Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AAConClient	40	23	12	0.00%	Show methods

Class AAConClient

Class AAConClient	Line # 40	Total Statements 23	Complexity 12	TOTAL Coverage 0.00%
AAConClient(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)   AAConClient(Jws2Instance,AlignFrame,WsParamSetI,List<Argument>)	4343	8.08	1.01	0.0 0.00%
getServiceActionText() : String   getServiceActionText() : String	5656	1.01	1.01	0.0 0.00%
updateResultAnnotation(boolean) : void   updateResultAnnotation(boolean) : void	6767	11.011	7.07	0.0 0.00%
checkValidInputSeqs(boolean,List<FastaSequence>) : boolean   checkValidInputSeqs(boolean,List<FastaSequence>) : boolean	107107	1.01	1.01	0.0 0.00%
getCalcId() : String   getCalcId() : String	113113	1.01	1.01	0.0 0.00%
getAlignAnalysisUITest() : AlignAnalysisUIText   getAlignAnalysisUITest() : AlignAnalysisUIText	121121	1.01	1.01	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.gui.AlignFrame;
25		import jalview.util.MessageManager;
26		import jalview.ws.jws2.jabaws2.Jws2Instance;
27		import jalview.ws.params.WsParamSetI;
28		import jalview.ws.uimodel.AlignAnalysisUIText;
29
30		import java.util.ArrayList;
31		import java.util.List;
32		import java.util.Map;
33		import java.util.Set;
34		import java.util.TreeSet;
35
36		import compbio.data.sequence.FastaSequence;
37		import compbio.data.sequence.Score;
38		import compbio.metadata.Argument;
39
		0% Uncovered Elements: 35 (35) Complexity: 12 Complexity Density: 0.52
40		public class AAConClient extends JabawsCalcWorker
41		{
42
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
43	0	public AAConClient(Jws2Instance service, AlignFrame alignFrame,...
44		WsParamSetI preset, List<Argument> paramset)
45		{
46	0	super(service, alignFrame, preset, paramset);
47	0	submitGaps = true;
48	0	alignedSeqs = true;
49	0	nucleotidesAllowed = false;
50	0	proteinAllowed = true;
51	0	filterNonStandardResidues = true;
52	0	gapMap = new boolean[0];
53	0	initViewportParams();
54		}
55
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	@Override...
57		public String getServiceActionText()
58		{
59	0	return "calculating Amino acid consensus using AACon service";
60		}
61
62		/**
63		* update the consensus annotation from the sequence profile data using
64		* current visualization settings.
65		*/
66
		0% Uncovered Elements: 17 (17) Complexity: 7 Complexity Density: 0.64
67	0	@Override...
68		public void updateResultAnnotation(boolean immediate)
69		{
70	0	if (immediate || !calcMan.isWorking(this) && scoremanager != null)
71		{
72	0	Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
73	0	int alWidth = alignViewport.getAlignment().getWidth();
74	0	ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
75	0	for (String score : scoremap.keySet())
76		{
77	0	Set<Score> scores = scoremap.get(score);
78	0	for (Score scr : scores)
79		{
80	0	if (scr.getRanges() != null && scr.getRanges().size() > 0)
81		{
82		/**
83		* annotation in range annotation = findOrCreate(scr.getMethod(),
84		* true, null, null); Annotation[] elm = new Annotation[alWidth];
85		* Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
86		* : scr.getRanges()) { float val = vals.next().floatValue(); for
87		* (int i = rng.from; i <= rng.to; i++) { elm[i] = new
88		* Annotation("", "", ' ', val); } } annotation.annotations = elm;
89		* annotation.validateRangeAndDisplay();
90		*/
91		}
92		else
93		{
94	0	createAnnotationRowsForScores(ourAnnot, getCalcId(), alWidth,
95		scr);
96		}
97		}
98		}
99
100	0	if (ourAnnot.size() > 0)
101		{
102	0	updateOurAnnots(ourAnnot);
103		}
104		}
105		}
106
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
107	0	@Override...
108		boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
109		{
110	0	return (seqs.size() > 1);
111		}
112
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
113	0	@Override...
114		public String getCalcId()
115		{
116	0	return CALC_ID;
117		}
118
119		private static String CALC_ID = "jabaws2.AACon";
120
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	public static AlignAnalysisUIText getAlignAnalysisUITest()...
122		{
123	0	return new AlignAnalysisUIText(
124		compbio.ws.client.Services.AAConWS.toString(),
125		jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
126		MessageManager.getString("label.aacon_calculations"),
127		MessageManager.getString("tooltip.aacon_calculations"),
128		MessageManager.getString("label.aacon_settings"),
129		MessageManager.getString("tooltip.aacon_settings"));
130		}
131		}