Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PhmmerTask	25	37	12	0.00%	Show methods

Class PhmmerTask

Class PhmmerTask	Line # 25	Total Statements 37	Complexity 12	TOTAL Coverage 0.00%
PhmmerTask(AlignmentWebServiceClientI,List<ArgumentI>,Credentials,AlignmentView)   PhmmerTask(AlignmentWebServiceClientI,List<ArgumentI>,Credentials,AlignmentView)	3030	3.03	1.01	0.0 0.00%
isInputValid() : boolean   isInputValid() : boolean	4747	1.01	1.01	0.0 0.00%
prepareJobs() : List<BaseJob>   prepareJobs() : List<BaseJob>	3838	6.06	1.01	0.0 0.00%
collectResult(List<BaseJob>) : AlignmentI   collectResult(List<BaseJob>) : AlignmentI	5757	16.016	5.05	0.0 0.00%
alignQeuryToReferencePositions(SequenceI,AlignmentAnnotation) : SequenceI   alignQeuryToReferencePositions(SequenceI,AlignmentAnnotation) : SequenceI	8787	11.011	4.04	0.0 0.00%

 

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1		package jalview.ws2.actions.hmmer;
2
3		import static jalview.util.Comparison.GapChars;
4
5		import java.io.IOException;
6		import java.util.List;
7
8		import jalview.analysis.AlignSeq;
9		import jalview.bin.Console;
10		import jalview.datamodel.AlignmentAnnotation;
11		import jalview.datamodel.AlignmentI;
12		import jalview.datamodel.AlignmentView;
13		import jalview.datamodel.Annotation;
14		import jalview.datamodel.Sequence;
15		import jalview.datamodel.SequenceI;
16		import jalview.util.Comparison;
17		import jalview.ws.params.ArgumentI;
18		import jalview.ws2.actions.BaseJob;
19		import jalview.ws2.actions.BaseTask;
20		import jalview.ws2.actions.ServiceInputInvalidException;
21		import jalview.ws2.api.Credentials;
22		import jalview.ws2.api.JobStatus;
23		import jalview.ws2.client.api.AlignmentWebServiceClientI;
24
		0% Uncovered Elements: 52 (52) Complexity: 12 Complexity Density: 0.32
25		class PhmmerTask extends BaseTask<BaseJob, AlignmentI>
26		{
27		private final AlignmentWebServiceClientI client;
28		private final AlignmentView view;
29
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
30	0	PhmmerTask(AlignmentWebServiceClientI client, List<ArgumentI> args,...
31		Credentials credentials, AlignmentView view)
32		{
33	0	super(client, args, credentials);
34	0	this.client = client;
35	0	this.view = view;
36		}
37
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
38	0	@Override...
39		protected List<BaseJob> prepareJobs() throws ServiceInputInvalidException
40		{
41	0	Console.info("Preparing sequence for phmmer job");
42	0	var sequence = view.getVisibleAlignment('-').getSequenceAt(0);
43	0	var seq = new Sequence(sequence.getName(),
44		AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString()));
45	0	var job = new BaseJob(List.of(seq))
46		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	@Override...
48		public boolean isInputValid()
49		{
50	0	return true;
51		}
52		};
53	0	job.setStatus(JobStatus.READY);
54	0	return List.of(job);
55		}
56
		0% Uncovered Elements: 22 (22) Complexity: 5 Complexity Density: 0.31
57	0	@Override...
58		protected AlignmentI collectResult(List<BaseJob> jobs) throws IOException
59		{
60	0	var job = jobs.get(0);
61	0	var status = job.getStatus();
62	0	Console.info(String.format("phmmer finished job \"%s\" with status %s",
63		job.getServerJob().getJobId(), status));
64	0	if (status != JobStatus.COMPLETED)
65	0	return null;
66	0	var outputAlignment = client.getAlignment(job.getServerJob());
67	0	var querySeq = job.getInputSequences().get(0).deriveSequence();
68		{
69	0	AlignmentAnnotation refpos = null;
70	0	for (var annot : outputAlignment.getAlignmentAnnotation())
71		{
72	0	if (annot.sequenceRef == null && annot.label.equals("Reference Positions"))
73		{
74	0	refpos = annot;
75	0	break;
76		}
77		}
78	0	if (refpos != null)
79		{
80	0	querySeq = alignQeuryToReferencePositions(querySeq, refpos);
81		}
82		}
83	0	outputAlignment.insertSequenceAt(0, querySeq);
84	0	return outputAlignment;
85		}
86
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.36
87	0	private SequenceI alignQeuryToReferencePositions(SequenceI query, AlignmentAnnotation refpos)...
88		{
89	0	var sequenceBuilder = new StringBuilder();
90	0	var index = 0;
91	0	for (Annotation a : refpos.annotations)
92		{
93		// TODO: we assume that the number of "x" annotations is equal to the number
94		// of residues. may need a safeguard against invalid input
95	0	if (a != null && a.displayCharacter.equals("x"))
96		{
97	0	char c;
98	0	do
99	0	c = query.getCharAt(index++);
100	0	while (Comparison.isGap(c));
101	0	sequenceBuilder.append(c);
102		}
103		else
104		{
105	0	sequenceBuilder.append(Comparison.GAP_DASH);
106		}
107		}
108	0	query.setSequence(sequenceBuilder.toString());
109	0	return query;
110		}
111		}