Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JabawsMsaInterfaceAlignCalcWorker	46	60	25	0.00%	Show methods

Class JabawsMsaInterfaceAlignCalcWorker

Class JabawsMsaInterfaceAlignCalcWorker	Line # 46	Total Statements 60	Complexity 25	TOTAL Coverage 0.00%
JabawsMsaInterfaceAlignCalcWorker(AlignViewportI,AlignmentViewPanel)   JabawsMsaInterfaceAlignCalcWorker(AlignViewportI,AlignmentViewPanel)	5555	1.01	1.01	0.0 0.00%
JabawsMsaInterfaceAlignCalcWorker(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)   JabawsMsaInterfaceAlignCalcWorker(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)	6161	6.06	1.01	0.0 0.00%
pullExecStatistics(String,long) : ChunkHolder   pullExecStatistics(String,long) : ChunkHolder	7474	1.01	1.01	0.0 0.00%
collectAnnotationResultsFor(String) : boolean   collectAnnotationResultsFor(String) : boolean	8080	4.04	2.02	0.0 0.00%
cancelJob(String) : boolean   cancelJob(String) : boolean	9292	1.01	1.01	0.0 0.00%
getJobStatus(String) : JobStatus   getJobStatus(String) : JobStatus	9898	1.01	1.01	0.0 0.00%
hasService() : boolean   hasService() : boolean	104104	1.01	1.01	0.0 0.00%
isInteractiveUpdate() : boolean   isInteractiveUpdate() : boolean	110110	1.01	1.01	0.0 0.00%
submitToService(List<compbio.data.sequence.FastaSequence>) : String   submitToService(List<compbio.data.sequence.FastaSequence>) : String	116116	7.07	4.04	0.0 0.00%
createAnnotationRowsForScores(List<AlignmentAnnotation>,String,int,Score) : void   createAnnotationRowsForScores(List<AlignmentAnnotation>,String,int,Score) : void	140140	4.04	2.02	0.0 0.00%
createAnnotationRowsForScores(List<AlignmentAnnotation>,String,String,SequenceI,int,Score) : AlignmentAnnotation   createAnnotationRowsForScores(List<AlignmentAnnotation>,String,String,SequenceI,int,Score) : AlignmentAnnotation	155155	8.08	1.01	0.0 0.00%
constructAnnotationFromScore(AlignmentAnnotation,int,int,Score) : void   constructAnnotationFromScore(AlignmentAnnotation,int,int,Score) : void	176176	25.025	9.09	0.0 0.00%

 

Contributing tests

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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.api.AlignViewportI;
24		import jalview.api.AlignmentViewPanel;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.Annotation;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.AlignFrame;
29		import jalview.util.MessageManager;
30		import jalview.ws.jws2.jabaws2.Jws2Instance;
31		import jalview.ws.params.WsParamSetI;
32
33		import java.util.Iterator;
34		import java.util.List;
35
36		import compbio.data.msa.MsaWS;
37		import compbio.data.sequence.Alignment;
38		import compbio.data.sequence.Score;
39		import compbio.metadata.Argument;
40		import compbio.metadata.ChunkHolder;
41		import compbio.metadata.JobStatus;
42		import compbio.metadata.JobSubmissionException;
43		import compbio.metadata.ResultNotAvailableException;
44		import compbio.metadata.WrongParameterException;
45
		0% Uncovered Elements: 92 (92) Complexity: 25 Complexity Density: 0.42
46		public abstract class JabawsMsaInterfaceAlignCalcWorker
47		extends AbstractJabaCalcWorker
48		{
49
50		@SuppressWarnings("unchecked")
51		protected MsaWS msaservice;
52
53		protected Alignment msascoreset;
54
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
55	0	public JabawsMsaInterfaceAlignCalcWorker(AlignViewportI alignViewport,...
56		AlignmentViewPanel alignPanel)
57		{
58	0	super(alignViewport, alignPanel);
59		}
60
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
61	0	public JabawsMsaInterfaceAlignCalcWorker(Jws2Instance service,...
62		AlignFrame alignFrame, WsParamSetI preset,
63		List<Argument> paramset)
64		{
65	0	this(alignFrame.getCurrentView(), alignFrame.alignPanel);
66	0	this.guiProgress = alignFrame;
67	0	this.preset = preset;
68	0	this.arguments = paramset;
69	0	this.service = service;
70	0	msaservice = (MsaWS) service.service;
71
72		}
73
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
74	0	@Override...
75		ChunkHolder pullExecStatistics(String rslt, long rpos)
76		{
77	0	return msaservice.pullExecStatistics(rslt, rpos);
78		}
79
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
80	0	@Override...
81		boolean collectAnnotationResultsFor(String rslt)
82		throws ResultNotAvailableException
83		{
84	0	msascoreset = msaservice.getResult(rslt);
85	0	if (msascoreset != null)
86		{
87	0	return true;
88		}
89	0	return false;
90		}
91
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
92	0	@Override...
93		boolean cancelJob(String rslt) throws Exception
94		{
95	0	return msaservice.cancelJob(rslt);
96		}
97
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
98	0	@Override...
99		protected JobStatus getJobStatus(String rslt) throws Exception
100		{
101	0	return msaservice.getJobStatus(rslt);
102		}
103
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
104	0	@Override...
105		boolean hasService()
106		{
107	0	return msaservice != null;
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		protected boolean isInteractiveUpdate()
112		{
113	0	return false; // this instanceof AAConClient;
114		}
115
		0% Uncovered Elements: 9 (9) Complexity: 4 Complexity Density: 0.57
116	0	@Override...
117		protected String submitToService(
118		List<compbio.data.sequence.FastaSequence> seqs)
119		throws JobSubmissionException
120		{
121	0	String rslt;
122	0	if (preset == null && arguments == null)
123		{
124	0	rslt = msaservice.align(seqs);
125		}
126		else
127		{
128	0	try
129		{
130	0	rslt = msaservice.customAlign(seqs, getJabaArguments());
131		} catch (WrongParameterException x)
132		{
133	0	throw new JobSubmissionException(MessageManager.getString(
134		"exception.jobsubmission_invalid_params_set"), x);
135		}
136		}
137	0	return rslt;
138		}
139
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
140	0	protected void createAnnotationRowsForScores(...
141		List<AlignmentAnnotation> ourAnnot, String calcId, int alWidth,
142		Score scr)
143		{
144		// simple annotation row
145	0	AlignmentAnnotation annotation = alignViewport.getAlignment()
146		.findOrCreateAnnotation(scr.getMethod(), calcId, true, null,
147		null);
148	0	if (alWidth == gapMap.length) // scr.getScores().size())
149		{
150	0	constructAnnotationFromScore(annotation, 0, alWidth, scr);
151	0	ourAnnot.add(annotation);
152		}
153		}
154
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
155	0	protected AlignmentAnnotation createAnnotationRowsForScores(...
156		List<AlignmentAnnotation> ourAnnot, String typeName,
157		String calcId, SequenceI dseq, int base, Score scr)
158		{
159	0	jalview.bin.Console.outPrintln("Creating annotation on dseq:"
160		+ dseq.getStart() + " base is " + base + " and length="
161		+ dseq.getLength() + " == " + scr.getScores().size());
162		// AlignmentAnnotation annotation = new AlignmentAnnotation(
163		// scr.getMethod(), typeName, new Annotation[]
164		// {}, 0, -1, AlignmentAnnotation.LINE_GRAPH);
165		// annotation.setCalcId(calcId);
166	0	AlignmentAnnotation annotation = alignViewport.getAlignment()
167		.findOrCreateAnnotation(typeName, calcId, false, dseq, null);
168	0	constructAnnotationFromScore(annotation, 0, dseq.getLength(), scr);
169	0	annotation.createSequenceMapping(dseq, base, false);
170	0	annotation.adjustForAlignment();
171	0	dseq.addAlignmentAnnotation(annotation);
172	0	ourAnnot.add(annotation);
173	0	return annotation;
174		}
175
		0% Uncovered Elements: 39 (39) Complexity: 9 Complexity Density: 0.36
176	0	private void constructAnnotationFromScore(AlignmentAnnotation annotation,...
177		int base, int alWidth, Score scr)
178		{
179	0	Annotation[] elm = new Annotation[alWidth];
180	0	Iterator<Float> vals = scr.getScores().iterator();
181	0	float m = 0f, x = 0f;
182	0	for (int i = 0; vals.hasNext(); i++)
183		{
184	0	float val = vals.next().floatValue();
185	0	if (i == 0)
186		{
187	0	m = val;
188	0	x = val;
189		}
190		else
191		{
192	0	if (m > val)
193		{
194	0	m = val;
195		}
196	0	;
197	0	if (x < val)
198		{
199	0	x = val;
200		}
201		}
202		// if we're at a gapped column then skip to next ungapped position
203	0	if (gapMap != null && gapMap.length > 0)
204		{
205	0	while (!gapMap[i])
206		{
207	0	elm[i++] = new Annotation("", "", ' ', Float.NaN);
208		}
209		}
210	0	elm[i] = new Annotation("", "" + val, ' ', val);
211		}
212
213	0	annotation.annotations = elm;
214	0	annotation.belowAlignment = true;
215	0	if (x < 0)
216		{
217	0	x = 0;
218		}
219	0	x += (x - m) * 0.1;
220	0	annotation.graphMax = x;
221	0	annotation.graphMin = m;
222	0	annotation.validateRangeAndDisplay();
223		}
224
225		}