Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
SeqCigarTest	35	64	12	2	0.9759036397.6%	Show methods

Class SeqCigarTest

Class SeqCigarTest	Line # 35	Total Statements 64	Complexity 12	Uncovered Elements 2	TOTAL Coverage 0.9759036397.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3838	2.02	1.01	0.00	1.0 1.0100%
testFindPosition() : void   testFindPosition() : void	4545	10.010	3.03	0.00	1.0 1.0100%
testSomething() : void   testSomething() : void	7474	46.046	5.05	0.00	1.0 1.0100%
testCigar_string(Sequence,String) : void   testCigar_string(Sequence,String) : void	183183	3.03	1.01	0.00	1.0 1.0100%
testSeqRecovery(SeqCigar,SequenceI) : void   testSeqRecovery(SeqCigar,SequenceI) : void	190190	3.03	2.02	2.02	0.6 0.660%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7590361	jalview.datamodel.SeqCigarTest.testSomethingjalview.datamodel.SeqCigarTest.testSomething	1PASS
	0.18072289	jalview.datamodel.SeqCigarTest.testFindPositionjalview.datamodel.SeqCigarTest.testFindPosition	1PASS

 

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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.datamodel;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25
26		import jalview.gui.JvOptionPane;
27		import jalview.util.Comparison;
28
29		import org.testng.annotations.BeforeClass;
30		import org.testng.annotations.Test;
31
32		/**
33		* Unit tests for SeqCigar
34		*/
		97.6% Uncovered Elements: 2 (83) Complexity: 12 Complexity Density: 0.19
35		public class SeqCigarTest
36		{
37
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
38	1	@BeforeClass(alwaysRun = true)...
39		public void setUpJvOptionPane()
40		{
41	1	JvOptionPane.setInteractiveMode(false);
42	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
43		}
44
		100% Uncovered Elements: 0 (14) Complexity: 3 Complexity Density: 0.3 1PASS
45	1	@Test(groups = { "Functional" })...
46		public void testFindPosition()
47		{
48	1	SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
49	1	oseq.createDatasetSequence();
50	1	SeqCigar cs = new SeqCigar(oseq);
51	1	assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
52	16	for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
53		{
54	15	int os_p = oseq.findPosition(c);
55	15	int cigar_p = cs.findPosition(c);
56	15	if (Comparison.isGap(oseq.getCharAt(c)))
57		{
58	6	assertEquals("Expected gap at position " + os_p + " column " + c,
59		-1, cigar_p);
60		}
61		else
62		{
63	9	assertEquals("Positions don't match for at column " + c, os_p,
64		cigar_p);
65		}
66		}
67		}
68
69		/*
70		* refactored 'as is' from main method
71		*
72		* TODO: split into separate tests
73		*/
		100% Uncovered Elements: 0 (54) Complexity: 5 Complexity Density: 0.11 1PASS
74	1	@Test(groups = { "Functional" })...
75		public void testSomething() throws Exception
76		{
77	1	String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
78	1	Sequence s = new Sequence("MySeq", o_seq, 39, 80);
79	1	String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
80	1	Sequence s_gapped = new Sequence("MySeq", orig_gapped, 39, 80);
81	1	String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
82	1	s_gapped.setDatasetSequence(s);
83	1	String sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh";
84	1	Sequence s_subsequence_gapped = new Sequence("MySeq", sub_gapped_s, 43,
85		77);
86	1	s_subsequence_gapped.setDatasetSequence(s);
87
88	1	SeqCigar c_null = new SeqCigar(s);
89	1	String cs_null = c_null.getCigarstring();
90	1	assertEquals("Failed to recover ungapped sequence cigar operations",
91		"42M", cs_null);
92	1	testCigar_string(s_gapped, ex_cs_gapped);
93	1	SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
94	1	assertEquals("Failed parseCigar", ex_cs_gapped,
95		gen_sgapped.getCigarstring());
96
97	1	testSeqRecovery(gen_sgapped, s_gapped);
98
99		/*
100		* Test dataset resolution
101		*/
102	1	SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
103	1	testSeqRecovery(sub_gapped, s_subsequence_gapped);
104
105		/*
106		* Test width functions
107		*/
108	1	assertEquals("Failed getWidth", sub_gapped_s.length(),
109		sub_gapped.getWidth());
110
111	1	sub_gapped.getFullWidth();
112	1	assertFalse("hasDeletedRegions is incorrect",
113		sub_gapped.hasDeletedRegions());
114
115		// Test start-end region SeqCigar
116	1	SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
117	1	assertEquals(
118		"SeqCigar(seq, start, end) not properly clipped alignsequence",
119		41, sub_se_gp.getWidth());
120
121		/*
122		* TODO: can we add assertions to the sysouts that follow?
123		*/
124	1	System.out.println("\nOriginal sequence align:\n" + sub_gapped_s
125		+ "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
126		+ sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
127		+ sub_se_gp.getCigarstring() + "\n");
128	1	SequenceI ssgp = sub_se_gp.getSeq('-');
129	1	System.out.println("\t " + ssgp.getSequenceAsString());
130	11	for (int r = 0; r < 10; r++)
131		{
132	10	sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
133	10	int sl = sub_se_gp.getWidth();
134	10	int st = sl - 1 - r;
135	110	for (int rs = 0; rs < 10; rs++)
136		{
137	100	int e = st + rs;
138	100	sub_se_gp.deleteRange(st, e);
139	100	String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
140	100	System.out.println(st + "," + e + "\t:" + ssgapedseq);
141	100	st -= 3;
142		}
143		}
144
145	1	SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
146		new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
147	1	Alignment al = new Alignment(set);
148	4	for (int i = 0; i < al.getHeight(); i++)
149		{
150	3	System.out.println("" + al.getSequenceAt(i).getName() + "\t"
151		+ al.getSequenceAt(i).getStart() + "\t"
152		+ al.getSequenceAt(i).getEnd() + "\t"
153		+ al.getSequenceAt(i).getSequenceAsString());
154		}
155
156	1	System.out.println("Gapped.");
157	1	set = new SeqCigar[] { new SeqCigar(s),
158		new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
159	1	set[0].deleteRange(20, 25);
160	1	al = new Alignment(set);
161	4	for (int i = 0; i < al.getHeight(); i++)
162		{
163	3	System.out.println("" + al.getSequenceAt(i).getName() + "\t"
164		+ al.getSequenceAt(i).getStart() + "\t"
165		+ al.getSequenceAt(i).getEnd() + "\t"
166		+ al.getSequenceAt(i).getSequenceAsString());
167		}
168
169		// if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
170		// System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
171		}
172
173		/**
174		* non rigorous testing
175		*
176		* @param seq
177		* Sequence
178		* @param ex_cs_gapped
179		* String
180		* @return String
181		*/
182
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
183	1	protected void testCigar_string(Sequence seq, String ex_cs_gapped)...
184		{
185	1	SeqCigar c_sgapped = new SeqCigar(seq);
186	1	String cs_gapped = c_sgapped.getCigarstring();
187	1	assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
188		}
189
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
190	2	protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)...
191		{
192		// this is non-rigorous - start and end recovery is not tested.
193	2	SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
194		// assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
195		// gen_sgapped_s);
196	2	if (!gen_sgapped_s.getSequenceAsString().equals(
197		s_gapped.getSequenceAsString()))
198		{
199		// TODO: investigate errors reported here, to allow full conversion to
200		// passing JUnit assertion form
201	0	System.err.println("Couldn't reconstruct sequence.\n"
202		+ gen_sgapped_s.getSequenceAsString() + "\n"
203		+ s_gapped.getSequenceAsString());
204		}
205		}
206
207		}