Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AAConSettings	43	37	21	0.00%	Show methods

Class AAConSettings

Class AAConSettings	Line # 43	Total Statements 37	Complexity 21	TOTAL Coverage 0.00%
AAConSettings(boolean,Jws2Instance,WsParamSetI,List<ArgumentI>)   AAConSettings(boolean,Jws2Instance,WsParamSetI,List<ArgumentI>)	4747	2.02	1.01	0.0 0.00%
getService() : Jws2Instance   getService() : Jws2Instance	5454	1.01	1.01	0.0 0.00%
setService(Jws2Instance) : void   setService(Jws2Instance) : void	5959	18.018	8.08	0.0 0.00%
getJobArgset() : List<Argument>   getJobArgset() : List<Argument>	102102	1.01	2.02	0.0 0.00%
setJobArgset(List<Argument>) : void   setJobArgset(List<Argument>) : void	108108	1.01	2.02	0.0 0.00%
getWsParamFile() : String   getWsParamFile() : String	115115	12.012	5.05	0.0 0.00%
getServiceURI() : String   getServiceURI() : String	142142	1.01	1.01	0.0 0.00%
getServiceURLs() : String[]   getServiceURLs() : String[]	148148	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.dm;
22
23		import jalview.util.MessageManager;
24		import jalview.ws.jws2.JabaParamStore;
25		import jalview.ws.jws2.JabaPreset;
26		import jalview.ws.jws2.ParameterUtils;
27		import jalview.ws.jws2.jabaws2.Jws2Instance;
28		import jalview.ws.params.ArgumentI;
29		import jalview.ws.params.WsParamSetI;
30
31		import java.util.ArrayList;
32		import java.util.List;
33
34		import compbio.metadata.Argument;
35		import compbio.metadata.Option;
36
37		/**
38		* preferences for running AACon service
39		*
40		* @author jprocter TODO: refactor to a generic 'last job and service run'
41		* container ?
42		*/
		0% Uncovered Elements: 65 (65) Complexity: 21 Complexity Density: 0.57
43		public class AAConSettings extends jalview.ws.params.AutoCalcSetting
44		{
45		Jws2Instance service;
46
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
47	0	public AAConSettings(boolean autoUpdate, Jws2Instance service,...
48		WsParamSetI preset, List<ArgumentI> jobArgset)
49		{
50	0	super(preset, jobArgset, autoUpdate);
51	0	this.service = service;
52		}
53
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	public Jws2Instance getService()...
55		{
56	0	return service;
57		}
58
		0% Uncovered Elements: 28 (28) Complexity: 8 Complexity Density: 0.44
59	0	public void setService(Jws2Instance service)...
60		{
61	0	this.service = service;
62	0	if (preset != null)
63		{
64		// migrate preset to new service
65	0	for (String url : preset.getApplicableUrls())
66		{
67	0	if (url.equals(service.getUri()))
68		{
69	0	return;
70		}
71		}
72	0	WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
73	0	if (pr instanceof JabaPreset && preset instanceof JabaPreset)
74		{
75		// easy - Presets are identical (we assume)
76	0	preset = pr;
77	0	return;
78		}
79	0	List<ArgumentI> oldargs = new ArrayList<ArgumentI>(),
80		newargs = new ArrayList<ArgumentI>();
81	0	oldargs.addAll(preset.getArguments());
82		// need to compare parameters
83	0	for (ArgumentI newparg : pr.getArguments())
84		{
85	0	if (!oldargs.remove(newparg))
86		{
87	0	newargs.add(newparg);
88		}
89		}
90	0	if (oldargs.size() == 0 && newargs.size() == 0)
91		{
92		// exact match.
93	0	preset = pr;
94	0	return;
95		}
96		// Try even harder to migrate arguments.
97	0	throw new Error(MessageManager
98		.getString("error.parameter_migration_not_implemented_yet"));
99		}
100		}
101
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
102	0	public List<Argument> getJobArgset()...
103		{
104	0	return jobArgset == null ? null
105		: JabaParamStore.getJabafromJwsArgs(jobArgset);
106		}
107
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
108	0	public void setJobArgset(List<Argument> jobArgset)...
109		{
110		// TODO: test if parameters valid for service
111	0	this.jobArgset = jobArgset == null ? null
112		: JabaParamStore.getJwsArgsfromJaba(jobArgset);
113		}
114
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
115	0	public String getWsParamFile()...
116		{
117	0	List<Option> opts = null;
118	0	if (jobArgset != null)
119		{
120	0	opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
121		}
122		else
123		{
124	0	if (preset != null)
125		{
126	0	opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
127		}
128		}
129	0	if (opts == null || opts.size() == 0)
130		{
131	0	return "";
132		}
133	0	StringBuffer pset = new StringBuffer();
134	0	for (String ps : ParameterUtils.writeParameterSet(opts, " "))
135		{
136	0	pset.append(ps);
137	0	pset.append("\n");
138		}
139	0	return pset.toString();
140		}
141
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		public String getServiceURI()
144		{
145	0	return service.getServiceTypeURI();
146		}
147
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	@Override...
149		public String[] getServiceURLs()
150		{
151	0	return new String[] { service.getUri() };
152		}
153		}