Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SecStructPredMsaTask	32	38	8	0.00%	Show methods
SecStructPredMsaTask.SecStructPredJob	118	6	3	0.00%	Show methods

Class SecStructPredMsaTask

Class SecStructPredMsaTask	Line # 32	Total Statements 38	Complexity 8	TOTAL Coverage 0.00%
SecStructPredMsaTask(SecStructPredWebServiceClientI,List<ArgumentI>,Credentials,AlignViewportI)   SecStructPredMsaTask(SecStructPredWebServiceClientI,List<ArgumentI>,Credentials,AlignViewportI)	4343	5.05	1.01	0.0 0.00%
prepareJobs() : List<SecStructPredJob>   prepareJobs() : List<SecStructPredJob>	5454	14.014	3.03	0.0 0.00%
collectResult(List<SecStructPredJob>) : AlignmentI   collectResult(List<SecStructPredJob>) : AlignmentI	7878	19.019	4.04	0.0 0.00%

 

Class SecStructPredMsaTask.SecStructPredJob

Class SecStructPredMsaTask.SecStructPredJob	Line # 118	Total Statements 6	Complexity 3	TOTAL Coverage 0.00%
SecStructPredJob(List<SequenceI>,SequenceI,int[],Map<String, SequenceInfo>)   SecStructPredJob(List<SequenceI>,SequenceI,int[],Map<String, SequenceInfo>)	126126	4.04	1.01	0.0 0.00%
isInputValid() : boolean   isInputValid() : boolean	135135	1.01	1.01	0.0 0.00%
getDelMap() : int[]   getDelMap() : int[]	141141	1.01	1.01	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.ws2.actions.secstructpred;
2
3		import java.io.IOException;
4		import java.util.ArrayList;
5		import java.util.Arrays;
6		import java.util.List;
7		import java.util.Map;
8
9		import jalview.analysis.AlignmentAnnotationUtils;
10		import jalview.analysis.SeqsetUtils;
11		import jalview.analysis.SeqsetUtils.SequenceInfo;
12		import jalview.api.AlignViewportI;
13		import jalview.bin.Console;
14		import jalview.datamodel.Alignment;
15		import jalview.datamodel.AlignmentAnnotation;
16		import jalview.datamodel.AlignmentI;
17		import jalview.datamodel.AlignmentView;
18		import jalview.datamodel.HiddenColumns;
19		import jalview.datamodel.SeqCigar;
20		import jalview.datamodel.SequenceI;
21		import jalview.io.AlignFile;
22		import jalview.io.JPredFile;
23		import jalview.io.JnetAnnotationMaker;
24		import jalview.ws.params.ArgumentI;
25		import jalview.ws2.actions.BaseJob;
26		import jalview.ws2.actions.BaseTask;
27		import jalview.ws2.actions.ServiceInputInvalidException;
28		import jalview.ws2.api.Credentials;
29		import jalview.ws2.api.JobStatus;
30		import jalview.ws2.client.api.SecStructPredWebServiceClientI;
31
		0% Uncovered Elements: 49 (49) Complexity: 8 Complexity Density: 0.21
32		public class SecStructPredMsaTask
33		extends BaseTask<SecStructPredMsaTask.SecStructPredJob, AlignmentI>
34		{
35		private final SecStructPredWebServiceClientI client;
36
37		private final AlignmentView alignmentView;
38
39		private final AlignmentI currentView;
40
41		private final char gapChar;
42
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
43	0	SecStructPredMsaTask(SecStructPredWebServiceClientI client,...
44		List<ArgumentI> args, Credentials credentials,
45		AlignViewportI viewport)
46		{
47	0	super(client, args, credentials);
48	0	this.client = client;
49	0	this.alignmentView = viewport.getAlignmentView(true);
50	0	this.currentView = viewport.getAlignment();
51	0	this.gapChar = viewport.getGapCharacter();
52		}
53
		0% Uncovered Elements: 18 (18) Complexity: 3 Complexity Density: 0.21
54	0	@Override...
55		protected List<SecStructPredJob> prepareJobs()
56		throws ServiceInputInvalidException
57		{
58	0	SeqCigar[] msf = alignmentView.getSequences();
59	0	SequenceI referenceSeq = msf[0].getSeq('-');
60	0	int[] delMap = alignmentView
61		.getVisibleContigMapFor(referenceSeq.gapMap());
62
63		// TODO: assume MSA for now
64	0	SequenceI[] sequences = new SequenceI[msf.length];
65	0	for (int i = 0; i < msf.length; i++)
66	0	sequences[i] = msf[i].getSeq('-');
67	0	var sequenceInfo = SeqsetUtils.uniquify(sequences, true);
68	0	referenceSeq.setSequence(alignmentView.getASequenceString('-', 0));
69	0	for (int i = 0; i < sequences.length; i++)
70	0	sequences[i].setSequence(alignmentView.getASequenceString('-', i));
71	0	var nonEmptySeqs = SeqsetUtils.getNonEmptySequenceSet(sequences);
72	0	var job = new SecStructPredJob(Arrays.asList(nonEmptySeqs),
73		referenceSeq, delMap, sequenceInfo);
74	0	job.setStatus(JobStatus.READY);
75	0	return List.of(job);
76		}
77
		0% Uncovered Elements: 23 (23) Complexity: 4 Complexity Density: 0.21
78	0	@Override...
79		protected AlignmentI collectResult(List<SecStructPredJob> jobs)
80		throws IOException
81		{
82	0	var job = jobs.get(0); // There shouldn't be more than one job
83	0	var status = job.getStatus();
84	0	Console.info(
85		String.format("sec str pred job \"%s\" finished with status %s",
86		job.getServerJob().getJobId(), status));
87	0	if (status != JobStatus.COMPLETED)
88	0	return null;
89	0	JPredFile predictionFile = client.getPredictionFile(job.getServerJob());
90	0	AlignFile alignmentFile = client.getAlignmentFile(job.getServerJob());
91
92	0	Object[] alnAndHiddenCols = alignmentView
93		.getAlignmentAndHiddenColumns(gapChar);
94	0	Alignment aln = new Alignment((SequenceI[]) alnAndHiddenCols[0]);
95	0	aln.setDataset(currentView.getDataset());
96	0	aln.setHiddenColumns((HiddenColumns) alnAndHiddenCols[1]);
97	0	try
98		{
99	0	JnetAnnotationMaker.add_annotation(predictionFile, aln, 0, false,
100		job.getDelMap());
101		} catch (Exception e)
102		{
103	0	throw new IOException(e);
104		}
105
106	0	for (AlignmentAnnotation alnAnnot : aln.getAlignmentAnnotation())
107		{
108	0	if (alnAnnot.sequenceRef != null)
109		{
110	0	AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(alnAnnot,
111		alnAnnot.label, getClass().getSimpleName());
112		}
113		}
114	0	aln.setSeqrep(aln.getSequenceAt(0));
115	0	return aln;
116		}
117
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.5
118		public static class SecStructPredJob extends BaseJob
119		{
120		private final int[] delMap;
121
122		private final SequenceI refSeq;
123
124		final Map<String, SequenceInfo> seqNames;
125
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
126	0	SecStructPredJob(List<SequenceI> sequences, SequenceI refSeq,...
127		int[] delMap, Map<String, SequenceInfo> seqNames)
128		{
129	0	super(sequences);
130	0	this.refSeq = refSeq;
131	0	this.delMap = delMap;
132	0	this.seqNames = seqNames;
133		}
134
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	@Override...
136		public boolean isInputValid()
137		{
138	0	return true;
139		}
140
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	public int[] getDelMap()...
142		{
143	0	return this.delMap;
144		}
145		}
146
147		}