Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AAConClient	38	12	7	0.1052631610.5%	Show methods

Class AAConClient

Class AAConClient	Line # 38	Total Statements 12	Complexity 7	TOTAL Coverage 0.1052631610.5%
getServiceActionText() : String   getServiceActionText() : String	4141	1.01	1.01	0.0 0.00%
getAlignAnalysisUIText() : AlignAnalysisUIText   getAlignAnalysisUIText() : AlignAnalysisUIText	5050	1.01	1.01	1.0 1.0100%
AAConClient(Jws2Instance)   AAConClient(Jws2Instance)	6262	1.01	1.01	0.0 0.00%
annotationFromScoreManager(AlignmentI,Map<String, FeatureColourI>,Map<String, FeatureMatcherSetI>) : List<AlignmentAnnotation>   annotationFromScoreManager(AlignmentI,Map<String, FeatureColourI>,Map<String, FeatureMatcherSetI>) : List<AlignmentAnnotation>	6767	1.01	1.01	0.0 0.00%
aacons_annotation(int,AlignmentI,boolean[]) : List<AlignmentAnnotation>   aacons_annotation(int,AlignmentI,boolean[]) : List<AlignmentAnnotation>	7575	8.08	3.03	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.10526316	jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest	1PASS
	0.10526316	jalview.bin.CommandsTest2.do_network_structureOpeningArgsTestjalview.bin.CommandsTest2.do_network_structureOpeningArgsTest	1PASS
	0.10526316	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	1PASS

 

Source view

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.jabaws2;
22
23		import jalview.api.FeatureColourI;
24		import jalview.datamodel.AlignmentAnnotation;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.features.FeatureMatcherSetI;
27		import jalview.util.MessageManager;
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.Score;
37
		10.5% Uncovered Elements: 17 (19) Complexity: 7 Complexity Density: 0.58
38		public class AAConClient extends JabawsAnnotationInstance
39		{
40		// configuration for factory
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
41	0	public static String getServiceActionText()...
42		{
43	0	return "calculating Amino acid consensus using AACon service";
44		}
45
46
47
48		private static String CALC_ID = "jabaws2.AACon";
49
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
50	4	public static AlignAnalysisUIText getAlignAnalysisUIText()...
51		{
52	4	return new AlignAnalysisUIText(
53		compbio.ws.client.Services.AAConWS.toString(),
54		AAConClient.class, CALC_ID, false, true, true, true,
55		true, 2, MessageManager.getString("label.aacon_calculations"),
56		MessageManager.getString("tooltip.aacon_calculations"),
57		MessageManager.getString("label.aacon_settings"),
58		MessageManager.getString("tooltip.aacon_settings"));
59		}
60
61		// instance
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public AAConClient(Jws2Instance handle)...
63		{
64	0	super(handle);
65		}
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
69		Map<String, FeatureColourI> featureColours,
70		Map<String, FeatureMatcherSetI> featureFilters)
71		{
72	0	return aacons_annotation(seqs.getWidth(), seqs, null);
73		}
74
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.38
75	0	private List<AlignmentAnnotation> aacons_annotation(int alWidth,...
76		AlignmentI alignViewport, boolean[] gapMap)
77		{
78	0	Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
79	0	ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
80	0	for (String score : scoremap.keySet())
81		{
82	0	Set<Score> scores = scoremap.get(score);
83	0	for (Score scr : scores)
84		{
85	0	if (scr.getRanges() != null && scr.getRanges().size() > 0)
86		{
87		/**
88		* annotation in range annotation = findOrCreate(scr.getMethod(),
89		* true, null, null); Annotation[] elm = new Annotation[alWidth];
90		* Iterator<Float> vals = scr.getScores().iterator(); for (Range rng :
91		* scr.getRanges()) { float val = vals.next().floatValue(); for (int i
92		* = rng.from; i <= rng.to; i++) { elm[i] = new Annotation("", "", '
93		* ', val); } } annotation.annotations = elm;
94		* annotation.validateRangeAndDisplay();
95		*/
96		}
97		else
98		{
99	0	createAnnotationRowsForScores(alignViewport, null, ourAnnot,
100		getCalcId(),
101		scr.getScores().size(), scr);
102		}
103		}
104		}
105	0	return ourAnnot;
106		}
107
108		}