Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
GStructureChooser	84	214	66	154	0.4726027347.3%	Show methods
GStructureChooser.FilterOption	683	13	10	10	0.565217456.5%	Show methods
GStructureChooser.AssociateSeqOptions	769	9	8	18	0.00%	Show methods
GStructureChooser.AssociateSeqPanel	825	10	6	11	0.352941235.3%	Show methods
GStructureChooser.CustomComboSeparatorsRenderer	883	8	4	0	1.0100%	Show methods

Class GStructureChooser

Class GStructureChooser	Line # 84	Total Statements 214	Complexity 66	Uncovered Elements 154	TOTAL Coverage 0.4726027347.3%
getScrollableTracksViewportWidth() : boolean   getScrollableTracksViewportWidth() : boolean	174174	1.01	1.01	0.00	1.0 1.0100%
doLayout() : void   doLayout() : void	181181	6.06	2.02	1.01	0.875 0.87587.5%
hasExcessWidth() : boolean   hasExcessWidth() : boolean	194194	1.01	1.01	0.00	1.0 1.0100%
columnMarginChanged(ChangeEvent) : void   columnMarginChanged(ChangeEvent) : void	199199	8.08	5.05	12.012	0.0 0.00%
getToolTipText(MouseEvent) : String   getToolTipText(MouseEvent) : String	219219	10.010	5.05	16.016	0.0 0.00%
GStructureChooser()   GStructureChooser()	248248	7.07	2.02	2.02	0.71428573 0.7142857371.4%
mouseClicked(MouseEvent) : void   mouseClicked(MouseEvent) : void	280280	1.01	1.01	1.01	0.0 0.00%
mouseReleased(MouseEvent) : void   mouseReleased(MouseEvent) : void	286286	1.01	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	294294	17.017	6.06	21.021	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	331331	1.01	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	339339	2.02	2.02	4.04	0.0 0.00%
mouseClicked(MouseEvent) : void   mouseClicked(MouseEvent) : void	353353	1.01	1.01	1.01	0.0 0.00%
mouseReleased(MouseEvent) : void   mouseReleased(MouseEvent) : void	359359	1.01	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	367367	19.019	7.07	25.025	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	410410	1.01	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	418418	2.02	2.02	4.04	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	432432	1.01	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	440440	2.02	2.02	4.04	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	455455	1.01	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	463463	2.02	2.02	4.04	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	486486	1.01	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	492492	1.01	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	498498	1.01	1.01	1.01	0.0 0.00%
addSeparatorAfter(JList,FilterOption,int) : boolean   addSeparatorAfter(JList,FilterOption,int) : boolean	513513	1.01	1.01	0.00	1.0 1.0100%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	559559	17.017	4.04	10.010	0.5652174 0.565217456.5%
internalFrameClosing(InternalFrameEvent) : void   internalFrameClosing(InternalFrameEvent) : void	622622	1.01	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	268268	95.095	5.05	4.04	0.96039605 0.9603960596%
closeAction(int) : void   closeAction(int) : void	640640	5.05	1.01	5.05	0.0 0.00%
wantedFieldsUpdated() : boolean   wantedFieldsUpdated() : boolean	654654	4.04	3.03	5.05	0.375 0.37537.5%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	668668	1.01	1.01	1.01	0.0 0.00%
getResultTable() : JTable   getResultTable() : JTable	866866	1.01	1.01	1.01	0.0 0.00%
getCmbFilterOption() : JComboBox<FilterOption>   getCmbFilterOption() : JComboBox<FilterOption>	871871	1.01	1.01	0.00	1.0 1.0100%

 

Class GStructureChooser.FilterOption

Class GStructureChooser.FilterOption	Line # 683	Total Statements 13	Complexity 10	Uncovered Elements 10	TOTAL Coverage 0.565217456.5%
FilterOption(String,String,String,boolean)   FilterOption(String,String,String,boolean)	706706	4.04	1.01	0.00	1.0 1.0100%
getName() : String   getName() : String	715715	1.01	1.01	0.00	1.0 1.0100%
setName(String) : void   setName(String) : void	720720	1.01	1.01	1.01	0.0 0.00%
getValue() : String   getValue() : String	725725	1.01	1.01	0.00	1.0 1.0100%
setValue(String) : void   setValue(String) : void	730730	1.01	1.01	1.01	0.0 0.00%
getView() : String   getView() : String	735735	1.01	1.01	1.01	0.0 0.00%
setView(String) : void   setView(String) : void	740740	1.01	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	745745	1.01	1.01	0.00	1.0 1.0100%
isAddSeparatorAfter() : boolean   isAddSeparatorAfter() : boolean	751751	1.01	1.01	0.00	1.0 1.0100%
setAddSeparatorAfter(boolean) : void   setAddSeparatorAfter(boolean) : void	756756	1.01	1.01	1.01	0.0 0.00%

 

Class GStructureChooser.AssociateSeqOptions

Class GStructureChooser.AssociateSeqOptions	Line # 769	Total Statements 9	Complexity 8	Uncovered Elements 18	TOTAL Coverage 0.00%
AssociateSeqOptions(SequenceI)   AssociateSeqOptions(SequenceI)	775775	2.02	2.02	4.04	0.0 0.00%
AssociateSeqOptions(String,SequenceI)   AssociateSeqOptions(String,SequenceI)	783783	2.02	1.01	2.02	0.0 0.00%
toString() : String   toString() : String	789789	1.01	1.01	1.01	0.0 0.00%
getName() : String   getName() : String	795795	1.01	1.01	1.01	0.0 0.00%
setName(String) : void   setName(String) : void	800800	1.01	1.01	1.01	0.0 0.00%
getSequence() : SequenceI   getSequence() : SequenceI	805805	1.01	1.01	1.01	0.0 0.00%
setSequence(SequenceI) : void   setSequence(SequenceI) : void	810810	1.01	1.01	1.01	0.0 0.00%

 

Class GStructureChooser.AssociateSeqPanel

Class GStructureChooser.AssociateSeqPanel	Line # 825	Total Statements 10	Complexity 6	Uncovered Elements 11	TOTAL Coverage 0.352941235.3%
AssociateSeqPanel()   AssociateSeqPanel()	831831	5.05	1.01	0.00	1.0 1.0100%
loadCmbAssSeq() : void   loadCmbAssSeq() : void	841841	1.01	1.01	1.01	0.0 0.00%
getCmb_assSeq() : JComboBox<AssociateSeqOptions>   getCmb_assSeq() : JComboBox<AssociateSeqOptions>	846846	1.01	1.01	1.01	0.0 0.00%
setCmb_assSeq(JComboBox<AssociateSeqOptions>) : void   setCmb_assSeq(JComboBox<AssociateSeqOptions>) : void	851851	1.01	1.01	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	856856	2.02	2.02	4.04	0.0 0.00%

 

Class GStructureChooser.CustomComboSeparatorsRenderer

Class GStructureChooser.CustomComboSeparatorsRenderer	Line # 883	Total Statements 8	Complexity 4	Uncovered Elements 0	TOTAL Coverage 1.0100%
CustomComboSeparatorsRenderer(ListCellRenderer<Object>)   CustomComboSeparatorsRenderer(ListCellRenderer<Object>)	892892	1.01	1.01	0.00	1.0 1.0100%
getListCellRendererComponent(JList,Object,int,boolean,boolean) : Component   getListCellRendererComponent(JList,Object,int,boolean,boolean) : Component	898898	7.07	3.03	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.46132597	jalview.gui.StructureChooserTest.populateFilterComboBoxTestjalview.gui.StructureChooserTest.populateFilterComboBoxTest	1PASS

 

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.ItemEvent;
44		import java.awt.event.ItemListener;
45		import java.awt.event.KeyAdapter;
46		import java.awt.event.KeyEvent;
47		import java.awt.event.MouseAdapter;
48		import java.awt.event.MouseEvent;
49		import java.util.Arrays;
50		import java.util.HashMap;
51		import java.util.Map;
52
53		import javax.swing.ImageIcon;
54		import javax.swing.JButton;
55		import javax.swing.JCheckBox;
56		import javax.swing.JComboBox;
57		import javax.swing.JFrame;
58		import javax.swing.JInternalFrame;
59		import javax.swing.JLabel;
60		import javax.swing.JList;
61		import javax.swing.JPanel;
62		import javax.swing.JScrollPane;
63		import javax.swing.JSeparator;
64		import javax.swing.JTabbedPane;
65		import javax.swing.JTable;
66		import javax.swing.JTextField;
67		import javax.swing.ListCellRenderer;
68		import javax.swing.event.ChangeEvent;
69		import javax.swing.event.ChangeListener;
70		import javax.swing.event.DocumentEvent;
71		import javax.swing.event.DocumentListener;
72		import javax.swing.event.InternalFrameEvent;
73		import javax.swing.table.TableColumn;
74
75		import net.miginfocom.swing.MigLayout;
76
77		@SuppressWarnings("serial")
78		/**
79		* GUI layout for structure chooser
80		*
81		* @author tcnofoegbu
82		*
83		*/
		47.3% Uncovered Elements: 154 (292) Complexity: 66 Complexity Density: 0.31
84		public abstract class GStructureChooser extends JPanel
85		implements ItemListener
86		{
87		private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
88
89		protected static final String VIEWS_FILTER = "VIEWS_FILTER";
90
91		protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
92
93		protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
94
95		/*
96		* 'cached' structure view
97		*/
98		protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
99
100		protected JPanel statusPanel = new JPanel();
101
102		public JLabel statusBar = new JLabel();
103
104		protected String frameTitle = MessageManager
105		.getString("label.structure_chooser");
106
107		protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
108
109		protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
110
111		protected AlignmentPanel ap;
112
113		protected StringBuilder errorWarning = new StringBuilder();
114
115		protected JButton btn_add;
116
117		protected JButton btn_newView;
118
119		protected JButton btn_pdbFromFile = new JButton();
120
121		protected JCheckBox chk_superpose = new JCheckBox(
122		MessageManager.getString("label.superpose_structures"));
123
124		protected JTextField txt_search = new JTextField(14);
125
126		protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
127
128		protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
129		.getLayout());
130
131		protected JCheckBox chk_invertFilter = new JCheckBox(
132		MessageManager.getString("label.invert"));
133
134		protected ImageIcon loadingImage = new ImageIcon(
135		getClass().getResource("/images/loading.gif"));
136
137		protected ImageIcon goodImage = new ImageIcon(
138		getClass().getResource("/images/good.png"));
139
140		protected ImageIcon errorImage = new ImageIcon(
141		getClass().getResource("/images/error.png"));
142
143		protected ImageIcon warningImage = new ImageIcon(
144		getClass().getResource("/images/warning.gif"));
145
146		protected JLabel lbl_loading = new JLabel(loadingImage);
147
148		protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
149
150		protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
151
152		protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel();
153
154		protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel();
155
156		protected JComboBox<StructureViewer> targetView = new JComboBox<>();
157
158		protected JTable tbl_local_pdb = new JTable();
159
160		protected JTabbedPane pnl_filter = jalview.jbgui.GDesktop.createTabbedPane();
161
162		protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
163		PreferenceSource.STRUCTURE_CHOOSER,
164		PDBFTSRestClient.getInstance());
165
166		protected FTSDataColumnI[] previousWantedFields;
167
168		protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
169
170		private JTable tbl_summary = new JTable()
171		{
172		private boolean inLayout;
173
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
174	11	@Override...
175		public boolean getScrollableTracksViewportWidth()
176		{
177	11	return hasExcessWidth();
178
179		}
180
		87.5% Uncovered Elements: 1 (8) Complexity: 2 Complexity Density: 0.33
181	2	@Override...
182		public void doLayout()
183		{
184	2	if (hasExcessWidth())
185		{
186	2	autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
187		}
188	2	inLayout = true;
189	2	super.doLayout();
190	2	inLayout = false;
191	2	autoResizeMode = AUTO_RESIZE_OFF;
192		}
193
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
194	13	protected boolean hasExcessWidth()...
195		{
196	13	return getPreferredSize().width < getParent().getWidth();
197		}
198
		0% Uncovered Elements: 12 (12) Complexity: 5 Complexity Density: 0.62
199	0	@Override...
200		public void columnMarginChanged(ChangeEvent e)
201		{
202	0	if (isEditing())
203		{
204	0	removeEditor();
205		}
206	0	TableColumn resizingColumn = getTableHeader().getResizingColumn();
207		// Need to do this here, before the parent's
208		// layout manager calls getPreferredSize().
209	0	if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
210		&& !inLayout)
211		{
212	0	resizingColumn.setPreferredWidth(resizingColumn.getWidth());
213	0	String colHeader = resizingColumn.getHeaderValue().toString();
214	0	tempUserPrefs.put(colHeader, resizingColumn.getWidth());
215		}
216	0	resizeAndRepaint();
217		}
218
		0% Uncovered Elements: 16 (16) Complexity: 5 Complexity Density: 0.5
219	0	@Override...
220		public String getToolTipText(MouseEvent evt)
221		{
222	0	String toolTipText = null;
223	0	java.awt.Point pnt = evt.getPoint();
224	0	int rowIndex = rowAtPoint(pnt);
225	0	int colIndex = columnAtPoint(pnt);
226
227	0	try
228		{
229	0	if (getValueAt(rowIndex, colIndex) == null)
230		{
231	0	return null;
232		}
233	0	toolTipText = getValueAt(rowIndex, colIndex).toString();
234		} catch (Exception e)
235		{
236		// e.printStackTrace();
237		}
238	0	toolTipText = (toolTipText == null ? null
239	0	: (toolTipText.length() > 500
240		? JvSwingUtils.wrapTooltip(true,
241		"\"" + toolTipText.subSequence(0, 500)
242		+ "...\"")
243		: JvSwingUtils.wrapTooltip(true, toolTipText)));
244	0	return toolTipText;
245		}
246		};
247
		71.4% Uncovered Elements: 2 (7) Complexity: 2 Complexity Density: 0.29
248	1	public GStructureChooser()...
249		{
250	1	try
251		{
252	1	jbInit();
253	1	mainFrame.setVisible(false);
254	1	mainFrame.invalidate();
255	1	mainFrame.pack();
256		} catch (Exception e)
257		{
258	0	System.out.println(e); // for JavaScript TypeError
259	0	e.printStackTrace();
260		}
261		}
262
263		/**
264		* Initializes the GUI default properties
265		*
266		* @throws Exception
267		*/
		96% Uncovered Elements: 4 (101) Complexity: 5 Complexity Density: 0.05
268	1	private void jbInit() throws Exception...
269		{
270	1	Integer width = tempUserPrefs.get("structureChooser.width") == null
271		? 800
272		: tempUserPrefs.get("structureChooser.width");
273	1	Integer height = tempUserPrefs.get("structureChooser.height") == null
274		? 400
275		: tempUserPrefs.get("structureChooser.height");
276	1	tbl_summary.setAutoCreateRowSorter(true);
277	1	tbl_summary.getTableHeader().setReorderingAllowed(false);
278	1	tbl_summary.addMouseListener(new MouseAdapter()
279		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
280	0	@Override...
281		public void mouseClicked(MouseEvent e)
282		{
283	0	validateSelections();
284		}
285
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
286	0	@Override...
287		public void mouseReleased(MouseEvent e)
288		{
289	0	validateSelections();
290		}
291		});
292	1	tbl_summary.addKeyListener(new KeyAdapter()
293		{
		0% Uncovered Elements: 21 (21) Complexity: 6 Complexity Density: 0.35
294	0	@Override...
295		public void keyPressed(KeyEvent evt)
296		{
297	0	validateSelections();
298	0	switch (evt.getKeyCode())
299		{
300	0	case KeyEvent.VK_ESCAPE: // escape key
301	0	mainFrame.dispose();
302	0	break;
303	0	case KeyEvent.VK_ENTER: // enter key
304	0	if (btn_add.isEnabled())
305		{
306	0	add_ActionPerformed();
307		}
308	0	break;
309	0	case KeyEvent.VK_TAB: // tab key
310	0	if (evt.isShiftDown())
311		{
312	0	pnl_filter.requestFocus();
313		}
314		else
315		{
316	0	btn_add.requestFocus();
317		}
318	0	evt.consume();
319	0	break;
320	0	default:
321	0	return;
322		}
323		}
324		});
325
326	1	JButton btn_cancel = new JButton(
327		MessageManager.getString("action.cancel"));
328	1	btn_cancel.setFont(VERDANA_12);
329	1	btn_cancel.addActionListener(new java.awt.event.ActionListener()
330		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
331	0	@Override...
332		public void actionPerformed(ActionEvent e)
333		{
334	0	closeAction(pnl_filter.getHeight());
335		}
336		});
337	1	btn_cancel.addKeyListener(new KeyAdapter()
338		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
339	0	@Override...
340		public void keyPressed(KeyEvent evt)
341		{
342	0	if (evt.getKeyCode() == KeyEvent.VK_ENTER)
343		{
344	0	closeAction(pnl_filter.getHeight());
345		}
346		}
347		});
348
349	1	tbl_local_pdb.setAutoCreateRowSorter(true);
350	1	tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
351	1	tbl_local_pdb.addMouseListener(new MouseAdapter()
352		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
353	0	@Override...
354		public void mouseClicked(MouseEvent e)
355		{
356	0	validateSelections();
357		}
358
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
359	0	@Override...
360		public void mouseReleased(MouseEvent e)
361		{
362	0	validateSelections();
363		}
364		});
365	1	tbl_local_pdb.addKeyListener(new KeyAdapter()
366		{
		0% Uncovered Elements: 25 (25) Complexity: 7 Complexity Density: 0.37
367	0	@Override...
368		public void keyPressed(KeyEvent evt)
369		{
370	0	validateSelections();
371	0	switch (evt.getKeyCode())
372		{
373	0	case KeyEvent.VK_ESCAPE: // escape key
374	0	mainFrame.dispose();
375	0	break;
376	0	case KeyEvent.VK_ENTER: // enter key
377	0	if (btn_add.isEnabled())
378		{
379	0	add_ActionPerformed();
380		}
381	0	break;
382	0	case KeyEvent.VK_TAB: // tab key
383	0	if (evt.isShiftDown())
384		{
385	0	cmb_filterOption.requestFocus();
386		}
387		else
388		{
389	0	if (btn_add.isEnabled())
390		{
391	0	btn_add.requestFocus();
392		}
393		else
394		{
395	0	btn_cancel.requestFocus();
396		}
397		}
398	0	evt.consume();
399	0	break;
400	0	default:
401	0	return;
402		}
403		}
404		});
405
406	1	btn_newView = new JButton(MessageManager.getString("action.new_view"));
407	1	btn_newView.setFont(VERDANA_12);
408	1	btn_newView.addActionListener(new java.awt.event.ActionListener()
409		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
410	0	@Override...
411		public void actionPerformed(ActionEvent e)
412		{
413	0	newView_ActionPerformed();
414		}
415		});
416	1	btn_newView.addKeyListener(new KeyAdapter()
417		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
418	0	@Override...
419		public void keyPressed(KeyEvent evt)
420		{
421	0	if (evt.getKeyCode() == KeyEvent.VK_ENTER)
422		{
423	0	newView_ActionPerformed();
424		}
425		}
426		});
427
428	1	btn_add = new JButton(MessageManager.getString("action.add"));
429	1	btn_add.setFont(VERDANA_12);
430	1	btn_add.addActionListener(new java.awt.event.ActionListener()
431		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
432	0	@Override...
433		public void actionPerformed(ActionEvent e)
434		{
435	0	add_ActionPerformed();
436		}
437		});
438	1	btn_add.addKeyListener(new KeyAdapter()
439		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
440	0	@Override...
441		public void keyPressed(KeyEvent evt)
442		{
443	0	if (evt.getKeyCode() == KeyEvent.VK_ENTER)
444		{
445	0	add_ActionPerformed();
446		}
447		}
448		});
449
450	1	btn_pdbFromFile.setFont(VERDANA_12);
451	1	String btn_title = MessageManager.getString("label.select_pdb_file");
452	1	btn_pdbFromFile.setText(btn_title + " ");
453	1	btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
454		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
455	0	@Override...
456		public void actionPerformed(ActionEvent e)
457		{
458	0	pdbFromFile_actionPerformed();
459		}
460		});
461	1	btn_pdbFromFile.addKeyListener(new KeyAdapter()
462		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
463	0	@Override...
464		public void keyPressed(KeyEvent evt)
465		{
466	0	if (evt.getKeyCode() == KeyEvent.VK_ENTER)
467		{
468	0	pdbFromFile_actionPerformed();
469		}
470		}
471		});
472
473	1	JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
474	1	scrl_foundStructures.setPreferredSize(new Dimension(width, height));
475
476	1	JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
477	1	scrl_localPDB.setPreferredSize(new Dimension(width, height));
478	1	scrl_localPDB.setHorizontalScrollBarPolicy(
479		JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
480
481	1	chk_invertFilter.setFont(VERDANA_12);
482	1	txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
483		MessageManager.getString("label.enter_pdb_id_tip")));
484	1	txt_search.getDocument().addDocumentListener(new DocumentListener()
485		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
486	0	@Override...
487		public void insertUpdate(DocumentEvent e)
488		{
489	0	txt_search_ActionPerformed();
490		}
491
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
492	0	@Override...
493		public void removeUpdate(DocumentEvent e)
494		{
495	0	txt_search_ActionPerformed();
496		}
497
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
498	0	@Override...
499		public void changedUpdate(DocumentEvent e)
500		{
501	0	txt_search_ActionPerformed();
502		}
503		});
504
505	1	cmb_filterOption.setFont(VERDANA_12);
506	1	cmb_filterOption.setToolTipText(
507		MessageManager.getString("info.select_filter_option"));
508	1	cmb_filterOption.addItemListener(this);
509		// add CustomComboSeparatorsRenderer to filter option combo-box
510	1	cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
511		(ListCellRenderer<Object>) cmb_filterOption.getRenderer())
512		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
513	16	@Override...
514		protected boolean addSeparatorAfter(JList list, FilterOption value,
515		int index)
516		{
517	16	return value.isAddSeparatorAfter();
518		}
519		});
520
521	1	chk_invertFilter.addItemListener(this);
522
523	1	targetView.setVisible(false);
524
525	1	JPanel actionsPanel = new JPanel(new MigLayout());
526	1	actionsPanel.add(targetView, "left");
527	1	actionsPanel.add(btn_add, "wrap");
528	1	actionsPanel.add(chk_superpose, "left");
529	1	actionsPanel.add(btn_newView);
530	1	actionsPanel.add(btn_cancel, "right");
531
532	1	JPanel pnl_main = new JPanel();
533	1	pnl_main.add(cmb_filterOption);
534	1	pnl_main.add(lbl_loading);
535	1	pnl_main.add(chk_invertFilter);
536	1	lbl_loading.setVisible(false);
537
538	1	JPanel pnl_fileChooser = new JPanel(new FlowLayout());
539	1	pnl_fileChooser.add(btn_pdbFromFile);
540	1	pnl_fileChooser.add(lbl_fromFileStatus);
541	1	JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
542	1	pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
543	1	pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
544
545	1	JPanel pnl_idInput = new JPanel(new FlowLayout());
546	1	pnl_idInput.add(txt_search);
547	1	pnl_idInput.add(lbl_pdbManualFetchStatus);
548
549	1	JPanel pnl_idInputBL = new JPanel(new BorderLayout());
550	1	pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
551	1	pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
552
553	1	final String foundStructureSummary = MessageManager
554		.getString("label.found_structures_summary");
555	1	final String configureCols = MessageManager
556		.getString("label.configure_displayed_columns");
557	1	ChangeListener changeListener = new ChangeListener()
558		{
		56.5% Uncovered Elements: 10 (23) Complexity: 4 Complexity Density: 0.24
559	1	@Override...
560		public void stateChanged(ChangeEvent changeEvent)
561		{
562	1	JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
563		.getSource();
564	1	int index = sourceTabbedPane.getSelectedIndex();
565	1	btn_add.setVisible(targetView.isVisible());
566	1	btn_newView.setVisible(true);
567	1	btn_cancel.setVisible(true);
568	1	if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
569		{
570	0	btn_add.setEnabled(false);
571	0	btn_cancel.setEnabled(false);
572	0	btn_add.setVisible(false);
573	0	btn_newView.setEnabled(false);
574	0	btn_cancel.setVisible(false);
575	0	previousWantedFields = pdbDocFieldPrefs
576		.getStructureSummaryFields()
577		.toArray(new FTSDataColumnI[0]);
578		}
579	1	if (sourceTabbedPane.getTitleAt(index)
580		.equals(foundStructureSummary))
581		{
582	1	btn_cancel.setEnabled(true);
583	1	if (wantedFieldsUpdated())
584		{
585	1	tabRefresh();
586		}
587		else
588		{
589	0	validateSelections();
590		}
591		}
592		}
593		};
594	1	pnl_filter.addChangeListener(changeListener);
595	1	pnl_filter.setPreferredSize(new Dimension(width, height));
596	1	pnl_filter.add(foundStructureSummary, scrl_foundStructures);
597	1	pnl_filter.add(configureCols, pdbDocFieldPrefs);
598
599	1	JPanel pnl_locPDB = new JPanel(new BorderLayout());
600	1	pnl_locPDB.add(scrl_localPDB);
601
602	1	pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
603	1	pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
604	1	pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
605	1	pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
606
607	1	this.setLayout(new BorderLayout());
608	1	this.add(pnl_main, java.awt.BorderLayout.NORTH);
609	1	this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
610		// this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
611	1	statusPanel.setLayout(new GridLayout());
612
613	1	JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
614	1	pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER);
615	1	pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
616	1	statusPanel.add(statusBar, null);
617	1	this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
618
619	1	mainFrame.addInternalFrameListener(
620		new javax.swing.event.InternalFrameAdapter()
621		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
622	0	@Override...
623		public void internalFrameClosing(InternalFrameEvent e)
624		{
625	0	closeAction(pnl_filter.getHeight());
626		}
627		});
628	1	mainFrame.setVisible(true);
629	1	mainFrame.setContentPane(this);
630	1	mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
631	1	Integer x = tempUserPrefs.get("structureChooser.x");
632	1	Integer y = tempUserPrefs.get("structureChooser.y");
633	1	if (x != null && y != null)
634		{
635	0	mainFrame.setLocation(x, y);
636		}
637	1	Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
638		}
639
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
640	0	protected void closeAction(int preferredHeight)...
641		{
642		// System.out.println(">>>>>>>>>> closing internal frame!!!");
643		// System.out.println("width : " + mainFrame.getWidth());
644		// System.out.println("heigh : " + mainFrame.getHeight());
645		// System.out.println("x : " + mainFrame.getX());
646		// System.out.println("y : " + mainFrame.getY());
647	0	tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
648	0	tempUserPrefs.put("structureChooser.height", preferredHeight);
649	0	tempUserPrefs.put("structureChooser.x", mainFrame.getX());
650	0	tempUserPrefs.put("structureChooser.y", mainFrame.getY());
651	0	mainFrame.dispose();
652		}
653
		37.5% Uncovered Elements: 5 (8) Complexity: 3 Complexity Density: 0.75
654	1	public boolean wantedFieldsUpdated()...
655		{
656	1	if (previousWantedFields == null)
657		{
658	1	return true;
659		}
660
661	0	FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
662		.getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
663	0	return Arrays.equals(currentWantedFields, previousWantedFields) ? false
664		: true;
665
666		}
667
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
668	0	@Override...
669		/**
670		* Event listener for the 'filter' combo-box and 'invert' check-box
671		*/
672		public void itemStateChanged(ItemEvent e)
673		{
674	0	stateChanged(e);
675		}
676
677		/**
678		* This inner class provides the data model for the structure filter combo-box
679		*
680		* @author tcnofoegbu
681		*
682		*/
		56.5% Uncovered Elements: 10 (23) Complexity: 10 Complexity Density: 0.77
683		public class FilterOption
684		{
685		private String name;
686
687		private String value;
688
689		private String view;
690
691		private boolean addSeparatorAfter;
692
693		/**
694		* Model for structure filter option
695		*
696		* @param name
697		* - the name of the Option
698		* @param value
699		* - the value of the option
700		* @param view
701		* - the category of the filter option
702		* @param addSeparatorAfter
703		* - if true, a horizontal separator is rendered immediately after
704		* this filter option, otherwise
705		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
706	26	public FilterOption(String name, String value, String view,...
707		boolean addSeparatorAfter)
708		{
709	26	this.name = name;
710	26	this.value = value;
711	26	this.view = view;
712	26	this.addSeparatorAfter = addSeparatorAfter;
713		}
714
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
715	1	public String getName()...
716		{
717	1	return name;
718		}
719
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
720	0	public void setName(String name)...
721		{
722	0	this.name = name;
723		}
724
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
725	1	public String getValue()...
726		{
727	1	return value;
728		}
729
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
730	0	public void setValue(String value)...
731		{
732	0	this.value = value;
733		}
734
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
735	0	public String getView()...
736		{
737	0	return view;
738		}
739
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
740	0	public void setView(String view)...
741		{
742	0	this.view = view;
743		}
744
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
745	22	@Override...
746		public String toString()
747		{
748	22	return this.name;
749		}
750
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
751	16	public boolean isAddSeparatorAfter()...
752		{
753	16	return addSeparatorAfter;
754		}
755
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
756	0	public void setAddSeparatorAfter(boolean addSeparatorAfter)...
757		{
758	0	this.addSeparatorAfter = addSeparatorAfter;
759		}
760		}
761
762		/**
763		* This inner class provides the provides the data model for associate
764		* sequence combo-box - cmb_assSeq
765		*
766		* @author tcnofoegbu
767		*
768		*/
		0% Uncovered Elements: 18 (18) Complexity: 8 Complexity Density: 0.89
769		public class AssociateSeqOptions
770		{
771		private SequenceI sequence;
772
773		private String name;
774
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
775	0	public AssociateSeqOptions(SequenceI seq)...
776		{
777	0	this.sequence = seq;
778	0	this.name = (seq.getName().length() >= 23)
779		? seq.getName().substring(0, 23)
780		: seq.getName();
781		}
782
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
783	0	public AssociateSeqOptions(String name, SequenceI seq)...
784		{
785	0	this.name = name;
786	0	this.sequence = seq;
787		}
788
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
789	0	@Override...
790		public String toString()
791		{
792	0	return name;
793		}
794
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
795	0	public String getName()...
796		{
797	0	return name;
798		}
799
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
800	0	public void setName(String name)...
801		{
802	0	this.name = name;
803		}
804
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
805	0	public SequenceI getSequence()...
806		{
807	0	return sequence;
808		}
809
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
810	0	public void setSequence(SequenceI sequence)...
811		{
812	0	this.sequence = sequence;
813		}
814
815		}
816
817		/**
818		* This inner class holds the Layout and configuration of the panel which
819		* handles association of manually fetched structures to a unique sequence
820		* when more than one sequence selection is made
821		*
822		* @author tcnofoegbu
823		*
824		*/
		35.3% Uncovered Elements: 11 (17) Complexity: 6 Complexity Density: 0.6
825		public class AssociateSeqPanel extends JPanel implements ItemListener
826		{
827		private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
828
829		private JLabel lbl_associateSeq = new JLabel();
830
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
831	2	public AssociateSeqPanel()...
832		{
833	2	this.setLayout(new FlowLayout());
834	2	this.add(cmb_assSeq);
835	2	this.add(lbl_associateSeq);
836	2	cmb_assSeq.setToolTipText(
837		MessageManager.getString("info.associate_wit_sequence"));
838	2	cmb_assSeq.addItemListener(this);
839		}
840
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
841	0	public void loadCmbAssSeq()...
842		{
843	0	populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
844		}
845
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
846	0	public JComboBox<AssociateSeqOptions> getCmb_assSeq()...
847		{
848	0	return cmb_assSeq;
849		}
850
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
851	0	public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)...
852		{
853	0	this.cmb_assSeq = cmb_assSeq;
854		}
855
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
856	0	@Override...
857		public void itemStateChanged(ItemEvent e)
858		{
859	0	if (e.getStateChange() == ItemEvent.SELECTED)
860		{
861	0	cmbAssSeqStateChanged();
862		}
863		}
864		}
865
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
866	0	public JTable getResultTable()...
867		{
868	0	return tbl_summary;
869		}
870
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
871	4	public JComboBox<FilterOption> getCmbFilterOption()...
872		{
873	4	return cmb_filterOption;
874		}
875
876		/**
877		* Custom ListCellRenderer for adding a separator between different categories
878		* of structure chooser filter option drop-down.
879		*
880		* @author tcnofoegbu
881		*
882		*/
		100% Uncovered Elements: 0 (12) Complexity: 4 Complexity Density: 0.5
883		public abstract class CustomComboSeparatorsRenderer
884		implements ListCellRenderer<Object>
885		{
886		private ListCellRenderer<Object> regent;
887
888		private JPanel separatorPanel = new JPanel(new BorderLayout());
889
890		private JSeparator jSeparator = new JSeparator();
891
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
892	1	public CustomComboSeparatorsRenderer(...
893		ListCellRenderer<Object> listCellRenderer)
894		{
895	1	this.regent = listCellRenderer;
896		}
897
		100% Uncovered Elements: 0 (9) Complexity: 3 Complexity Density: 0.43
898	25	@Override...
899		public Component getListCellRendererComponent(JList list, Object value,
900		int index, boolean isSelected, boolean cellHasFocus)
901		{
902
903	25	Component comp = regent.getListCellRendererComponent(list, value,
904		index, isSelected, cellHasFocus);
905	25	if (index != -1
906		&& addSeparatorAfter(list, (FilterOption) value, index))
907		{
908	1	separatorPanel.removeAll();
909	1	separatorPanel.add(comp, BorderLayout.CENTER);
910	1	separatorPanel.add(jSeparator, BorderLayout.SOUTH);
911	1	return separatorPanel;
912		}
913		else
914		{
915	24	return comp;
916		}
917		}
918
919		protected abstract boolean addSeparatorAfter(JList list,
920		FilterOption value, int index);
921		}
922
923		protected abstract void stateChanged(ItemEvent e);
924
925		protected abstract void add_ActionPerformed();
926
927		protected abstract void newView_ActionPerformed();
928
929		protected abstract void pdbFromFile_actionPerformed();
930
931		protected abstract void txt_search_ActionPerformed();
932
933		protected abstract void populateCmbAssociateSeqOptions(
934		JComboBox<AssociateSeqOptions> cmb_assSeq,
935		JLabel lbl_associateSeq);
936
937		protected abstract void cmbAssSeqStateChanged();
938
939		protected abstract void tabRefresh();
940
941		protected abstract void validateSelections();
942		}