Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GFinder	47	73	23	0.00%	Show methods

Class GFinder

Class GFinder	Line # 47	Total Statements 73	Complexity 23	TOTAL Coverage 0.00%
GFinder()   GFinder()	7474	3.03	2.02	0.0 0.00%
caretUpdate(CaretEvent) : void   caretUpdate(CaretEvent) : void	132132	1.01	1.01	0.0 0.00%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	140140	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	181181	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	192192	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	204204	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	216216	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	8888	52.052	1.01	0.0 0.00%
copyToClipboard_actionPerformed() : void   copyToClipboard_actionPerformed() : void	228228	0.00	1.01	-1.0 -1.0 -
textfield_keyPressed(KeyEvent) : void   textfield_keyPressed(KeyEvent) : void	232232	4.04	3.03	0.0 0.00%
findNext_actionPerformed() : void   findNext_actionPerformed() : void	244244	0.00	1.01	-1.0 -1.0 -
findAll_actionPerformed() : void   findAll_actionPerformed() : void	248248	0.00	1.01	-1.0 -1.0 -
createFeatures_actionPerformed() : void   createFeatures_actionPerformed() : void	252252	0.00	1.01	-1.0 -1.0 -
run() : void   run() : void	263263	6.06	4.04	0.0 0.00%
textfield_caretUpdate() : void   textfield_caretUpdate() : void	256256	2.02	3.03	0.0 0.00%

 

Contributing tests

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.jbgui;
22
23		import java.awt.BorderLayout;
24		import java.awt.Font;
25		import java.awt.GridLayout;
26		import java.awt.event.ActionEvent;
27		import java.awt.event.ActionListener;
28		import java.awt.event.KeyAdapter;
29		import java.awt.event.KeyEvent;
30
31		import javax.swing.JButton;
32		import javax.swing.JCheckBox;
33		import javax.swing.JLabel;
34		import javax.swing.JPanel;
35		import javax.swing.SwingConstants;
36		import javax.swing.SwingUtilities;
37		import javax.swing.event.CaretEvent;
38		import javax.swing.event.CaretListener;
39
40		import jalview.datamodel.AlignmentI;
41		import jalview.io.DataSourceType;
42		import jalview.io.FileFormat;
43		import jalview.io.FormatAdapter;
44		import jalview.io.cache.JvCacheableInputBox;
45		import jalview.util.MessageManager;
46
		0% Uncovered Elements: 96 (96) Complexity: 23 Complexity Density: 0.32
47		public class GFinder extends JPanel
48		{
49		private static final java.awt.Font VERDANA_12 = new Font("Verdana",
50		Font.PLAIN, 12);
51
52		private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
53
54		/*
55		* if more checkboxes are wanted, increase this value
56		* and add to centrePanel in jbInit()
57		*/
58		private static final int PANEL_ROWS = 4;
59
60		protected JButton createFeatures;
61
62		protected JButton copyToClipboard;
63
64		protected JvCacheableInputBox<String> searchBox;
65
66		protected JCheckBox caseSensitive;
67
68		protected JCheckBox searchDescription;
69
70		protected JCheckBox searchFeatures;
71
72		protected JCheckBox ignoreHidden;
73
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
74	0	public GFinder()...
75		{
76	0	try
77		{
78	0	jbInit();
79		} catch (Exception e)
80		{
81	0	e.printStackTrace();
82		}
83		}
84
85		/**
86		* Constructs the widgets and adds them to the layout
87		*/
		0% Uncovered Elements: 52 (52) Complexity: 1 Complexity Density: 0.02
88	0	private void jbInit() throws Exception...
89		{
90		/*
91		* border layout
92		* West: 4 rows
93		* first row 'Find'
94		* remaining rows empty
95		* Center: 4 rows
96		* first row search box
97		* second row 'match case' checkbox
98		* third row 'include description' checkbox
99		* fourth row 'ignore hidden' checkbox
100		* East: four rows
101		* first row 'find next' button
102		* second row 'find all' button
103		* third row 'new feature' button
104		* fourth row empty
105		*/
106	0	this.setLayout(new BorderLayout());
107	0	JPanel eastPanel = new JPanel();
108	0	eastPanel.setLayout(new GridLayout(PANEL_ROWS, 1));
109	0	this.add(eastPanel, BorderLayout.EAST);
110	0	JPanel centrePanel = new JPanel();
111	0	centrePanel.setLayout(new GridLayout(PANEL_ROWS, 1));
112	0	this.add(centrePanel, BorderLayout.CENTER);
113	0	JPanel westPanel = new JPanel();
114	0	westPanel.setLayout(new GridLayout(PANEL_ROWS, 1));
115	0	this.add(westPanel, BorderLayout.WEST);
116
117		/*
118		* 'Find' prompt goes top left
119		*/
120	0	JLabel findLabel = new JLabel(
121		" " + MessageManager.getString("label.find") + " ");
122	0	findLabel.setFont(VERDANA_12);
123	0	westPanel.add(findLabel);
124
125		/*
126		* search box
127		*/
128	0	searchBox = new JvCacheableInputBox<>(FINDER_CACHE_KEY, 25);
129	0	searchBox.getComponent().setFont(VERDANA_12);
130	0	searchBox.addCaretListener(new CaretListener()
131		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
132	0	@Override...
133		public void caretUpdate(CaretEvent e)
134		{
135	0	textfield_caretUpdate();
136		}
137		});
138	0	searchBox.addKeyListener(new KeyAdapter()
139		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	@Override...
141		public void keyPressed(KeyEvent e)
142		{
143	0	textfield_keyPressed(e);
144		}
145		});
146	0	centrePanel.add(searchBox.getComponent());
147
148		/*
149		* search options checkboxes
150		*/
151	0	caseSensitive = new JCheckBox();
152	0	caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
153	0	caseSensitive.setText(MessageManager.getString("label.match_case"));
154
155	0	searchDescription = new JCheckBox();
156	0	searchDescription
157		.setText(MessageManager.getString("label.include_description"));
158
159	0	searchFeatures = new JCheckBox();
160	0	searchFeatures
161		.setText(MessageManager.getString("label.include_features"));
162
163	0	ignoreHidden = new JCheckBox();
164	0	ignoreHidden.setText(MessageManager.getString("label.ignore_hidden"));
165	0	ignoreHidden.setToolTipText(
166		MessageManager.getString("label.ignore_hidden_tooltip"));
167
168	0	centrePanel.add(caseSensitive);
169	0	centrePanel.add(searchDescription);
170	0	centrePanel.add(searchFeatures);
171	0	centrePanel.add(ignoreHidden);
172
173		/*
174		* action buttons
175		*/
176	0	JButton findAll = new JButton(
177		MessageManager.getString("action.find_all"));
178	0	findAll.setFont(VERDANA_12);
179	0	findAll.addActionListener(new ActionListener()
180		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
181	0	@Override...
182		public void actionPerformed(ActionEvent e)
183		{
184	0	findAll_actionPerformed();
185		}
186		});
187	0	JButton findNext = new JButton(
188		MessageManager.getString("action.find_next"));
189	0	findNext.setFont(VERDANA_12);
190	0	findNext.addActionListener(new ActionListener()
191		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
192	0	@Override...
193		public void actionPerformed(ActionEvent e)
194		{
195	0	findNext_actionPerformed();
196		}
197		});
198	0	createFeatures = new JButton();
199	0	createFeatures.setEnabled(false);
200	0	createFeatures.setFont(VERDANA_12);
201	0	createFeatures.setText(MessageManager.getString("label.new_feature"));
202	0	createFeatures.addActionListener(new ActionListener()
203		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
204	0	@Override...
205		public void actionPerformed(ActionEvent e)
206		{
207	0	createFeatures_actionPerformed();
208		}
209		});
210	0	copyToClipboard = new JButton();
211	0	copyToClipboard.setEnabled(false);
212	0	copyToClipboard.setFont(VERDANA_12);
213	0	copyToClipboard.setText(MessageManager.getString("label.copy"));
214	0	copyToClipboard.addActionListener(new ActionListener()
215		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
216	0	@Override...
217		public void actionPerformed(ActionEvent e)
218		{
219	0	copyToClipboard_actionPerformed();
220		}
221		});
222	0	eastPanel.add(findNext);
223	0	eastPanel.add(findAll);
224	0	eastPanel.add(createFeatures);
225	0	eastPanel.add(copyToClipboard);
226		}
227
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
228	0	protected void copyToClipboard_actionPerformed()...
229		{
230		}
231
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
232	0	protected void textfield_keyPressed(KeyEvent e)...
233		{
234	0	if (e.getKeyCode() == KeyEvent.VK_ENTER)
235		{
236	0	if (!searchBox.isPopupVisible())
237		{
238	0	e.consume();
239	0	findNext_actionPerformed();
240		}
241		}
242		}
243
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
244	0	protected void findNext_actionPerformed()...
245		{
246		}
247
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
248	0	protected void findAll_actionPerformed()...
249		{
250		}
251
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
252	0	public void createFeatures_actionPerformed()...
253		{
254		}
255
		0% Uncovered Elements: 4 (4) Complexity: 3 Complexity Density: 1.5
256	0	public void textfield_caretUpdate()...
257		{
258		// disabled as appears to be running a non-functional
259	0	if (false && searchBox.getUserInput().indexOf(">") > -1)
260		{
261	0	SwingUtilities.invokeLater(new Runnable()
262		{
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 0.67
263	0	@Override...
264		public void run()
265		{
266	0	String str = searchBox.getUserInput();
267	0	AlignmentI al = null;
268	0	try
269		{
270	0	al = new FormatAdapter().readFile(str, DataSourceType.PASTE,
271		FileFormat.Fasta);
272		} catch (Exception ex)
273		{
274		}
275	0	if (al != null && al.getHeight() > 0)
276		{
277	0	str = jalview.analysis.AlignSeq.extractGaps(
278		jalview.util.Comparison.GapChars,
279		al.getSequenceAt(0).getSequenceAsString());
280		// todo and what? set str as searchBox text?
281		}
282		}
283		});
284		}
285		}
286
287		}