Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AutoCalcSetting	29	39	20	0.00%	Show methods

Class AutoCalcSetting

Class AutoCalcSetting	Line # 29	Total Statements 39	Complexity 20	TOTAL Coverage 0.00%
AutoCalcSetting(ServiceWithParameters,WsParamSetI,List<ArgumentI>,boolean)   AutoCalcSetting(ServiceWithParameters,WsParamSetI,List<ArgumentI>,boolean)	4040	4.04	1.01	0.0 0.00%
isAutoUpdate() : boolean   isAutoUpdate() : boolean	5050	1.01	1.01	0.0 0.00%
setAutoUpdate(boolean) : void   setAutoUpdate(boolean) : void	5555	1.01	1.01	0.0 0.00%
getPreset() : WsParamSetI   getPreset() : WsParamSetI	6060	1.01	1.01	0.0 0.00%
setPreset(WsParamSetI) : void   setPreset(WsParamSetI) : void	6565	1.01	1.01	0.0 0.00%
getArgumentSet() : List<ArgumentI>   getArgumentSet() : List<ArgumentI>	7171	1.01	1.01	0.0 0.00%
getServiceURI() : String   getServiceURI() : String	8383	1.01	1.01	0.0 0.00%
getServiceURLs() : String[]   getServiceURLs() : String[]	9696	1.01	1.01	0.0 0.00%
getWsParamFile() : String   getWsParamFile() : String	107107	12.012	5.05	0.0 0.00%
getService() : ServiceWithParameters   getService() : ServiceWithParameters	133133	1.01	1.01	0.0 0.00%
setService(ServiceWithParameters) : void   setService(ServiceWithParameters) : void	138138	15.015	6.06	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.params;
22
23		import jalview.util.MessageManager;
24		import jalview.ws.api.ServiceWithParameters;
25
26		import java.util.ArrayList;
27		import java.util.List;
28
		0% Uncovered Elements: 64 (64) Complexity: 20 Complexity Density: 0.51
29		public class AutoCalcSetting
30		{
31
32		protected boolean autoUpdate;
33
34		protected WsParamSetI preset;
35
36		protected List<ArgumentI> jobArgset;
37
38		protected ServiceWithParameters service;
39
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
40	0	public AutoCalcSetting(ServiceWithParameters service2,...
41		WsParamSetI preset2, List<ArgumentI> jobArgset2,
42		boolean autoUpdate2)
43		{
44	0	service = service2;
45	0	autoUpdate = autoUpdate2;
46	0	preset = preset2;
47	0	jobArgset = jobArgset2;
48		}
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	public boolean isAutoUpdate()...
51		{
52	0	return autoUpdate;
53		}
54
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
55	0	public void setAutoUpdate(boolean autoUpdate)...
56		{
57	0	this.autoUpdate = autoUpdate;
58		}
59
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
60	0	public WsParamSetI getPreset()...
61		{
62	0	return preset;
63		}
64
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
65	0	public void setPreset(WsParamSetI preset)...
66		{
67		// TODO: test if service URL is in presets
68	0	this.preset = preset;
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	public List<ArgumentI> getArgumentSet()...
72		{
73	0	return jobArgset;
74		}
75
76		/**
77		* TODO: refactor to ServiceWithParameters ?
78		*
79		* @return characteristic URI for this service. The URI should reflect the
80		* type and version of this service, enabling the service client code
81		* to recover the correct client for this calculation.
82		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	public String getServiceURI()...
84		{
85	0	return service.getNameURI();
86		}
87
88		/**
89		* TODO: refactor to ServiceWithParameters ?
90		*
91		* return any concrete service endpoints associated with this calculation.
92		* built in services should return a zero length array
93		*
94		* @return
95		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	public String[] getServiceURLs()...
97		{
98	0	return new String[] { service.getUri() };
99		}
100
101		/**
102		* default WsParamFile generator method - clients with custom formats should
103		* override and implement their own
104		*
105		* @return stringified representation of the parameters for this setting
106		*/
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
107	0	public String getWsParamFile()...
108		{
109	0	List<ArgumentI> opts = null;
110	0	if (jobArgset != null)
111		{
112	0	opts = jobArgset;
113		}
114		else
115		{
116	0	if (preset != null)
117		{
118	0	opts = preset.getArguments();
119		}
120		}
121	0	if (opts == null || opts.size() == 0)
122		{
123	0	return "";
124		}
125	0	StringBuffer pset = new StringBuffer();
126	0	for (ArgumentI ps : opts)
127		{
128	0	pset.append(ps.getName() + "\t" + ps.getValue());
129	0	pset.append("\n");
130		}
131	0	return pset.toString();
132		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	public ServiceWithParameters getService()...
134		{
135	0	return service;
136		}
137
		0% Uncovered Elements: 23 (23) Complexity: 6 Complexity Density: 0.4
138	0	public void setService(ServiceWithParameters service)...
139		{
140	0	this.service = service;
141	0	if (preset != null)
142		{
143		// check if we need to migrate preset to a new service URL
144	0	for (String url : preset.getApplicableUrls())
145		{
146	0	if (url.equals(service.getUri()))
147		{
148		// preset already verified
149	0	return;
150		}
151		}
152	0	WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
153
154		// TODO: decide of this distinction between preset and args are needed.
155		//
156		// if (pr instanceof JabaPreset && preset instanceof JabaPreset)
157		// {
158		// // easy - Presets are identical (we assume)
159		// preset = pr;
160		// return;
161		// }
162
163		// this verifies that all arguments in the existing preset are the same as
164		// the parameters for the preset provided by the service parameter store.
165		// ie the LastUsed settings or a predefined preset.
166
167	0	List<ArgumentI> oldargs = new ArrayList<>(),
168		newargs = new ArrayList<>();
169	0	oldargs.addAll(preset.getArguments());
170		// need to compare parameters
171	0	for (ArgumentI newparg : pr.getArguments())
172		{
173	0	if (!oldargs.remove(newparg))
174		{
175	0	newargs.add(newparg);
176		}
177		}
178	0	if (oldargs.size() == 0 && newargs.size() == 0)
179		{
180		// exact match.
181	0	preset = pr;
182	0	return;
183		}
184		// Try even harder to migrate arguments.
185	0	throw new Error(MessageManager
186		.getString("error.parameter_migration_not_implemented_yet"));
187		}
188		}
189
190		}