Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AAConSettings	39	13	6	0.00%	Show methods

Class AAConSettings

Class AAConSettings	Line # 39	Total Statements 13	Complexity 6	TOTAL Coverage 0.00%
AAConSettings(boolean,ServiceWithParameters,WsParamSetI,List<ArgumentI>)   AAConSettings(boolean,ServiceWithParameters,WsParamSetI,List<ArgumentI>)	4141	1.01	1.01	0.0 0.00%
getWsParamFile() : String   getWsParamFile() : String	4747	12.012	5.05	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.dm;
22
23		import jalview.ws.api.ServiceWithParameters;
24		import jalview.ws.jws2.JabaParamStore;
25		import jalview.ws.jws2.ParameterUtils;
26		import jalview.ws.params.ArgumentI;
27		import jalview.ws.params.WsParamSetI;
28
29		import java.util.List;
30
31		import compbio.metadata.Option;
32
33		/**
34		* preferences for running AACon service
35		*
36		* @author jprocter TODO: refactor to a generic 'last job and service run'
37		* container ?
38		*/
		0% Uncovered Elements: 21 (21) Complexity: 6 Complexity Density: 0.46
39		public class AAConSettings extends jalview.ws.params.AutoCalcSetting
40		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
41	0	public AAConSettings(boolean autoUpdate, ServiceWithParameters service2,...
42		WsParamSetI preset, List<ArgumentI> jobArgset)
43		{
44	0	super(service2, preset, jobArgset, autoUpdate);
45		}
46
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
47	0	@Override...
48		public String getWsParamFile()
49		{
50	0	List<Option> opts = null;
51	0	if (jobArgset != null)
52		{
53	0	opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
54		}
55		else
56		{
57	0	if (preset != null)
58		{
59	0	opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
60		}
61		}
62	0	if (opts == null || opts.size() == 0)
63		{
64	0	return "";
65		}
66	0	StringBuffer pset = new StringBuffer();
67	0	for (String ps : ParameterUtils.writeParameterSet(opts, " "))
68		{
69	0	pset.append(ps);
70	0	pset.append("\n");
71		}
72	0	return pset.toString();
73		}
74		}