Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CountReader	18	17	5	0.00%	Show methods

Class CountReader

Class CountReader	Line # 18	Total Statements 17	Complexity 5	TOTAL Coverage 0.00%
getBackgroundFrequencies(AlignmentPanel,SequenceI) : ResidueCount   getBackgroundFrequencies(AlignmentPanel,SequenceI) : ResidueCount	2020	17.017	5.05	0.0 0.00%

 

Contributing tests

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1		package jalview.io;
2
3		import jalview.bin.Jalview;
4		import jalview.datamodel.AlignmentI;
5		import jalview.datamodel.ResidueCount;
6		import jalview.datamodel.SequenceI;
7		import jalview.gui.AlignmentPanel;
8		import jalview.gui.Desktop;
9		import jalview.gui.JvOptionPane;
10		import jalview.util.MessageManager;
11
12		import java.io.File;
13		import java.io.IOException;
14		import java.net.MalformedURLException;
15
16		import javax.swing.JFileChooser;
17
		0% Uncovered Elements: 24 (24) Complexity: 5 Complexity Density: 0.29
18		public class CountReader
19		{
		0% Uncovered Elements: 23 (23) Complexity: 5 Complexity Density: 0.29
20	0	public static ResidueCount getBackgroundFrequencies(AlignmentPanel ap, SequenceI seq) throws MalformedURLException, IOException...
21		{
22	0	JFileChooser bkgdFreqChooser = new JFileChooser();
23
24	0	bkgdFreqChooser.showOpenDialog(ap);
25
26	0	File file = bkgdFreqChooser.getSelectedFile();
27	0	if (file == null)
28		{
29	0	return null;
30		}
31
32	0	IdentifyFile identifier = new IdentifyFile();
33	0	FileFormatI format = null;
34	0	try
35		{
36	0	format = identifier.identify(file.getPath(), DataSourceType.FILE);
37		} catch (Exception e)
38		{
39
40		}
41
42	0	if (format == null)
43		{
44	0	if (!Jalview.isHeadlessMode())
45		{
46	0	JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
47		MessageManager.getString("label.couldnt_read_data") + " in "
48		+ file + "\n"
49		+ AppletFormatAdapter.getSupportedFormats(),
50		MessageManager.getString("label.couldnt_read_data"),
51		JvOptionPane.WARNING_MESSAGE);
52		}
53		}
54
55	0	FileParse parser = new FileParse(file.getPath(), DataSourceType.FILE);
56	0	AlignmentI al = new FormatAdapter().readFromFile(parser, format);
57	0	parser.close();
58
59	0	ResidueCount counts = new ResidueCount(al.getSequences());
60
61	0	return counts;
62		}
63		}