Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Finder	50	103	26	0.00%	Show methods

Class Finder

Class Finder	Line # 50	Total Statements 103	Complexity 26	TOTAL Coverage 0.00%
windowClosing(WindowEvent) : void   windowClosing(WindowEvent) : void	9797	1.01	1.01	0.0 0.00%
Finder(AlignmentPanel)   Finder(AlignmentPanel)	7575	12.012	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	106106	8.08	5.05	0.0 0.00%
createFeatures_actionPerformed() : void   createFeatures_actionPerformed() : void	129129	10.010	2.02	0.0 0.00%
doSearch(boolean) : void   doSearch(boolean) : void	151151	31.031	13.013	0.0 0.00%
keyTyped(KeyEvent) : void   keyTyped(KeyEvent) : void	246246	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	235235	39.039	1.01	0.0 0.00%
textfield_keyTyped() : void   textfield_keyTyped() : void	288288	1.01	1.01	0.0 0.00%

 

Contributing tests

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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.appletgui;
22
23		import jalview.api.AlignViewportI;
24		import jalview.api.FinderI;
25		import jalview.datamodel.SearchResultMatchI;
26		import jalview.datamodel.SearchResultsI;
27		import jalview.datamodel.SequenceFeature;
28		import jalview.datamodel.SequenceI;
29		import jalview.util.MessageManager;
30
31		import java.awt.Button;
32		import java.awt.Checkbox;
33		import java.awt.Font;
34		import java.awt.Frame;
35		import java.awt.GridLayout;
36		import java.awt.Label;
37		import java.awt.Panel;
38		import java.awt.Rectangle;
39		import java.awt.TextField;
40		import java.awt.event.ActionEvent;
41		import java.awt.event.ActionListener;
42		import java.awt.event.KeyEvent;
43		import java.awt.event.WindowAdapter;
44		import java.awt.event.WindowEvent;
45		import java.util.ArrayList;
46		import java.util.HashMap;
47		import java.util.List;
48		import java.util.Map;
49
		0% Uncovered Elements: 139 (139) Complexity: 26 Complexity Density: 0.25
50		public class Finder extends Panel implements ActionListener
51		{
52		private AlignViewportI av;
53
54		private AlignmentPanel ap;
55
56		private TextField textfield = new TextField();
57
58		private Button findAll = new Button();
59
60		private Button findNext = new Button();
61
62		private Button createFeatures = new Button();
63
64		private Checkbox caseSensitive = new Checkbox();
65
66		private Checkbox searchDescription = new Checkbox();
67
68		private SearchResultsI searchResults;
69
70		/*
71		* Finder agent per viewport searched
72		*/
73		Map<AlignViewportI, FinderI> finders;
74
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.17
75	0	public Finder(final AlignmentPanel ap)...
76		{
77	0	finders = new HashMap<>();
78
79	0	try
80		{
81	0	jbInit();
82
83		} catch (Exception e)
84		{
85	0	e.printStackTrace();
86		}
87
88	0	this.av = ap.av;
89	0	this.ap = ap;
90	0	Frame frame = new Frame();
91	0	frame.add(this);
92	0	jalview.bin.JalviewLite.addFrame(frame,
93		MessageManager.getString("action.find"), 340, 120);
94	0	frame.repaint();
95	0	frame.addWindowListener(new WindowAdapter()
96		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	@Override...
98		public void windowClosing(WindowEvent evt)
99		{
100	0	ap.highlightSearchResults(null);
101		}
102		});
103	0	textfield.requestFocus();
104		}
105
		0% Uncovered Elements: 16 (16) Complexity: 5 Complexity Density: 0.62
106	0	@Override...
107		public void actionPerformed(ActionEvent evt)
108		{
109	0	if (evt.getSource() == textfield)
110		{
111	0	doSearch(false);
112		}
113
114	0	else if (evt.getSource() == findNext)
115		{
116	0	doSearch(false);
117		}
118
119	0	else if (evt.getSource() == findAll)
120		{
121	0	doSearch(true);
122		}
123	0	else if (evt.getSource() == createFeatures)
124		{
125	0	createFeatures_actionPerformed();
126		}
127		}
128
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
129	0	public void createFeatures_actionPerformed()...
130		{
131	0	List<SequenceI> seqs = new ArrayList<>();
132	0	List<SequenceFeature> features = new ArrayList<>();
133	0	String searchString = textfield.getText().trim();
134
135	0	for (SearchResultMatchI match : searchResults.getResults())
136		{
137	0	seqs.add(match.getSequence().getDatasetSequence());
138	0	features.add(new SequenceFeature(searchString, "Search Results",
139		match.getStart(), match.getEnd(), "Search Results"));
140		}
141
142	0	if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
143		features, true, ap))
144		{
145	0	ap.alignFrame.sequenceFeatures.setState(true);
146	0	av.setShowSequenceFeatures(true);
147	0	ap.highlightSearchResults(null);
148		}
149		}
150
		0% Uncovered Elements: 49 (49) Complexity: 13 Complexity Density: 0.42
151	0	void doSearch(boolean doFindAll)...
152		{
153	0	if (ap.av.applet.currentAlignFrame != null)
154		{
155	0	ap = ap.av.applet.currentAlignFrame.alignPanel;
156	0	av = ap.av;
157		}
158	0	createFeatures.setEnabled(false);
159	0	FinderI finder = finders.get(av);
160	0	if (finder == null)
161		{
162		/*
163		* first time we searched this viewport
164		*/
165	0	finder = new jalview.analysis.Finder(av);
166	0	finders.put(av, finder);
167		}
168
169	0	String searchString = textfield.getText();
170	0	boolean isCaseSensitive = caseSensitive.getState();
171	0	boolean doSearchDescription = searchDescription.getState();
172	0	if (doFindAll)
173		{
174	0	finder.findAll(searchString, isCaseSensitive, doSearchDescription);
175		}
176		else
177		{
178	0	finder.findNext(searchString, isCaseSensitive, doSearchDescription);
179		}
180
181	0	searchResults = finder.getSearchResults();
182
183	0	List<SequenceI> idMatches = finder.getIdMatches();
184	0	ap.idPanel.highlightSearchResults(idMatches);
185
186	0	if (searchResults.isEmpty())
187		{
188	0	searchResults = null;
189		}
190		else
191		{
192	0	createFeatures.setEnabled(true);
193		}
194
195		// if allResults is null, this effectively switches displaySearch flag in
196		// seqCanvas
197	0	ap.highlightSearchResults(searchResults);
198		// TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
199		// 'SelectRegion' selection
200	0	if (idMatches.isEmpty() && searchResults == null)
201		{
202	0	ap.alignFrame.statusBar.setText(
203		MessageManager.getString("label.finished_searching"));
204		}
205		else
206		{
207	0	if (doFindAll)
208		{
209	0	String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
210		: "";
211	0	if (idMatches.size() > 0 && searchResults != null
212		&& searchResults.getSize() > 0)
213		{
214	0	message += " and ";
215		}
216	0	if (searchResults != null)
217		{
218	0	message += searchResults.getSize() + " subsequence matches.";
219		}
220	0	ap.alignFrame.statusBar.setText(MessageManager
221		.formatMessage("label.search_results", new String[]
222		{ searchString, message }));
223
224		}
225		else
226		{
227		// TODO: indicate sequence and matching position in status bar
228	0	ap.alignFrame.statusBar.setText(MessageManager
229		.formatMessage("label.found_match_for", new String[]
230		{ searchString }));
231		}
232		}
233		}
234
		0% Uncovered Elements: 39 (39) Complexity: 1 Complexity Density: 0.03
235	0	private void jbInit() throws Exception...
236		{
237	0	Label jLabel1 = new Label(MessageManager.getString("action.find"));
238	0	jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
239	0	jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
240	0	this.setLayout(null);
241	0	textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
242	0	textfield.setText("");
243	0	textfield.setBounds(new Rectangle(40, 17, 133, 21));
244	0	textfield.addKeyListener(new java.awt.event.KeyAdapter()
245		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
246	0	@Override...
247		public void keyTyped(KeyEvent e)
248		{
249	0	textfield_keyTyped();
250		}
251		});
252	0	textfield.addActionListener(this);
253	0	findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
254	0	findAll.setLabel(MessageManager.getString("action.find_all"));
255	0	findAll.addActionListener(this);
256	0	findNext.setEnabled(false);
257	0	findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
258	0	findNext.setLabel(MessageManager.getString("action.find_next"));
259	0	findNext.addActionListener(this);
260
261	0	Panel actionsPanel = new Panel();
262	0	actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
263	0	GridLayout gridLayout1 = new GridLayout();
264	0	actionsPanel.setLayout(gridLayout1);
265	0	gridLayout1.setHgap(0);
266	0	gridLayout1.setRows(3);
267	0	gridLayout1.setVgap(2);
268	0	createFeatures.setEnabled(false);
269	0	createFeatures.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
270	0	createFeatures.setLabel(MessageManager.getString("label.new_feature"));
271	0	createFeatures.addActionListener(this);
272	0	caseSensitive.setLabel(MessageManager.getString("label.match_case"));
273	0	caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
274
275	0	searchDescription.setLabel(
276		MessageManager.getString("label.include_description"));
277	0	searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
278	0	actionsPanel.add(findNext, null);
279	0	actionsPanel.add(findAll, null);
280	0	actionsPanel.add(createFeatures, null);
281	0	this.add(caseSensitive);
282	0	this.add(textfield, null);
283	0	this.add(jLabel1, null);
284	0	this.add(actionsPanel, null);
285	0	this.add(searchDescription);
286		}
287
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
288	0	void textfield_keyTyped()...
289		{
290	0	findNext.setEnabled(true);
291		}
292
293		}