Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
A3mFile	8	8	6	0.7333333573.3%	Show methods

Class A3mFile

Class A3mFile	Line # 8	Total Statements 8	Complexity 6	TOTAL Coverage 0.7333333573.3%
A3mFile()   A3mFile()	1414	0.00	1.01	-1.0 -1.0 -
A3mFile(String,DataSourceType)   A3mFile(String,DataSourceType)	2929	1.01	1.01	0.0 0.00%
A3mFile(FileParse)   A3mFile(FileParse)	3535	1.01	1.01	1.0 1.0100%
A3mFile(FileParse,boolean)   A3mFile(FileParse,boolean)	4040	1.01	1.01	1.0 1.0100%
getSeqsAsArray() : SequenceI[]   getSeqsAsArray() : SequenceI[]	4646	5.05	2.02	0.85714287 0.8571428785.7%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.73333335	jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine	1PASS

 

Source view

1		package jalview.io;
2
3		import java.io.IOException;
4
5		import jalview.analysis.AlignmentUtils;
6		import jalview.datamodel.SequenceI;
7
		73.3% Uncovered Elements: 4 (15) Complexity: 6 Complexity Density: 0.75
8		public class A3mFile extends FastaFile
9		{
10
11		/**
12		* Creates a new FastaFile object.
13		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
14	0	public A3mFile()...
15		{
16		}
17
18		/**
19		* Creates a new FastaFile object.
20		*
21		* @param inFile
22		* DOCUMENT ME!
23		* @param sourceType
24		* DOCUMENT ME!
25		*
26		* @throws IOException
27		* DOCUMENT ME!
28		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
29	0	public A3mFile(String inFile, DataSourceType sourceType)...
30		throws IOException
31		{
32	0	super(inFile, sourceType);
33		}
34
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
35	1	public A3mFile(FileParse source) throws IOException...
36		{
37	1	this(source, true);
38		}
39
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
40	1	public A3mFile(FileParse source, boolean closeData) throws IOException...
41		{
42	1	super(source, closeData);
43		}
44
45		boolean expanded=false;
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
46	1	@Override...
47		public SequenceI[] getSeqsAsArray()
48		{
49	1	SequenceI[] seqs = super.getSeqsAsArray();
50	1	if (!expanded)
51		{
52	1	AlignmentUtils.a3mToMSA(seqs);
53	1	expanded=true;
54		}
55	1	return seqs;
56		}
57
58		}