolean addSeparatorAfter;
717   
718    /**
719    * Model for structure filter option
720    *
721    * @param name
722    * - the name of the Option
723    * @param value
724    * - the value of the option
725    * @param view
726    * - the category of the filter option
727    * @param addSeparatorAfter
728    * - if true, a horizontal separator is rendered immediately after
729    * this filter option, otherwise
730    */
 
731  26 toggle public FilterOption(String name, String value, String view,
732    boolean addSeparatorAfter)
733    {
734  26 this.name = name;
735  26 this.value = value;
736  26 this.view = view;
737  26 this.addSeparatorAfter = addSeparatorAfter;
738    }
739   
 
740  1 toggle public String getName()
741    {
742  1 return name;
743    }
744   
 
745  0 toggle public void setName(String name)
746    {
747  0 this.name = name;
748    }
749   
 
750  1 toggle public String getValue()
751    {
752  1 return value;
753    }
754   
 
755  0 toggle public void setValue(String value)
756    {
757  0 this.value = value;
758    }
759   
 
760  6 toggle public String getView()
761    {
762  6 return view;
763    }
764   
 
765  0 toggle public void setView(String view)
766    {
767  0 this.view = view;
768    }
769   
 
770  19 toggle @Override
771    public String toString()
772    {
773  19 return this.name;
774    }
775   
 
776  16 toggle public boolean isAddSeparatorAfter()
777    {
778  16 return addSeparatorAfter;
779    }
780   
 
781  0 toggle public void setAddSeparatorAfter(boolean addSeparatorAfter)
782    {
783  0 this.addSeparatorAfter = addSeparatorAfter;
784    }
785    }
786   
787    /**
788    * This inner class provides the provides the data model for associate
789    * sequence combo-box - cmb_assSeq
790    *
791    * @author tcnofoegbu
792    *
793    */
 
794    public class AssociateSeqOptions
795    {
796    private SequenceI sequence;
797   
798    private String name;
799   
 
800  0 toggle public AssociateSeqOptions(SequenceI seq)
801    {
802  0 this.sequence = seq;
803  0 this.name = (seq.getName().length() >= 23)
804    ? seq.getName().substring(0, 23)
805    : seq.getName();
806    }
807   
 
808  2 toggle public AssociateSeqOptions(String name, SequenceI seq)
809    {
810  2 this.name = name;
811  2 this.sequence = seq;
812    }
813   
 
814  2 toggle @Override
815    public String toString()
816    {
817  2 return name;
818    }
819   
 
820  0 toggle public String getName()
821    {
822  0 return name;
823    }
824   
 
825  0 toggle public void setName(String name)
826    {
827  0 this.name = name;
828    }
829   
 
830  0 toggle public SequenceI getSequence()
831    {
832  0 return sequence;
833    }
834   
 
835  0 toggle public void setSequence(SequenceI sequence)
836    {
837  0 this.sequence = sequence;
838    }
839   
840    }
841   
842    /**
843    * This inner class holds the Layout and configuration of the panel which
844    * handles association of manually fetched structures to a unique sequence
845    * when more than one sequence selection is made
846    *
847    * @author tcnofoegbu
848    *
849    */
 
850    public class AssociateSeqPanel extends JPanel implements ItemListener
851    {
852    private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
853   
854    private JLabel lbl_associateSeq = new JLabel();
855   
 
856  2 toggle public AssociateSeqPanel()
857    {
858  2 this.setLayout(new FlowLayout());
859  2 this.add(cmb_assSeq);
860  2 this.add(lbl_associateSeq);
861  2 cmb_assSeq.setToolTipText(
862    MessageManager.getString("info.associate_wit_sequence"));
863  2 cmb_assSeq.addItemListener(this);
864    }
865   
 
866  2 toggle public void loadCmbAssSeq()
867    {
868  2 populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
869    }
870   
 
871  3 toggle public JComboBox<AssociateSeqOptions> getCmb_assSeq()
872    {
873  3 return cmb_assSeq;
874    }
875   
 
876  0 toggle public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
877    {
878  0 this.cmb_assSeq = cmb_assSeq;
879    }
880   
 
881  2 toggle @Override
882    public void itemStateChanged(ItemEvent e)
883    {
884  2 if (e.getStateChange() == ItemEvent.SELECTED)
885    {
886  2 cmbAssSeqStateChanged();
887    }
888    }
889    }
890   
 
891  0 toggle public JTable getResultTable()
892    {
893  0 return tbl_summary;
894    }
895   
 
896  4 toggle public JComboBox<FilterOption> getCmbFilterOption()
897    {
898  4 return cmb_filterOption;
899    }
900   
901    /**
902    * Custom ListCellRenderer for adding a separator between different categories
903    * of structure chooser filter option drop-down.
904    *
905    * @author tcnofoegbu
906    *
907    */
 
908    public abstract class CustomComboSeparatorsRenderer
909    implements ListCellRenderer<Object>
910    {
911    private ListCellRenderer<Object> regent;
912   
913    private JPanel separatorPanel = new JPanel(new BorderLayout());
914   
915    private JSeparator jSeparator = new JSeparator();
916   
 
917  1 toggle public CustomComboSeparatorsRenderer(
918    ListCellRenderer<Object> listCellRenderer)
919    {
920  1 this.regent = listCellRenderer;
921    }
922   
 
923  18 toggle @Override
924    public Component getListCellRendererComponent(JList list, Object value,
925    int index, boolean isSelected, boolean cellHasFocus)
926    {
927   
928  18 Component comp = regent.getListCellRendererComponent(list, value,
929    index, isSelected, cellHasFocus);
930  18 if (index != -1
931    && addSeparatorAfter(list, (FilterOption) value, index))
932    {
933  1 separatorPanel.removeAll();
934  1 separatorPanel.add(comp, BorderLayout.CENTER);
935  1 separatorPanel.add(jSeparator, BorderLayout.SOUTH);
936  1 return separatorPanel;
937    }
938    else
939    {
940  17 return comp;
941    }
942    }
943   
944    protected abstract boolean addSeparatorAfter(JList list,
945    FilterOption value, int index);
946    }
947   
948    protected abstract void stateChanged(ItemEvent e);
949   
950    protected abstract void add_ActionPerformed();
951   
952    protected abstract void newView_ActionPerformed();
953   
954    protected abstract void pdbFromFile_actionPerformed();
955   
956    protected abstract void txt_search_ActionPerformed();
957   
958    protected abstract void populateCmbAssociateSeqOptions(
959    JComboBox<AssociateSeqOptions> cmb_assSeq,
960    JLabel lbl_associateSeq);
961   
962    protected abstract void cmbAssSeqStateChanged();
963   
964    protected abstract void tabRefresh();
965   
966    protected abstract void validateSelections();
967    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.