Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JabawsCalcWorker	44	65	28	101	0.00%	Show methods

Class JabawsCalcWorker

Class JabawsCalcWorker	Line # 44	Total Statements 65	Complexity 28	Uncovered Elements 101	TOTAL Coverage 0.00%
JabawsCalcWorker(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)   JabawsCalcWorker(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)	5252	2.02	1.01	2.02	0.0 0.00%
pullExecStatistics(String,long) : ChunkHolder   pullExecStatistics(String,long) : ChunkHolder	5959	1.01	1.01	1.01	0.0 0.00%
collectAnnotationResultsFor(String) : boolean   collectAnnotationResultsFor(String) : boolean	6565	4.04	2.02	6.06	0.0 0.00%
cancelJob(String) : boolean   cancelJob(String) : boolean	7777	1.01	1.01	1.01	0.0 0.00%
getJobStatus(String) : JobStatus   getJobStatus(String) : JobStatus	8383	1.01	1.01	1.01	0.0 0.00%
hasService() : boolean   hasService() : boolean	8989	1.01	1.01	1.01	0.0 0.00%
isInteractiveUpdate() : boolean   isInteractiveUpdate() : boolean	9595	1.01	1.01	1.01	0.0 0.00%
submitToService(List<compbio.data.sequence.FastaSequence>) : String   submitToService(List<compbio.data.sequence.FastaSequence>) : String	101101	7.07	4.04	9.09	0.0 0.00%
createAnnotationRowsForScores(List<AlignmentAnnotation>,String,int,Score) : void   createAnnotationRowsForScores(List<AlignmentAnnotation>,String,int,Score) : void	126126	4.04	2.02	6.06	0.0 0.00%
createAnnotationRowsForScores(List<AlignmentAnnotation>,String,String,SequenceI,int,Score) : AlignmentAnnotation   createAnnotationRowsForScores(List<AlignmentAnnotation>,String,String,SequenceI,int,Score) : AlignmentAnnotation	141141	8.08	1.01	8.08	0.0 0.00%
replaceAnnotationOnAlignmentWith(AlignmentAnnotation,String,String,SequenceI) : void   replaceAnnotationOnAlignmentWith(AlignmentAnnotation,String,String,SequenceI) : void	162162	10.010	4.04	14.014	0.0 0.00%
constructAnnotationFromScore(AlignmentAnnotation,int,int,Score) : void   constructAnnotationFromScore(AlignmentAnnotation,int,int,Score) : void	186186	25.025	9.09	39.039	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ws.jws2;
22
23		import jalview.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.Annotation;
25		import jalview.datamodel.SequenceI;
26		import jalview.gui.AlignFrame;
27		import jalview.util.MessageManager;
28		import jalview.ws.jws2.jabaws2.Jws2Instance;
29		import jalview.ws.params.WsParamSetI;
30
31		import java.util.Iterator;
32		import java.util.List;
33
34		import compbio.data.msa.SequenceAnnotation;
35		import compbio.data.sequence.Score;
36		import compbio.data.sequence.ScoreManager;
37		import compbio.metadata.Argument;
38		import compbio.metadata.ChunkHolder;
39		import compbio.metadata.JobStatus;
40		import compbio.metadata.JobSubmissionException;
41		import compbio.metadata.ResultNotAvailableException;
42		import compbio.metadata.WrongParameterException;
43
		0% Uncovered Elements: 101 (101) Complexity: 28 Complexity Density: 0.43
44		public abstract class JabawsCalcWorker extends AbstractJabaCalcWorker
45		{
46
47		@SuppressWarnings("unchecked")
48		protected SequenceAnnotation aaservice;
49
50		protected ScoreManager scoremanager;
51
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
52	0	public JabawsCalcWorker(Jws2Instance service, AlignFrame alignFrame,...
53		WsParamSetI preset, List<Argument> paramset)
54		{
55	0	super(service, alignFrame, preset, paramset);
56	0	aaservice = (SequenceAnnotation) service.service;
57		}
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	@Override...
60		ChunkHolder pullExecStatistics(String rslt, long rpos)
61		{
62	0	return aaservice.pullExecStatistics(rslt, rpos);
63		}
64
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
65	0	@Override...
66		boolean collectAnnotationResultsFor(String rslt)
67		throws ResultNotAvailableException
68		{
69	0	scoremanager = aaservice.getAnnotation(rslt);
70	0	if (scoremanager != null)
71		{
72	0	return true;
73		}
74	0	return false;
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		boolean cancelJob(String rslt) throws Exception
79		{
80	0	return aaservice.cancelJob(rslt);
81		}
82
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	@Override...
84		protected JobStatus getJobStatus(String rslt) throws Exception
85		{
86	0	return aaservice.getJobStatus(rslt);
87		}
88
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
89	0	@Override...
90		boolean hasService()
91		{
92	0	return aaservice != null;
93		}
94
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	@Override...
96		protected boolean isInteractiveUpdate()
97		{
98	0	return this instanceof AAConClient;
99		}
100
		0% Uncovered Elements: 9 (9) Complexity: 4 Complexity Density: 0.57
101	0	@Override...
102		protected String submitToService(
103		List<compbio.data.sequence.FastaSequence> seqs)
104		throws JobSubmissionException
105		{
106	0	String rslt;
107	0	if (preset == null && arguments == null)
108		{
109	0	rslt = aaservice.analize(seqs);
110		}
111		else
112		{
113	0	try
114		{
115	0	rslt = aaservice.customAnalize(seqs, getJabaArguments());
116		} catch (WrongParameterException x)
117		{
118	0	throw new JobSubmissionException(MessageManager.getString(
119		"exception.jobsubmission_invalid_params_set"), x);
120
121		}
122		}
123	0	return rslt;
124		}
125
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
126	0	protected void createAnnotationRowsForScores(...
127		List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
128		Score scr)
129		{
130		// simple annotation row
131	0	AlignmentAnnotation annotation = alignViewport.getAlignment()
132		.findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
133		null);
134	0	if (alWidth == gapMap.length) // scr.getScores().size())
135		{
136	0	constructAnnotationFromScore(annotation, 0, alWidth, scr);
137	0	ourAnnot.add(annotation);
138		}
139		}
140
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
141	0	protected AlignmentAnnotation createAnnotationRowsForScores(...
142		List<AlignmentAnnotation> ourAnnot, String typeName,
143		String calcId, SequenceI dseq, int base, Score scr)
144		{
145	0	System.out.println("Creating annotation on dseq:" + dseq.getStart()
146		+ " base is " + base + " and length=" + dseq.getLength()
147		+ " == " + scr.getScores().size());
148		// AlignmentAnnotation annotation = new AlignmentAnnotation(
149		// scr.getMethod(), typeName, new Annotation[]
150		// {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
151		// annotation.setCalcId(calcId);
152	0	AlignmentAnnotation annotation = alignViewport.getAlignment()
153		.findOrCreateAnnotation(typeName, calcId, false, dseq, null);
154	0	constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
155	0	annotation.createSequenceMapping(dseq, base, false);
156	0	annotation.adjustForAlignment();
157	0	dseq.addAlignmentAnnotation(annotation);
158	0	ourAnnot.add(annotation);
159	0	return annotation;
160		}
161
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.4
162	0	protected void replaceAnnotationOnAlignmentWith(...
163		AlignmentAnnotation newAnnot, String typeName, String calcId,
164		SequenceI aSeq)
165		{
166	0	SequenceI dsseq = aSeq.getDatasetSequence();
167	0	while (dsseq.getDatasetSequence() != null)
168		{
169	0	dsseq = dsseq.getDatasetSequence();
170		}
171		// look for same annotation on dataset and lift this one over
172	0	List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
173		typeName);
174	0	if (dsan != null && dsan.size() > 0)
175		{
176	0	for (AlignmentAnnotation dssan : dsan)
177		{
178	0	dsseq.removeAlignmentAnnotation(dssan);
179		}
180		}
181	0	AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
182	0	dsseq.addAlignmentAnnotation(dssan);
183	0	dssan.adjustForAlignment();
184		}
185
		0% Uncovered Elements: 39 (39) Complexity: 9 Complexity Density: 0.36
186	0	private void constructAnnotationFromScore(AlignmentAnnotation annotation,...
187		int base, int alWidth, Score scr)
188		{
189	0	Annotation[] elm = new Annotation[alWidth];
190	0	Iterator<Float> vals = scr.getScores().iterator();
191	0	float m = 0f, x = 0f;
192	0	for (int i = 0; vals.hasNext(); i++)
193		{
194	0	float val = vals.next().floatValue();
195	0	if (i == 0)
196		{
197	0	m = val;
198	0	x = val;
199		}
200		else
201		{
202	0	if (m > val)
203		{
204	0	m = val;
205		}
206	0	;
207	0	if (x < val)
208		{
209	0	x = val;
210		}
211		}
212		// if we're at a gapped column then skip to next ungapped position
213	0	if (gapMap != null && gapMap.length > 0)
214		{
215	0	while (!gapMap[i])
216		{
217	0	elm[i++] = new Annotation("", "", ' ', Float.NaN);
218		}
219		}
220	0	elm[i] = new Annotation("", "" + val, ' ', val);
221		}
222
223	0	annotation.annotations = elm;
224	0	annotation.belowAlignment = true;
225	0	if (x < 0)
226		{
227	0	x = 0;
228		}
229	0	x += (x - m) * 0.1;
230	0	annotation.graphMax = x;
231	0	annotation.graphMin = m;
232	0	annotation.validateRangeAndDisplay();
233		}
234
235		}