Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JabawsAnnotationInstance	30	64	29	0.00%	Show methods

Class JabawsAnnotationInstance

Class JabawsAnnotationInstance	Line # 30	Total Statements 64	Complexity 29	TOTAL Coverage 0.00%
JabawsAnnotationInstance(Jws2Instance)   JabawsAnnotationInstance(Jws2Instance)	4040	1.01	1.01	0.0 0.00%
getCalcId() : String   getCalcId() : String	5353	1.01	2.02	0.0 0.00%
submitToService(List<SequenceI>,WsParamSetI,List<ArgumentI>) : JobId   submitToService(List<SequenceI>,WsParamSetI,List<ArgumentI>) : JobId	5959	18.018	9.09	0.0 0.00%
getAnnotationResult(JobId,List<SequenceI>,Map<String, FeatureColourI>,Map<String, FeatureMatcherSetI>) : List<AlignmentAnnotation>   getAnnotationResult(JobId,List<SequenceI>,Map<String, FeatureColourI>,Map<String, FeatureMatcherSetI>) : List<AlignmentAnnotation>	112112	7.07	3.03	0.0 0.00%
createAnnotationRowsForScores(AlignmentI,boolean[],List<AlignmentAnnotation>,String,int,Score) : void   createAnnotationRowsForScores(AlignmentI,boolean[],List<AlignmentAnnotation>,String,int,Score) : void	164164	4.04	3.03	0.0 0.00%
createAnnotationRowsForScores(AlignmentI,boolean[],List<AlignmentAnnotation>,String,String,SequenceI,int,Score) : AlignmentAnnotation   createAnnotationRowsForScores(AlignmentI,boolean[],List<AlignmentAnnotation>,String,String,SequenceI,int,Score) : AlignmentAnnotation	194194	8.08	1.01	0.0 0.00%
constructAnnotationFromScore(boolean[],AlignmentAnnotation,int,int,Score) : void   constructAnnotationFromScore(boolean[],AlignmentAnnotation,int,int,Score) : void	227227	25.025	10.010	0.0 0.00%

 

Contributing tests

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1		package jalview.ws.jws2.jabaws2;
2
3		import jalview.api.FeatureColourI;
4		import jalview.datamodel.Alignment;
5		import jalview.datamodel.AlignmentAnnotation;
6		import jalview.datamodel.AlignmentI;
7		import jalview.datamodel.Annotation;
8		import jalview.datamodel.SequenceI;
9		import jalview.datamodel.features.FeatureMatcherSetI;
10		import jalview.util.MessageManager;
11		import jalview.ws.api.JobId;
12		import jalview.ws.api.SequenceAnnotationServiceI;
13		import jalview.ws.jws2.JabaParamStore;
14		import jalview.ws.jws2.JabaPreset;
15		import jalview.ws.params.ArgumentI;
16		import jalview.ws.params.WsParamSetI;
17
18		import java.util.ArrayList;
19		import java.util.Iterator;
20		import java.util.List;
21		import java.util.Map;
22
23		import compbio.data.msa.SequenceAnnotation;
24		import compbio.data.sequence.FastaSequence;
25		import compbio.data.sequence.Score;
26		import compbio.data.sequence.ScoreManager;
27		import compbio.metadata.JobSubmissionException;
28		import compbio.metadata.WrongParameterException;
29
		0% Uncovered Elements: 103 (103) Complexity: 29 Complexity Density: 0.45
30		public abstract class JabawsAnnotationInstance
31		extends JabawsServiceInstance<SequenceAnnotation>
32		implements SequenceAnnotationServiceI
33		{
34
35		/**
36		* holds last results obtained when non-null. TODO: remove this as a field ?
37		*/
38		protected ScoreManager scoremanager = null;
39
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
40	0	public JabawsAnnotationInstance(Jws2Instance handle)...
41		{
42	0	super(handle);
43		}
44
45
46		/**
47		*
48		* @return the calcId for this Jabaws Service (convenience method).
49		*
50		* TODO: decide if this is really convenient since manager and
51		* instance have same method !
52		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
53	0	public String getCalcId()...
54		{
55	0	return our.getAlignAnalysisUI() == null ? null
56		: our.getAlignAnalysisUI().getCalcId();
57		}
58
		0% Uncovered Elements: 28 (28) Complexity: 9 Complexity Density: 0.5
59	0	@Override...
60		public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset,
61		List<ArgumentI> arguments) throws Throwable
62		{
63	0	String rslt = null;
64	0	scoremanager = null;
65	0	List<FastaSequence> jabaseqs = new ArrayList(seqs.size());
66	0	for (SequenceI seq : seqs)
67		{
68	0	jabaseqs.add(
69		new FastaSequence(seq.getName(), seq.getSequenceAsString()));
70		}
71	0	if (preset == null && arguments == null)
72		{
73	0	rslt = service.analize(jabaseqs);
74		}
75	0	if (preset != null)
76		{
77	0	if (preset instanceof JabaPreset)
78		{
79		// TODO: verify behaviour is really the same, since preset analyze was
80		// never called in Jalview 2.11.x
81	0	rslt = service.presetAnalize(jabaseqs,
82		((JabaPreset) preset).getJabaPreset());
83		}
84		else
85		{
86	0	rslt = service.customAnalize(jabaseqs,
87		JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
88		}
89		}
90	0	else if (arguments != null && arguments.size() > 0)
91		{
92	0	try
93		{
94	0	rslt = service.customAnalize(jabaseqs,
95		JabaParamStore.getJabafromJwsArgs(arguments));
96		} catch (WrongParameterException x)
97		{
98	0	throw new JobSubmissionException(MessageManager.getString(
99		"exception.jobsubmission_invalid_params_set"), x);
100
101		}
102		}
103
104	0	if (rslt == null)
105		{
106	0	return null;
107		}
108	0	return new JobId(our.getServiceType(), our.getName(), rslt);
109		}
110
111
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
112	0	@Override...
113		public
114		List<AlignmentAnnotation> getAnnotationResult(JobId job,
115		List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
116		Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
117		{
118	0	if (scoremanager == null)
119		{
120		// TODO: raise annotation unavailable exception ?
121	0	scoremanager = service.getAnnotation(job.getJobId());
122		}
123	0	if (scoremanager == null)
124		{
125	0	return List.of();
126		}
127		/**
128		* dummy alignment to perform annotation on
129		*/
130	0	AlignmentI newal = new Alignment(seqs.toArray(new SequenceI[0]));
131	0	List<AlignmentAnnotation> ourAnnot = annotationFromScoreManager(newal,
132		featureColours, featureFilters);
133	0	return ourAnnot;
134		}
135
136		/**
137		* service specific annotation creation method
138		*
139		* @param seqs
140		* - sequences to be annotated with results
141		* @param featureColours
142		* - - updated with any colours imported during result processing
143		* @param featureFilters
144		* - updated with any filters imported during result processing
145		*
146		* @return
147		*/
148		abstract List<AlignmentAnnotation> annotationFromScoreManager(
149		AlignmentI seqs, Map<String, FeatureColourI> featureColours,
150		Map<String, FeatureMatcherSetI> featureFilters);
151
152
153		/**
154		* create and complete an annotation row from a JABAWS score object
155		*
156		* @param alignViewport
157		* @param gapMap
158		* @param ourAnnot
159		* @param calcId
160		* @param alWidth
161		* @param scr
162		*/
163
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
164	0	protected void createAnnotationRowsForScores(AlignmentI al_result,...
165		boolean[] gapMap, List<AlignmentAnnotation> ourAnnot,
166		String calcId,
167		int alWidth, Score scr)
168		{
169		// simple annotation row
170	0	AlignmentAnnotation annotation = al_result
171		.findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
172		null);
173	0	if (gapMap == null || alWidth == gapMap.length) // scr.getScores().size())
174		{
175	0	constructAnnotationFromScore(gapMap, annotation, 0,
176		alWidth, scr);
177	0	ourAnnot.add(annotation);
178		}
179		}
180
181		/**
182		* create a sequence associated annotation row for JABAWS score object scr
183		*
184		* @param alignViewport
185		* @param gapMap
186		* @param ourAnnot
187		* @param typeName
188		* @param calcId
189		* @param dseq
190		* @param base
191		* @param scr
192		* @return
193		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
194	0	protected AlignmentAnnotation createAnnotationRowsForScores(...
195		AlignmentI alignment, boolean[] gapMap,
196		List<AlignmentAnnotation> ourAnnot, String typeName,
197		String calcId, SequenceI dseq, int base, Score scr)
198		{
199	0	System.out.println("Creating annotation on dseq:" + dseq.getStart()
200		+ " base is " + base + " and length=" + dseq.getLength()
201		+ " == " + scr.getScores().size());
202		// AlignmentAnnotation annotation = new AlignmentAnnotation(
203		// scr.getMethod(), typeName, new Annotation[]
204		// {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
205		// annotation.setCalcId(calcId);
206	0	AlignmentAnnotation annotation = alignment
207		.findOrCreateAnnotation(typeName, calcId, false, dseq, null);
208	0	constructAnnotationFromScore(gapMap, annotation, 0, dseq.getLength(),
209		scr);
210	0	annotation.createSequenceMapping(dseq, base, false);
211	0	annotation.adjustForAlignment();
212	0	dseq.addAlignmentAnnotation(annotation);
213	0	ourAnnot.add(annotation);
214	0	return annotation;
215		}
216
217		/**
218		* create column annotation elements from Jabaws score object
219		*
220		* @param gapMap
221		* @param annotation
222		* @param base
223		* @param alWidth
224		* @param scr
225		* JABAWS score object
226		*/
		0% Uncovered Elements: 39 (39) Complexity: 10 Complexity Density: 0.4
227	0	protected void constructAnnotationFromScore(boolean[] gapMap,...
228		AlignmentAnnotation annotation,
229		int base, int alWidth, Score scr)
230		{
231	0	Annotation[] elm = new Annotation[alWidth];
232	0	Iterator<Float> vals = scr.getScores().iterator();
233	0	float m = 0f, x = 0f;
234	0	for (int i = 0; vals.hasNext(); i++)
235		{
236	0	float val = vals.next().floatValue();
237	0	if (i == 0)
238		{
239	0	m = val;
240	0	x = val;
241		}
242		else
243		{
244	0	if (m > val)
245		{
246	0	m = val;
247		}
248	0	;
249	0	if (x < val)
250		{
251	0	x = val;
252		}
253		}
254		// if we're at a gapped column then skip to next ungapped position
255	0	if (gapMap != null && gapMap.length > 0)
256		{
257		// if gapMap is a different length to the result then it may be out of
258		// sync with the job.
259	0	while (i < gapMap.length && !gapMap[i])
260		{
261	0	elm[i++] = new Annotation("", "", ' ', Float.NaN);
262		}
263		}
264	0	elm[i] = new Annotation("", "" + val, ' ', val);
265		}
266
267	0	annotation.annotations = elm;
268	0	annotation.belowAlignment = true;
269	0	if (x < 0)
270		{
271	0	x = 0;
272		}
273	0	x += (x - m) * 0.1;
274	0	annotation.graphMax = x;
275	0	annotation.graphMin = m;
276	0	annotation.validateRangeAndDisplay();
277		}
278
279		}