Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FormatAdapterTest	39	32	10	0.00%	Show methods

Class FormatAdapterTest

Class FormatAdapterTest	Line # 39	Total Statements 32	Complexity 10	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	0.0 0.00%
testRoundTrip(FileFormatI) : void   testRoundTrip(FileFormatI) : void	5454	16.016	2.02	0.0 0.00%
adjustForGapTreatment(String,char,FileFormatI) : String   adjustForGapTreatment(String,char,FileFormatI) : String	110110	3.03	2.02	0.0 0.00%
getFormats() : Object[][]   getFormats() : Object[][]	130130	10.010	4.04	0.0 0.00%
testOneFormatRoundTrip() : void   testOneFormatRoundTrip() : void	158158	1.01	1.01	0.0 0.00%

 

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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.io;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.fail;
26
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.SequenceI;
29		import jalview.gui.JvOptionPane;
30
31		import java.io.IOException;
32		import java.util.ArrayList;
33		import java.util.List;
34
35		import org.testng.annotations.BeforeClass;
36		import org.testng.annotations.DataProvider;
37		import org.testng.annotations.Test;
38
		0% Uncovered Elements: 41 (41) Complexity: 10 Complexity Density: 0.31
39		public class FormatAdapterTest
40		{
41
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
42	0	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	0	JvOptionPane.setInteractiveMode(false);
46	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
49		/**
50		* Test saving and re-reading in a specified format
51		*
52		* @throws IOException
53		*/
		0% Uncovered Elements: 16 (16) Complexity: 2 Complexity Density: 0.12 4-
54	0	@Test(groups = { "Functional" }, dataProvider = "formats")...
55		public void testRoundTrip(FileFormatI format) throws IOException
56		{
57	0	try
58		{
59	0	AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
60		DataSourceType.FILE, FileFormat.Fasta);
61
62		/*
63		* 'gap' is the gap character used in the alignment data file here,
64		* not the user preferred gap character
65		*/
66	0	char gap = al.getGapCharacter();
67	0	assertNotNull(al);
68
69	0	SequenceI[] seqs = al.getSequencesArray();
70	0	String formatted = new FormatAdapter().formatSequences(format, al,
71		false);
72
73	0	AlignmentI reloaded = new FormatAdapter().readFile(formatted,
74		DataSourceType.PASTE, format);
75	0	List<SequenceI> reread = reloaded.getSequences();
76	0	assertEquals("Wrong number of reloaded sequences", seqs.length,
77		reread.size());
78
79	0	int i = 0;
80	0	for (SequenceI seq : reread)
81		{
82	0	String sequenceString = seq.getSequenceAsString();
83
84		/*
85		* special case: MSF always uses '.' as gap character
86		*/
87	0	sequenceString = adjustForGapTreatment(sequenceString, gap, format);
88	0	assertEquals(String.format("Sequence %d: %s", i, seqs[i].getName()),
89		seqs[i].getSequenceAsString(), sequenceString);
90	0	i++;
91		}
92		} catch (IOException e)
93		{
94	0	fail(String.format("Format %s failed with %s", format,
95		e.getMessage()));
96		}
97		}
98
99		/**
100		* Optionally change the gap character in the string to the given character,
101		* depending on the sequence file format
102		*
103		* @param sequenceString
104		* a sequence (as written in 'format' format)
105		* @param gap
106		* the sequence's original gap character
107		* @param format
108		* @return
109		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
110	0	String adjustForGapTreatment(String sequenceString, char gap,...
111		FileFormatI format)
112		{
113	0	if (FileFormat.MSF.equals(format))
114		{
115		/*
116		* MSF forces gap character to '.', so change it back
117		* for comparison purposes
118		*/
119	0	sequenceString = sequenceString.replace('.', gap);
120		}
121	0	return sequenceString;
122		}
123
124		/**
125		* Data provider that serves alignment formats that are both readable and
126		* (text) writable
127		*
128		* @return
129		*/
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.4
130	0	@DataProvider(name = "formats")...
131		static Object[][] getFormats()
132		{
133	0	List<FileFormatI> both = new ArrayList<FileFormatI>();
134	0	for (FileFormatI format : FileFormats.getInstance().getFormats())
135		{
136	0	if (format.isReadable() && format.isWritable()
137		&& format.isTextFormat())
138		{
139	0	both.add(format);
140		}
141		}
142
143	0	Object[][] formats = new Object[both.size()][];
144	0	int i = 0;
145	0	for (FileFormatI format : both)
146		{
147	0	formats[i] = new Object[] { format };
148	0	i++;
149		}
150	0	return formats;
151		}
152
153		/**
154		* Enable this to isolate testing to a single file format
155		*
156		* @throws IOException
157		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 4-
158	0	@Test(groups = { "Functional" }, enabled = false)...
159		public void testOneFormatRoundTrip() throws IOException
160		{
161	0	testRoundTrip(FileFormat.Json);
162		}
163		}