Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Jws2Instance	40	56	34	0.00%	Show methods

Class Jws2Instance

Class Jws2Instance	Line # 40	Total Statements 56	Complexity 34	TOTAL Coverage 0.00%
Jws2Instance(String,String,String,String,JABAService)   Jws2Instance(String,String,String,String,JABAService)	6060	16.016	8.08	0.0 0.00%
getPresets() : PresetManager   getPresets() : PresetManager	111111	8.08	5.05	0.0 0.00%
getRunnerConfig() : RunnerConfig   getRunnerConfig() : RunnerConfig	142142	5.05	3.03	0.0 0.00%
close() : void   close() : void	158158	3.03	3.03	0.0 0.00%
getParamStore() : ParamDatastoreI   getParamStore() : ParamDatastoreI	174174	6.06	4.04	0.0 0.00%
hasParameters() : boolean   hasParameters() : boolean	197197	5.05	3.03	0.0 0.00%
initParamStore(ParamManager) : void   initParamStore(ParamManager) : void	220220	2.02	2.02	0.0 0.00%
getEndpoint() : Object   getEndpoint() : Object	234234	11.011	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.jws2.jabaws2;
22
23		import jalview.gui.Desktop;
24		import jalview.util.MessageManager;
25		import jalview.ws.api.JalviewServiceEndpointProviderI;
26		import jalview.ws.api.ServiceWithParameters;
27		import jalview.ws.jws2.JabaParamStore;
28		import jalview.ws.params.ParamDatastoreI;
29		import jalview.ws.params.ParamManager;
30
31		import java.io.Closeable;
32		import java.net.URL;
33
34		import compbio.data.msa.JABAService;
35		import compbio.data.msa.MsaWS;
36		import compbio.data.msa.SequenceAnnotation;
37		import compbio.metadata.PresetManager;
38		import compbio.metadata.RunnerConfig;
39
		0% Uncovered Elements: 104 (104) Complexity: 34 Complexity Density: 0.61
40		public class Jws2Instance extends ServiceWithParameters
41		implements JalviewServiceEndpointProviderI, AutoCloseable
42		{
43
44		public JABAService service;
45
46		/**
47		*
48		* @param hosturl
49		* Service endpoint
50		* @param serviceType
51		* Category for this service's analysis
52		* @param action
53		* text describing their action that service performs (eg 'aligning',
54		* 'analysing')
55		* @param description
56		* Description from JABAWS registry
57		* @param service
58		* JABAWS registry ID for service
59		*/
		0% Uncovered Elements: 28 (28) Complexity: 8 Complexity Density: 0.5
60	0	public Jws2Instance(String hosturl, String serviceType, String action,...
61		String description, JABAService service)
62		{
63	0	super(action, action, serviceType, description, hosturl);
64	0	this.service = service;
65	0	if (service instanceof MsaWS<?>)
66		{
67	0	style = ServiceClient.MSAWSCLIENT;
68		}
69	0	else if (service instanceof SequenceAnnotation<?>)
70		{
71	0	style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
72		}
73
74	0	int p = description.indexOf("MORE INFORMATION:");
75	0	if (p > -1)
76		{
77	0	String docUrl = description.substring(description.indexOf("http", p))
78		.trim();
79	0	if (docUrl.indexOf('\n') > -1)
80		{
81	0	docUrl = docUrl.substring(0, docUrl.indexOf("\n")).trim();
82		}
83	0	if (docUrl.length() > 0)
84		{
85	0	try
86		{
87	0	URL url = new URL(docUrl);
88	0	if (url != null)
89		{
90	0	setDocumentationUrl(docUrl);
91		}
92		} catch (Exception x)
93		{
94
95		}
96		}
97
98		}
99		}
100
101		PresetManager presets = null;
102
103		public JabaParamStore paramStore = null;
104
105		/**
106		* non thread safe - gets the presets for this service (blocks whilst it calls
107		* the service to get the preset set)
108		*
109		* @return service presets or null if exceptions were raised.
110		*/
		0% Uncovered Elements: 14 (14) Complexity: 5 Complexity Density: 0.62
111	0	public PresetManager getPresets()...
112		{
113	0	if (presets == null)
114		{
115	0	try
116		{
117	0	if (service instanceof MsaWS<?>)
118		{
119	0	presets = ((MsaWS) service).getPresets();
120
121		}
122	0	if (service instanceof SequenceAnnotation<?>)
123		{
124	0	presets = ((SequenceAnnotation) service).getPresets();
125		}
126		} catch (Exception ex)
127		{
128	0	jalview.bin.Console
129		.errPrintln("Exception when retrieving presets for service "
130		+ getServiceType() + " at " + getHostURL());
131		}
132		}
133	0	return presets;
134		}
135
136		/**
137		* non-thread safe - blocks whilst accessing service to get complete set of
138		* available options and parameters
139		*
140		* @return
141		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
142	0	public RunnerConfig getRunnerConfig()...
143		{
144	0	if (service instanceof MsaWS<?>)
145		{
146	0	return ((MsaWS) service).getRunnerOptions();
147		}
148	0	if (service instanceof SequenceAnnotation<?>)
149		{
150	0	return ((SequenceAnnotation) service).getRunnerOptions();
151		}
152	0	throw new Error(MessageManager.formatMessage(
153		"error.implementation_error_runner_config_not_available",
154		new String[]
155		{ getServiceType(), service.getClass().toString() }));
156		}
157
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
158	0	@Override...
159		public void close()
160		{
161	0	if (service != null)
162		{
163	0	try
164		{
165	0	((Closeable) service).close();
166		} catch (Throwable t)
167		{
168		// ignore
169		}
170		}
171		// super.finalize();
172		}
173
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
174	0	@Override...
175		public ParamDatastoreI getParamStore()
176		{
177	0	if (paramStore == null)
178		{
179	0	try
180		{
181	0	paramStore = new JabaParamStore(this,
182	0	(Desktop.getInstance() != null ? Desktop.getUserParameterStore()
183		: null));
184		} catch (Exception ex)
185		{
186	0	jalview.bin.Console.errPrintln(
187		"Unexpected exception creating JabaParamStore.");
188	0	ex.printStackTrace();
189		}
190
191		}
192	0	return paramStore;
193		}
194
195		private boolean hasParams = false, lookedForParams = false;
196
		0% Uncovered Elements: 7 (7) Complexity: 3 Complexity Density: 0.6
197	0	@Override...
198		public boolean hasParameters()
199		{
200	0	if (!lookedForParams)
201		{
202	0	lookedForParams = true;
203	0	try
204		{
205	0	hasParams = (getRunnerConfig().getArguments().size() > 0);
206		} catch (Exception e)
207		{
208
209		}
210		}
211	0	return hasParams;
212		}
213
214		/**
215		* initialise a parameter store for this service
216		*
217		* @param userParameterStore
218		* - the user ParamManager (e.g. Desktop.getUserParameterStore() )
219		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
220	0	@Override...
221		public void initParamStore(ParamManager userParameterStore)
222		{
223	0	if (paramStore == null)
224		{
225	0	paramStore = new JabaParamStore(this, userParameterStore);
226		}
227		}
228
229		/**
230		* an object that implements one or more interfaces in jalview.ws.api
231		*
232		* @return
233		*/
		0% Uncovered Elements: 19 (19) Complexity: 6 Complexity Density: 0.55
234	0	@Override...
235		public Object getEndpoint()
236		{
237	0	if (service instanceof MsaWS<?>)
238		{
239	0	if (aaui != null)
240		{
241	0	throw new Error(
242		"JABAWS MsaWS based instant calculation not implemented.");
243
244		}
245		else
246		{
247	0	return new JabawsMsaInstance(this);
248		}
249		}
250		else
251		{
252	0	if (service instanceof compbio.data.msa.SequenceAnnotation)
253		{
254	0	if (aaui != null)
255		{
256	0	try
257		{
258		// probably a factory would be nicer but..
259	0	return aaui.getClient().getConstructor(getClass())
260		.newInstance(this);
261		} catch (Throwable t)
262		{
263	0	throw new Error("Implementation Error in web service framework",
264		t);
265		}
266		}
267	0	return new AADisorderClient(this);
268		}
269	0	return null;
270		}
271		}
272		}