Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentJob	28	33	16	0.00%	Show methods

Class AlignmentJob

Class AlignmentJob	Line # 28	Total Statements 33	Complexity 16	TOTAL Coverage 0.00%
AlignmentJob(List<SequenceI>,List<SequenceI>,Map<String, SequenceInfo>)   AlignmentJob(List<SequenceI>,List<SequenceI>,Map<String, SequenceInfo>)	3636	3.03	1.01	0.0 0.00%
create(SequenceI[],int,boolean) : AlignmentJob   create(SequenceI[],int,boolean) : AlignmentJob	4444	24.024	9.09	0.0 0.00%
isInputValid() : boolean   isInputValid() : boolean	8484	1.01	1.01	0.0 0.00%
getEmptySequences() : List<SequenceI>   getEmptySequences() : List<SequenceI>	9090	1.01	1.01	0.0 0.00%
getNames() : Map<String, SequenceInfo>   getNames() : Map<String, SequenceInfo>	9595	1.01	1.01	0.0 0.00%
hasResult() : boolean   hasResult() : boolean	100100	1.01	1.01	0.0 0.00%
getAlignmentResult() : AlignmentI   getAlignmentResult() : AlignmentI	105105	1.01	1.01	0.0 0.00%
setAlignmentResult(AlignmentI) : void   setAlignmentResult(AlignmentI) : void	110110	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.ws2.actions.alignment;
2
3		import java.util.ArrayList;
4		import java.util.Collections;
5		import java.util.LinkedHashMap;
6		import java.util.List;
7		import java.util.Map;
8
9		import jalview.analysis.AlignSeq;
10		import jalview.analysis.SeqsetUtils;
11		import jalview.analysis.SeqsetUtils.SequenceInfo;
12		import jalview.datamodel.AlignmentI;
13		import jalview.datamodel.Sequence;
14		import jalview.datamodel.SequenceI;
15		import jalview.util.Comparison;
16		import jalview.ws2.actions.BaseJob;
17		import jalview.ws2.api.WebServiceJobHandle;
18
19		/**
20		* A wrapper class that extends basic job container with data specific to
21		* alignment services. It stores input and empty sequences (with uniquified
22		* names) along the original sequence information. {@link AlignmentJob} objects
23		* are created by {@link AlignmentTask} during a preparation stage.
24		*
25		* @author mmwarowny
26		*
27		*/
		0% Uncovered Elements: 55 (55) Complexity: 16 Complexity Density: 0.48
28		class AlignmentJob extends BaseJob
29		{
30		private final List<SequenceI> emptySeqs;
31
32		private final Map<String, SequenceInfo> names;
33
34		private AlignmentI alignmentResult;
35
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
36	0	AlignmentJob(List<SequenceI> inputSeqs, List<SequenceI> emptySeqs,...
37		Map<String, SequenceInfo> names)
38		{
39	0	super(Collections.unmodifiableList(inputSeqs));
40	0	this.emptySeqs = Collections.unmodifiableList(emptySeqs);
41	0	this.names = Collections.unmodifiableMap(names);
42		}
43
		0% Uncovered Elements: 38 (38) Complexity: 9 Complexity Density: 0.38
44	0	public static AlignmentJob create(SequenceI[] seqs, int minlen, boolean keepGaps)...
45		{
46	0	int nseqs = 0;
47	0	for (int i = 0; i < seqs.length; i++)
48		{
49	0	if (seqs[i].getEnd() - seqs[i].getStart() >= minlen)
50	0	nseqs++;
51		}
52	0	boolean valid = nseqs > 1; // need at least two sequences
53	0	Map<String, SequenceInfo> names = new LinkedHashMap<>();
54	0	List<SequenceI> inputSeqs = new ArrayList<>();
55	0	List<SequenceI> emptySeqs = new ArrayList<>();
56	0	for (int i = 0; i < seqs.length; i++)
57		{
58	0	SequenceI seq = seqs[i];
59	0	String newName = SeqsetUtils.unique_name(i);
60	0	names.put(newName, SeqsetUtils.SeqCharacterHash(seq));
61	0	if (valid && seq.getEnd() - seq.getStart() >= minlen)
62		{
63		// make new input sequence
64	0	String seqString = seq.getSequenceAsString();
65	0	if (!keepGaps)
66	0	seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString);
67	0	inputSeqs.add(new Sequence(newName, seqString));
68		}
69		else
70		{
71	0	String seqString = "";
72	0	if (seq.getEnd() >= seq.getStart()) // true if gaps only
73		{
74	0	seqString = seq.getSequenceAsString();
75	0	if (!keepGaps)
76	0	seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString);
77		}
78	0	emptySeqs.add(new Sequence(newName, seqString));
79		}
80		}
81	0	return new AlignmentJob(inputSeqs, emptySeqs, names);
82		}
83
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
84	0	@Override...
85		public boolean isInputValid()
86		{
87	0	return inputSeqs.size() >= 2;
88		}
89
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
90	0	List<SequenceI> getEmptySequences()...
91		{
92	0	return emptySeqs;
93		}
94
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	Map<String, SequenceInfo> getNames()...
96		{
97	0	return names;
98		}
99
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
100	0	boolean hasResult()...
101		{
102	0	return alignmentResult != null;
103		}
104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	AlignmentI getAlignmentResult()...
106		{
107	0	return alignmentResult;
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	void setAlignmentResult(AlignmentI alignment)...
111		{
112	0	this.alignmentResult = alignment;
113		}
114		}