Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HMMFileTest	26	259	23	0.993150799.3%	Show methods

Class HMMFileTest

Class HMMFileTest	Line # 26	Total Statements 259	Complexity 23	TOTAL Coverage 0.993150799.3%
setUp() : void   setUp() : void	3434	3.03	1.01	1.0 1.0100%
testParse() : void   testParse() : void	4747	49.049	1.01	1.0 1.0100%
testParse_minimalFile() : void   testParse_minimalFile() : void	124124	14.014	1.01	1.0 1.0100%
testParseHeaderLines_amino() : void   testParseHeaderLines_amino() : void	172172	30.030	1.01	1.0 1.0100%
testParseHeaderLines_dna() : void   testParseHeaderLines_dna() : void	212212	30.030	1.01	1.0 1.0100%
testFillList() : void   testFillList() : void	252252	25.025	3.03	1.0 1.0100%
testParseModel() : void   testParseModel() : void	294294	25.025	2.02	1.0 1.0100%
testParseAnnotations() : void   testParseAnnotations() : void	346346	30.030	1.01	1.0 1.0100%
testPrint_roundTrip() : void   testPrint_roundTrip() : void	392392	5.05	1.01	1.0 1.0100%
checkModelsMatch(HiddenMarkovModel,HiddenMarkovModel) : void   checkModelsMatch(HiddenMarkovModel,HiddenMarkovModel) : void	410410	10.010	3.03	1.0 1.0100%
testAppendProperties() : void   testAppendProperties() : void	437437	7.07	1.01	1.0 1.0100%
testAppendModelAsString() : void   testAppendModelAsString() : void	463463	13.013	1.01	1.0 1.0100%
findValue(int,int,int,String) : String   findValue(int,int,int,String) : String	496496	18.018	6.06	0.9285714 0.928571492.9%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.17123288	jalview.io.HMMFileTest.testParsejalview.io.HMMFileTest.testParse	1PASS
	0.14041096	jalview.io.HMMFileTest.testAppendModelAsStringjalview.io.HMMFileTest.testAppendModelAsString	1PASS
	0.10616438	jalview.io.HMMFileTest.testParseHeaderLines_dnajalview.io.HMMFileTest.testParseHeaderLines_dna	1PASS
	0.10616438	jalview.io.HMMFileTest.testParseAnnotationsjalview.io.HMMFileTest.testParseAnnotations	1PASS
	0.10616438	jalview.io.HMMFileTest.testParseHeaderLines_aminojalview.io.HMMFileTest.testParseHeaderLines_amino	1PASS
	0.10273973	jalview.io.HMMFileTest.testFillListjalview.io.HMMFileTest.testFillList	1PASS
	0.09589041	jalview.io.HMMFileTest.testParseModeljalview.io.HMMFileTest.testParseModel	1PASS
	0.07191781	jalview.io.HMMFileTest.testPrint_roundTripjalview.io.HMMFileTest.testPrint_roundTrip	1PASS
	0.051369864	jalview.io.HMMFileTest.testParse_minimalFilejalview.io.HMMFileTest.testParse_minimalFile	1PASS
	0.02739726	jalview.io.HMMFileTest.testAppendPropertiesjalview.io.HMMFileTest.testAppendProperties	1PASS

 

Source view

1		package jalview.io;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertFalse;
5		import static org.testng.Assert.assertNotNull;
6		import static org.testng.Assert.assertNull;
7		import static org.testng.Assert.assertTrue;
8
9		import jalview.datamodel.HMMNode;
10		import jalview.datamodel.HiddenMarkovModel;
11
12		import java.io.BufferedReader;
13		import java.io.File;
14		import java.io.FileNotFoundException;
15		import java.io.FileReader;
16		import java.io.IOException;
17		import java.util.ArrayList;
18		import java.util.List;
19		import java.util.Scanner;
20
21		import org.testng.annotations.BeforeClass;
22		import org.testng.annotations.Test;
23
24		import junit.extensions.PA;
25
		99.3% Uncovered Elements: 2 (292) Complexity: 23 Complexity Density: 0.09
26		public class HMMFileTest {
27
28		HMMFile fn3;
29
30		HMMFile pKinase;
31
32		HMMFile made1;
33
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
34	1	@BeforeClass(alwaysRun = true)...
35		public void setUp() throws IOException
36		{
37	1	fn3 = new HMMFile("test/jalview/io/test_fn3_hmm.txt",
38		DataSourceType.FILE);
39
40	1	pKinase = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
41		DataSourceType.FILE);
42
43	1	made1 = new HMMFile("test/jalview/io/test_MADE1_hmm.txt",
44		DataSourceType.FILE);
45		}
46
		100% Uncovered Elements: 0 (49) Complexity: 1 Complexity Density: 0.02 1PASS
47	1	@Test(groups = "Functional")...
48		public void testParse() throws IOException
49		{
50	1	HiddenMarkovModel hmm = pKinase.getHMM();
51	1	assertEquals(hmm.getName(), "Pkinase");
52	1	assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00069.17");
53	1	assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
54		"Protein kinase domain");
55	1	assertEquals(hmm.getLength(), 260);
56	1	assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
57	1	assertEquals(hmm.getAlphabetType(), "amino");
58	1	assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
59	1	assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
60	1	assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
61	1	assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
62	1	assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
63	1	assertEquals(hmm.getProperty(HMMFile.DATE), "Thu Jun 16 11:44:06 2011");
64	1	assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
65	1	assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "54");
66	1	assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
67		"3.358521");
68	1	assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3106786190");
69	1	assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
70		"70.30 70.30");
71	1	assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "70.30 70.30");
72	1	assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "70.20 70.20");
73
74	1	assertEquals(hmm.getSymbols(), "ACDEFGHIKLMNPQRSTVWY");
75
76	1	assertEquals(hmm.getMatchEmissionProbability(0, 'Y'), 0.16102, 0.001d);
77	1	assertEquals(hmm.getMatchEmissionProbability(11, 'P'), 0.0130, 0.001d);
78	1	assertEquals(hmm.getMatchEmissionProbability(24, 'I'), 0.02583, 0.001d);
79	1	assertEquals(hmm.getMatchEmissionProbability(83, 'C'), 0.008549,
80		0.001d);
81	1	assertEquals(hmm.getMatchEmissionProbability(332, 'E'), 0.07998,
82		0.001d);
83	1	assertEquals(hmm.getMatchEmissionProbability(381, 'D'), 0.014465,
84		0.001d);
85	1	assertEquals(hmm.getMatchEmissionProbability(475, 'Y'), 0.02213,
86		0.001d);
87
88	1	assertEquals(hmm.getInsertEmissionProbability(1, 'C'), 0.012, 0.001d);
89	1	assertEquals(hmm.getInsertEmissionProbability(14, 'H'), 0.02411,
90		0.001d);
91	1	assertEquals(hmm.getInsertEmissionProbability(23, 'L'), 0.06764,
92		0.001d);
93	1	assertEquals(hmm.getInsertEmissionProbability(90, 'D'), 0.0623, 0.001d);
94	1	assertEquals(hmm.getInsertEmissionProbability(374, 'T'), 0.0623,
95		0.001d);
96	1	assertEquals(hmm.getInsertEmissionProbability(470, 'P'), 0.0647,
97		0.001d);
98
99	1	assertEquals(hmm.getStateTransitionProbability(2, 6), 0.3848, 0.001d);
100	1	assertEquals(hmm.getStateTransitionProbability(38, 3), 0.5382, 0.001d);
101	1	assertEquals(hmm.getStateTransitionProbability(305, 3), 0.2916, 0.001d);
102	1	assertEquals(hmm.getStateTransitionProbability(380, 0), 0.99, 0.001d);
103	1	assertEquals(hmm.getStateTransitionProbability(453, 1), 0.0066, 0.001d);
104
105	1	assertEquals(hmm.getNodeMapPosition(3), 3);
106	1	assertEquals(hmm.getReferenceAnnotation(7), '-');
107	1	assertEquals(hmm.getConsensusResidue(23), 't');
108	1	assertEquals(hmm.getMaskedValue(30), '-');
109	1	assertEquals(hmm.getConsensusStructure(56), 'S');
110
111	1	assertEquals(hmm.getNodeMapPosition(78), 136);
112	1	assertEquals(hmm.getReferenceAnnotation(93), '-');
113	1	assertEquals(hmm.getConsensusResidue(145), 'a');
114	1	assertEquals(hmm.getMaskedValue(183), '-');
115	1	assertEquals(hmm.getConsensusStructure(240), 'H');
116		}
117
118		/**
119		* Test that Jalview can parse an HMM file even with a bunch of 'mandatory'
120		* fields missing (including no MAP annotation or // terminator line)
121		*
122		* @throws IOException
123		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
124	1	@Test(groups = "Functional")...
125		public void testParse_minimalFile() throws IOException
126		{
127		/*
128		* ALPH is absent, alphabet inferred from HMM header line
129		* Optional COMPO line is absent
130		* first line after HMM is a guide line for readability
131		* next line is BEGIN node insert emissions
132		* next line is BEGIN node transitions
133		* next line is first sequence node match emissions 1.1 1.2 1.3
134		* next line is first sequence node insert emissions 1.4 1.5 1.6
135		* last line is first sequence node transitions
136		*/
137		//@formatter:off
138	1	String hmmData =
139		"HMMER3\n" +
140		"HMM P M J\n" +
141		// both spec and parser require a line after the HMM line
142		" m->m m->i m->d i->m i->i d->m d->d\n" +
143		" 0.1 0.2 0.3\n" +
144		" 0.4 0.5 0.6 0.7 0.8 0.9 0.95\n" +
145		" 1 1.1 1.2 1.3 - - - - -\n" +
146		" 1.4 1.5 1.6\n" +
147		" 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n" +
148		" 2 1.01 1.02 1.03 - - - - -\n" +
149		" 1.04 1.05 1.06\n" +
150		" 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n";
151		//@formatter:on
152	1	HMMFile parser = new HMMFile(hmmData, DataSourceType.PASTE);
153	1	HiddenMarkovModel hmm = parser.getHMM();
154	1	assertNotNull(hmm);
155	1	assertEquals(hmm.getSymbols(), "PMJ");
156		// no LENG property: this should return node count excluding BEGIN node
157	1	assertEquals(hmm.getLength(), 2);
158
159		// node 1 (implicitly mapped to column 0)
160	1	double prob = hmm.getMatchEmissionProbability(0, 'p');
161	1	assertEquals(prob, Math.pow(Math.E, -1.1));
162	1	prob = hmm.getInsertEmissionProbability(0, 'J');
163	1	assertEquals(prob, Math.pow(Math.E, -1.6));
164
165		// node 2 (implicitly mapped to column 1)
166	1	prob = hmm.getMatchEmissionProbability(1, 'M');
167	1	assertEquals(prob, Math.pow(Math.E, -1.02));
168	1	prob = hmm.getInsertEmissionProbability(1, 'm');
169	1	assertEquals(prob, Math.pow(Math.E, -1.05));
170		}
171
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
172	1	@Test(groups = "Functional")...
173		public void testParseHeaderLines_amino() throws IOException
174		{
175	1	FileReader fr = new FileReader(
176		new File("test/jalview/io/test_fn3_hmm.txt"));
177	1	BufferedReader br = new BufferedReader(fr);
178	1	HiddenMarkovModel hmm = new HiddenMarkovModel();
179	1	HMMFile testee = new HMMFile();
180	1	PA.setValue(testee, "hmm", hmm);
181	1	testee.parseHeaderLines(br);
182	1	br.close();
183	1	fr.close();
184
185	1	assertEquals(hmm.getName(), "fn3");
186	1	assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00041.13");
187	1	assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
188		"Fibronectin type III domain");
189	1	assertEquals(hmm.getProperty(HMMFile.LENGTH), "86");
190	1	assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
191	1	assertEquals(hmm.getAlphabetType(), "amino");
192	1	assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
193	1	assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
194	1	assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
195	1	assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
196
197	1	assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
198	1	assertEquals(hmm.getProperty(HMMFile.DATE), "Fri Jun 20 08:22:31 2014");
199	1	assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
200	1	assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "106");
201	1	assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
202		"11.415833");
203	1	assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3564431818");
204	1	assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD), "8.00 7.20");
205	1	assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "8.00 7.20");
206	1	assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "7.90 7.90");
207	1	assertEquals(hmm.getViterbi(), "-9.7737 0.71847");
208	1	assertEquals(hmm.getMSV(), "-9.4043 0.71847");
209	1	assertEquals(hmm.getForward(), "-3.8341 0.71847");
210		}
211
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
212	1	@Test(groups = "Functional")...
213		public void testParseHeaderLines_dna() throws IOException
214		{
215	1	FileReader fr = new FileReader(
216		new File("test/jalview/io/test_MADE1_hmm.txt"));
217	1	BufferedReader br = new BufferedReader(fr);
218	1	HiddenMarkovModel hmm = new HiddenMarkovModel();
219	1	HMMFile testee = new HMMFile();
220	1	PA.setValue(testee, "hmm", hmm);
221	1	testee.parseHeaderLines(br);
222	1	br.close();
223	1	fr.close();
224
225	1	assertEquals(hmm.getName(), "MADE1");
226	1	assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER),
227		"DF0000629.2");
228	1	assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
229		"MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon");
230	1	assertEquals(hmm.getProperty(HMMFile.LENGTH), "80");
231	1	assertEquals(hmm.getProperty(HMMFile.MAX_LENGTH), "426");
232	1	assertEquals(hmm.getAlphabetType(), "DNA");
233	1	assertTrue(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
234	1	assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
235	1	assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
236	1	assertFalse(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
237	1	assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
238	1	assertEquals(hmm.getProperty(HMMFile.DATE), "Tue Feb 19 20:33:41 2013");
239	1	assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
240	1	assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "1997");
241	1	assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES), "3.911818");
242	1	assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3015610723");
243	1	assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
244		"2.324 4.234");
245	1	assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "2.343 1.212");
246	1	assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "2.354 5.456");
247	1	assertEquals(hmm.getViterbi(), "-9.3632 0.71858");
248	1	assertEquals(hmm.getMSV(), "-8.5786 0.71858");
249	1	assertEquals(hmm.getForward(), "-3.4823 0.71858");
250		}
251
		100% Uncovered Elements: 0 (29) Complexity: 3 Complexity Density: 0.12 1PASS
252	1	@Test(groups = "Functional")...
253		public void testFillList() throws IOException
254		{
255	1	Scanner scanner1 = new Scanner("1.3 2.4 5.3 3.9 9.8 4.7 4.3 2.3 6.9");
256	1	ArrayList<Double> filledArray = new ArrayList<>();
257
258	1	filledArray.add(0.27253);
259	1	filledArray.add(0.0907);
260	1	filledArray.add(0.00499);
261	1	filledArray.add(0.02024);
262	1	filledArray.add(0.00005);
263	1	filledArray.add(0.00909);
264	1	filledArray.add(0.01357);
265	1	filledArray.add(0.10026);
266	1	filledArray.add(0.001);
267
268	1	double[] testList = HMMFile.parseDoubles(scanner1, 9);
269
270	10	for (int i = 0; i < 9; i++)
271		{
272	9	assertEquals(testList[i], filledArray.get(i), 0.001d);
273		}
274
275	1	filledArray.clear();
276	1	scanner1.close();
277
278	1	Scanner scanner2 = new Scanner(
279		"1.346 5.554 35.345 5.64 1.4");
280	1	filledArray.add(0.2603);
281	1	filledArray.add(0.00387);
282	1	filledArray.add(0d);
283	1	filledArray.add(0.00355);
284	1	filledArray.add(0.2466);
285
286	1	testList = HMMFile.parseDoubles(scanner2, 5);
287
288	6	for (int i = 0; i < 5; i++)
289		{
290	5	assertEquals(testList[i], filledArray.get(i), 0.001d);
291		}
292		}
293
		100% Uncovered Elements: 0 (27) Complexity: 2 Complexity Density: 0.08 1PASS
294	1	@Test(groups = "Functional")...
295		public void testParseModel() throws IOException
296		{
297	1	FileReader fr = new FileReader(
298		new File("test/jalview/io/test_MADE1_hmm.txt"));
299	1	BufferedReader br = new BufferedReader(fr);
300	1	HiddenMarkovModel testHMM = new HiddenMarkovModel();
301	1	String line = null;
302	1	do
303		{
304	23	line = br.readLine(); // skip header lines up to HMM plus one
305	23	} while (!line.startsWith("HMM "));
306	1	br.readLine();
307
308	1	made1.parseModel(br);
309	1	testHMM = made1.getHMM();
310
311	1	br.close();
312	1	fr.close();
313
314	1	assertEquals(testHMM.getMatchEmissionProbability(1, 'C'), 0.09267,
315		0.001d);
316	1	assertEquals(testHMM.getMatchEmissionProbability(25, 'G'), 0.07327,
317		0.001d);
318	1	assertEquals(testHMM.getMatchEmissionProbability(1092, 'C'), 0.04184,
319		0.001d);
320	1	assertEquals(testHMM.getMatchEmissionProbability(1107, 'G'), 0.07,
321		0.001d);
322
323	1	assertEquals(testHMM.getInsertEmissionProbability(0, 'G'), 0.25,
324		0.001d);
325	1	assertEquals(testHMM.getInsertEmissionProbability(247, 'T'), 0.2776,
326		0.001d);
327	1	assertEquals(testHMM.getInsertEmissionProbability(1096, 'T'), 0.25,
328		0.001d);
329	1	assertEquals(testHMM.getInsertEmissionProbability(1111, 'T'), 0.25,
330		0.001d);
331
332	1	assertEquals(testHMM.getStateTransitionProbability(1, 0), 0.9634,
333		0.001d);
334	1	assertEquals(testHMM.getStateTransitionProbability(5, 1), 0.0203,
335		0.001d);
336	1	assertEquals(testHMM.getStateTransitionProbability(14, 3), 0.2515,
337		0.001d);
338	1	assertEquals(testHMM.getStateTransitionProbability(65, 4), 0.78808,
339		0.001d);
340	1	assertEquals(testHMM.getStateTransitionProbability(1080, 2), 0.01845,
341		0.001d);
342	1	assertEquals(testHMM.getStateTransitionProbability(1111, 6),
343		Double.NEGATIVE_INFINITY);
344		}
345
		100% Uncovered Elements: 0 (30) Complexity: 1 Complexity Density: 0.03 1PASS
346	1	@Test(groups = "Functional")...
347		public void testParseAnnotations()
348		{
349	1	HMMFile testFile = new HMMFile();
350	1	HiddenMarkovModel hmm = new HiddenMarkovModel();
351	1	PA.setValue(testFile, "hmm", hmm);
352
353	1	List<HMMNode> nodes = new ArrayList<>();
354	1	nodes.add(new HMMNode()); // BEGIN node
355
356	1	hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
357	1	hmm.setProperty(HMMFile.MAP, "yes");
358	1	hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
359	1	hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "yes");
360	1	hmm.setProperty(HMMFile.MASKED_VALUE, "yes");
361	1	Scanner scanner = new Scanner("1345 t t t t");
362	1	HMMNode node = new HMMNode();
363	1	nodes.add(node);
364	1	testFile.parseAnnotations(scanner, node);
365
366	1	hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
367	1	hmm.setProperty(HMMFile.MAP, "no");
368	1	hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
369	1	hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "no");
370	1	hmm.setProperty(HMMFile.MASKED_VALUE, "no");
371	1	Scanner scanner2 = new Scanner("- y x - -");
372	1	node = new HMMNode();
373	1	nodes.add(node);
374	1	testFile.parseAnnotations(scanner2, node);
375
376	1	hmm.setNodes(nodes);
377
378	1	assertEquals(hmm.getNodeMapPosition(1), 1345);
379	1	assertEquals(hmm.getConsensusResidue(1), 't');
380	1	assertEquals(hmm.getReferenceAnnotation(1), 't');
381	1	assertEquals(hmm.getMaskedValue(1), 't');
382	1	assertEquals(hmm.getConsensusStructure(1), 't');
383
384	1	scanner.close();
385		}
386
387		/**
388		* tests to see if file produced by the output matches the file from the input
389		*
390		* @throws IOException
391		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
392	1	@Test(groups = "Functional")...
393		public void testPrint_roundTrip() throws IOException
394		{
395	1	String output = pKinase.print();
396	1	HMMFile pKinaseClone = new HMMFile(
397		new FileParse(output, DataSourceType.PASTE));
398	1	HiddenMarkovModel pKinaseHMM = pKinase.getHMM();
399	1	HiddenMarkovModel pKinaseCloneHMM = pKinaseClone.getHMM();
400
401	1	checkModelsMatch(pKinaseHMM, pKinaseCloneHMM);
402		}
403
404		/**
405		* A helper method to check two HMM models have the same values
406		*
407		* @param model1
408		* @param model2
409		*/
		100% Uncovered Elements: 0 (14) Complexity: 3 Complexity Density: 0.3
410	1	protected void checkModelsMatch(HiddenMarkovModel model1,...
411		HiddenMarkovModel model2)
412		{
413	1	assertEquals(model1.getLength(), model2.getLength());
414
415	261	for (int i = 0; i < model1.getLength(); i++)
416		{
417	260	String msg = "For Node" + i;
418	260	assertEquals(model1.getNode(i).getMatchEmissions(),
419		model2.getNode(i).getMatchEmissions(), msg);
420	260	assertEquals(model1.getNode(i).getInsertEmissions(),
421		model2.getNode(i).getInsertEmissions(), msg);
422	260	assertEquals(model1.getNode(i).getStateTransitions(),
423		model2.getNode(i).getStateTransitions(), msg);
424
425	260	if (i > 0)
426		{
427	259	assertEquals(model1.getNodeMapPosition(i),
428		model2.getNodeMapPosition(i), msg);
429	259	assertEquals(model1.getReferenceAnnotation(i),
430		model2.getReferenceAnnotation(i), msg);
431	259	assertEquals(model1.getConsensusResidue(i),
432		model2.getConsensusResidue(i), msg);
433		}
434		}
435		}
436
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
437	1	@Test(groups = "Functional")...
438		public void testAppendProperties() throws FileNotFoundException
439		{
440	1	StringBuilder sb = new StringBuilder();
441	1	fn3.appendProperties(sb);
442
443	1	Scanner testScanner = new Scanner(sb.toString());
444
445	1	String[] expected = new String[] { "HMMER3/f [3.1b1 | May 2013]",
446		"NAME fn3", "ACC PF00041.13",
447		"DESC Fibronectin type III domain", "LENG 86", "ALPH amino",
448		"RF no", "MM no", "CONS yes", "CS yes", "MAP yes",
449		"DATE Fri Jun 20 08:22:31 2014", "NSEQ 106", "EFFN 11.415833",
450		"CKSUM 3564431818", "GA 8.00 7.20", "TC 8.00 7.20",
451		"NC 7.90 7.90", "STATS LOCAL MSV -9.4043 0.71847",
452		"STATS LOCAL VITERBI -9.7737 0.71847",
453		"STATS LOCAL FORWARD -3.8341 0.71847" };
454
455	1	for (String value : expected)
456		{
457	21	assertEquals(testScanner.nextLine(), value);
458		}
459
460	1	testScanner.close();
461		}
462
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
463	1	@Test(groups = "Functional")...
464		public void testAppendModelAsString() throws FileNotFoundException
465		{
466	1	StringBuilder sb = new StringBuilder();
467	1	fn3.appendModelAsString(sb);
468	1	String string = sb.toString();
469
470	1	assertEquals(findValue(2, 2, 2, string), "4.42225");
471	1	assertEquals(findValue(12, 14, 1, string), "2.79307");
472	1	assertEquals(findValue(6, 24, 3, string), "0.48576");
473	1	assertEquals(findValue(19, 33, 2, string), "4.58477");
474	1	assertEquals(findValue(20, 64, 2, string), "3.61505");
475	1	assertEquals(findValue(3, 72, 3, string), "6.81068");
476	1	assertEquals(findValue(10, 80, 2, string), "2.69355");
477	1	assertEquals(findValue(16, 65, 1, string), "2.81003");
478	1	assertEquals(findValue(14, 3, 1, string), "2.69012");
479	1	assertEquals(findValue(11, 32, 1, string), "4.34805");
480		}
481
482		/**
483		* A helper method to find a token in the model string
484		*
485		* @param symbolIndex
486		* index of symbol being searched. First symbol has index 1.
487		* @param nodeIndex
488		* index of node being searched. Begin node has index 0. First node
489		* has index 1.
490		* @param line
491		* index of line being searched in node. First line has index 1.
492		* @param model
493		* string model being searched
494		* @return value at specified position
495		*/
		92.9% Uncovered Elements: 2 (28) Complexity: 6 Complexity Density: 0.33
496	10	private String findValue(int symbolIndex, int nodeIndex, int line,...
497		String model)
498		{
499	10	String value = "";
500	10	Scanner scanner = new Scanner(model);
501	10	scanner.nextLine();
502	10	scanner.nextLine();
503
504	18	for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
505		{
506	8	scanner.nextLine();
507		}
508	399	for (int node = 0; node < nodeIndex; node++)
509		{
510	389	scanner.nextLine();
511	389	scanner.nextLine();
512	389	scanner.nextLine();
513		}
514
515	123	for (int symbol = 0; symbol < symbolIndex; symbol++)
516		{
517	113	value = scanner.next();
518	113	if ("COMPO".equals(value))
519		{
520	0	scanner.next();
521		}
522	113	else if (value.length() < 7)
523		{
524	4	scanner.next();
525		}
526		}
527	10	scanner.close();
528	10	return value;
529		}
530		}
531