Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JabaWsParamSet	33	36	23	0.00%	Show methods

Class JabaWsParamSet

Class JabaWsParamSet	Line # 33	Total Statements 36	Complexity 23	TOTAL Coverage 0.00%
JabaWsParamSet(String,String,List)   JabaWsParamSet(String,String,List)	4242	11.011	4.04	0.0 0.00%
JabaWsParamSet()   JabaWsParamSet()	7272	0.00	1.01	-1.0 -1.0 -
allJaba(List) : boolean   allJaba(List) : boolean	7777	7.07	3.03	0.0 0.00%
getName() : String   getName() : String	9696	1.01	1.01	0.0 0.00%
getDescription() : String   getDescription() : String	102102	1.01	1.01	0.0 0.00%
setName(String) : void   setName(String) : void	112112	1.01	1.01	0.0 0.00%
setDescription(String) : void   setDescription(String) : void	121121	1.01	1.01	0.0 0.00%
setApplicableUrls(String[]) : void   setApplicableUrls(String[]) : void	130130	1.01	1.01	0.0 0.00%
setModifiable(boolean) : void   setModifiable(boolean) : void	139139	1.01	1.01	0.0 0.00%
getApplicableUrls() : String[]   getApplicableUrls() : String[]	144144	1.01	1.01	0.0 0.00%
getSourceFile() : String   getSourceFile() : String	150150	1.01	1.01	0.0 0.00%
setSourceFile(String) : void   setSourceFile(String) : void	156156	1.01	1.01	0.0 0.00%
isModifiable() : boolean   isModifiable() : boolean	164164	1.01	1.01	0.0 0.00%
getArguments() : List<ArgumentI>   getArguments() : List<ArgumentI>	170170	1.01	1.01	0.0 0.00%
setArguments(List<ArgumentI>) : void   setArguments(List<ArgumentI>) : void	176176	5.05	2.02	0.0 0.00%
getjabaArguments() : List<Option>   getjabaArguments() : List<Option>	191191	1.01	1.01	0.0 0.00%
setjabaArguments(List<Option>) : void   setjabaArguments(List<Option>) : void	196196	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.params.ArgumentI;
26		import jalview.ws.params.WsParamSetI;
27
28		import java.util.ArrayList;
29		import java.util.List;
30
31		import compbio.metadata.Option;
32
		0% Uncovered Elements: 63 (63) Complexity: 23 Complexity Density: 0.64
33		public class JabaWsParamSet implements WsParamSetI
34		{
35		/**
36		* raw jaba arguments.
37		*/
38		List<Option> jabaArguments;
39
40		String name, description, applicableUrls[], sourceFile;
41
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.36
42	0	public JabaWsParamSet(String storeSetName, String descr, List jobParams)...
43		{
44	0	if (jobParams.size() > 0)
45		{
46	0	if (jobParams.get(0) instanceof Option)
47		{
48	0	jabaArguments = new ArrayList<Option>();
49		// if classCastExceptions are raised then there has been an
50		// implementation error.
51	0	jabaArguments.addAll((List<Option>) jobParams);
52		}
53		else
54		{
55	0	if (!allJaba(jobParams))
56		{
57	0	throw new Error(MessageManager
58		.getString("error.cannot_create_jabaws_param_set"));
59		}
60		else
61		{
62	0	jabaArguments = JabaParamStore.getJabafromJwsArgs(jobParams);
63		}
64		}
65		}
66	0	name = storeSetName;
67	0	description = descr;
68	0	sourceFile = null;
69	0	applicableUrls = null;
70		}
71
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
72	0	public JabaWsParamSet()...
73		{
74
75		}
76
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
77	0	private boolean allJaba(List jobParams)...
78		{
79
80	0	boolean allJaba = true;
81	0	for (Object jp : jobParams)
82		{
83	0	if (jp instanceof JabaParameter || jp instanceof JabaOption)
84		{
85	0	allJaba &= true;
86		}
87		else
88		{
89	0	allJaba = false;
90	0	break;
91		}
92		}
93	0	return allJaba;
94		}
95
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	@Override...
97		public String getName()
98		{
99	0	return name;
100		}
101
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
102	0	@Override...
103		public String getDescription()
104		{
105	0	return description;
106		}
107
108		/**
109		* @param name
110		* the name to set
111		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
112	0	public void setName(String name)...
113		{
114	0	this.name = name;
115		}
116
117		/**
118		* @param description
119		* the description to set
120		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	public void setDescription(String description)...
122		{
123	0	this.description = description;
124		}
125
126		/**
127		* @param applicableUrls
128		* the applicableUrls to set
129		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	public void setApplicableUrls(String[] applicableUrls)...
131		{
132	0	this.applicableUrls = applicableUrls;
133		}
134
135		/**
136		* @param modifiable
137		* the modifiable to set
138		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
139	0	public void setModifiable(boolean modifiable)...
140		{
141	0	this.modifiable = modifiable;
142		}
143
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
144	0	@Override...
145		public String[] getApplicableUrls()
146		{
147	0	return applicableUrls;
148		}
149
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
150	0	@Override...
151		public String getSourceFile()
152		{
153	0	return sourceFile;
154		}
155
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
156	0	@Override...
157		public void setSourceFile(String newfile)
158		{
159	0	sourceFile = newfile;
160		}
161
162		boolean modifiable = true;
163
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
164	0	@Override...
165		public boolean isModifiable()
166		{
167	0	return modifiable;
168		}
169
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	@Override...
171		public List<ArgumentI> getArguments()
172		{
173	0	return JabaParamStore.getJwsArgsfromJaba(jabaArguments);
174		}
175
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
176	0	@Override...
177		public void setArguments(List<ArgumentI> args)
178		{
179	0	if (!allJaba(args))
180		{
181	0	throw new Error(MessageManager
182		.getString("error.cannot_set_arguments_to_jabaws_param_set"));
183		}
184	0	jabaArguments = new ArrayList<Option>();
185	0	for (ArgumentI rg : args)
186		{
187	0	jabaArguments.add(((JabaOption) rg).opt);
188		}
189		}
190
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
191	0	public List<Option> getjabaArguments()...
192		{
193	0	return jabaArguments;
194		}
195
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
196	0	public void setjabaArguments(List<Option> args)...
197		{
198	0	jabaArguments = args;
199		}
200
201		}