Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Jws2Instance	41	47	30	0.00%	Show methods

Class Jws2Instance

Class Jws2Instance	Line # 41	Total Statements 47	Complexity 30	TOTAL Coverage 0.00%
Jws2Instance(String,String,String,String,JABAService)   Jws2Instance(String,String,String,String,JABAService)	6969	11.011	3.03	0.0 0.00%
getPresets() : PresetManager   getPresets() : PresetManager	100100	8.08	5.05	0.0 0.00%
getHost() : String   getHost() : String	125125	1.01	1.01	0.0 0.00%
getActionText() : String   getActionText() : String	140140	1.01	1.01	0.0 0.00%
getRunnerConfig() : RunnerConfig   getRunnerConfig() : RunnerConfig	151151	5.05	3.03	0.0 0.00%
close() : void   close() : void	167167	3.03	3.03	0.0 0.00%
getParamStore() : ParamDatastoreI   getParamStore() : ParamDatastoreI	183183	6.06	4.04	0.0 0.00%
getUri() : String   getUri() : String	203203	1.01	2.02	0.0 0.00%
hasParameters() : boolean   hasParameters() : boolean	214214	5.05	3.03	0.0 0.00%
attachWSMenuEntry(JMenu,AlignFrame) : void   attachWSMenuEntry(JMenu,AlignFrame) : void	230230	4.04	3.03	0.0 0.00%
getServiceTypeURI() : String   getServiceTypeURI() : String	243243	1.01	1.01	0.0 0.00%
getAlignAnalysisUI() : jalview.ws.uimodel.AlignAnalysisUIText   getAlignAnalysisUI() : jalview.ws.uimodel.AlignAnalysisUIText	250250	1.01	1.01	0.0 0.00%

 

Contributing tests

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.gui.AlignFrame;
24		import jalview.gui.Desktop;
25		import jalview.util.MessageManager;
26		import jalview.ws.jws2.JabaParamStore;
27		import jalview.ws.jws2.MsaWSClient;
28		import jalview.ws.jws2.SequenceAnnotationWSClient;
29		import jalview.ws.params.ParamDatastoreI;
30
31		import java.io.Closeable;
32
33		import javax.swing.JMenu;
34
35		import compbio.data.msa.JABAService;
36		import compbio.data.msa.MsaWS;
37		import compbio.data.msa.SequenceAnnotation;
38		import compbio.metadata.PresetManager;
39		import compbio.metadata.RunnerConfig;
40
		0% Uncovered Elements: 87 (87) Complexity: 30 Complexity Density: 0.64
41		public class Jws2Instance implements AutoCloseable
42		{
43		public String hosturl;
44
45		public String serviceType;
46
47		public String action;
48
49		public JABAService service;
50
51		public String description;
52
53		public String docUrl;
54
55		/**
56		*
57		* @param hosturl
58		* Service endpoint
59		* @param serviceType
60		* Category for this service's analysis
61		* @param action
62		* text describing their action that service performs (eg 'aligning',
63		* 'analysing')
64		* @param description
65		* Description from JABAWS registry
66		* @param service
67		* JABAWS registry ID for service
68		*/
		0% Uncovered Elements: 15 (15) Complexity: 3 Complexity Density: 0.27
69	0	public Jws2Instance(String hosturl, String serviceType, String action,...
70		String description, JABAService service)
71		{
72	0	super();
73	0	this.hosturl = hosturl;
74	0	this.serviceType = serviceType;
75	0	this.service = service;
76	0	this.action = action;
77	0	this.description = description;
78	0	int p = description.indexOf("MORE INFORMATION:");
79	0	if (p > -1)
80		{
81	0	docUrl = description.substring(description.indexOf("http", p)).trim();
82	0	if (docUrl.indexOf('\n') > -1)
83		{
84	0	docUrl = docUrl.substring(0, docUrl.indexOf("\n")).trim();
85		}
86
87		}
88		}
89
90		PresetManager presets = null;
91
92		public JabaParamStore paramStore = null;
93
94		/**
95		* non thread safe - gets the presets for this service (blocks whilst it calls
96		* the service to get the preset set)
97		*
98		* @return service presets or null if exceptions were raised.
99		*/
		0% Uncovered Elements: 14 (14) Complexity: 5 Complexity Density: 0.62
100	0	public PresetManager getPresets()...
101		{
102	0	if (presets == null)
103		{
104	0	try
105		{
106	0	if (service instanceof MsaWS<?>)
107		{
108	0	presets = ((MsaWS) service).getPresets();
109
110		}
111	0	if (service instanceof SequenceAnnotation<?>)
112		{
113	0	presets = ((SequenceAnnotation) service).getPresets();
114		}
115		} catch (Exception ex)
116		{
117	0	jalview.bin.Console
118		.errPrintln("Exception when retrieving presets for service "
119		+ serviceType + " at " + hosturl);
120		}
121		}
122	0	return presets;
123		}
124
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
125	0	public String getHost()...
126		{
127	0	return hosturl;
128		/*
129		* try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80) {
130		* return serviceurl.getHost()+":"+serviceurl.getPort(); } return
131		* serviceurl.getHost(); } catch (Exception e) {
132		* jalview.bin.Console.errPrintln("Failed to parse service URL '" + hosturl +
133		* "' as a valid URL!"); } return null;
134		*/
135		}
136
137		/**
138		* @return short description of what the service will do
139		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	public String getActionText()...
141		{
142	0	return action + " with " + serviceType;
143		}
144
145		/**
146		* non-thread safe - blocks whilst accessing service to get complete set of
147		* available options and parameters
148		*
149		* @return
150		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
151	0	public RunnerConfig getRunnerConfig()...
152		{
153	0	if (service instanceof MsaWS<?>)
154		{
155	0	return ((MsaWS) service).getRunnerOptions();
156		}
157	0	if (service instanceof SequenceAnnotation<?>)
158		{
159	0	return ((SequenceAnnotation) service).getRunnerOptions();
160		}
161	0	throw new Error(MessageManager.formatMessage(
162		"error.implementation_error_runner_config_not_available",
163		new String[]
164		{ serviceType, service.getClass().toString() }));
165		}
166
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
167	0	@Override...
168		public void close()
169		{
170	0	if (service != null)
171		{
172	0	try
173		{
174	0	((Closeable) service).close();
175		} catch (Throwable t)
176		{
177		// ignore
178		}
179		}
180		// super.finalize();
181		}
182
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
183	0	public ParamDatastoreI getParamStore()...
184		{
185	0	if (paramStore == null)
186		{
187	0	try
188		{
189	0	paramStore = new JabaParamStore(this,
190	0	(Desktop.instance != null ? Desktop.getUserParameterStore()
191		: null));
192		} catch (Exception ex)
193		{
194	0	jalview.bin.Console.errPrintln(
195		"Unexpected exception creating JabaParamStore.");
196	0	ex.printStackTrace();
197		}
198
199		}
200	0	return paramStore;
201		}
202
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
203	0	public String getUri()...
204		{
205		// this is only valid for Jaba 1.0 - this formula might have to change!
206	0	return hosturl
207	0	+ (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? ""
208		: "/")
209		+ serviceType;
210		}
211
212		private boolean hasParams = false, lookedForParams = false;
213
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
214	0	public boolean hasParameters()...
215		{
216	0	if (!lookedForParams)
217		{
218	0	lookedForParams = true;
219	0	try
220		{
221	0	hasParams = (getRunnerConfig().getArguments().size() > 0);
222		} catch (Exception e)
223		{
224
225		}
226		}
227	0	return hasParams;
228		}
229
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
230	0	public void attachWSMenuEntry(JMenu atpoint, AlignFrame alignFrame)...
231		{
232	0	if (service instanceof MsaWS<?>)
233		{
234	0	new MsaWSClient().attachWSMenuEntry(atpoint, this, alignFrame);
235		}
236	0	else if (service instanceof SequenceAnnotation<?>)
237		{
238	0	new SequenceAnnotationWSClient().attachWSMenuEntry(atpoint, this,
239		alignFrame);
240		}
241		}
242
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
243	0	public String getServiceTypeURI()...
244		{
245	0	return "java:" + serviceType;
246		}
247
248		jalview.ws.uimodel.AlignAnalysisUIText aaui;
249
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
250	0	public jalview.ws.uimodel.AlignAnalysisUIText getAlignAnalysisUI()...
251		{
252	0	return aaui;
253		}
254		}