Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
MuscleWSSoapBindingStub	23	203	33	249	0.00%	Show methods

Class MuscleWSSoapBindingStub

Class MuscleWSSoapBindingStub	Line # 23	Total Statements 203	Complexity 33	Uncovered Elements 249	TOTAL Coverage 0.00%
<clinit>, line 28()   <clinit>, line 28()	2828	2.02	1.01	2.02	0.0 0.00%
MuscleWSSoapBindingStub()   MuscleWSSoapBindingStub()	4242	1.01	1.01	1.01	0.0 0.00%
MuscleWSSoapBindingStub(java.net.URL,javax.xml.rpc.Service)   MuscleWSSoapBindingStub(java.net.URL,javax.xml.rpc.Service)	4747	2.02	1.01	2.02	0.0 0.00%
MuscleWSSoapBindingStub(javax.xml.rpc.Service)   MuscleWSSoapBindingStub(javax.xml.rpc.Service)	5454	63.063	2.02	65.065	0.0 0.00%
_initOperationDesc1() : void   _initOperationDesc1() : void	154154	37.037	1.01	37.037	0.0 0.00%
createCall() : org.apache.axis.client.Call   createCall() : org.apache.axis.client.Call	218218	30.030	11.011	48.048	0.0 0.00%
align(vamsas.objects.simple.SequenceSet) : vamsas.objects.simple.WsJobId   align(vamsas.objects.simple.SequenceSet) : vamsas.objects.simple.WsJobId	299299	17.017	4.04	21.021	0.0 0.00%
getalign(java.lang.String) : vamsas.objects.simple.Alignment   getalign(java.lang.String) : vamsas.objects.simple.Alignment	340340	17.017	4.04	21.021	0.0 0.00%
getResult(java.lang.String) : vamsas.objects.simple.MsaResult   getResult(java.lang.String) : vamsas.objects.simple.MsaResult	381381	17.017	4.04	21.021	0.0 0.00%
cancel(java.lang.String) : vamsas.objects.simple.WsJobId   cancel(java.lang.String) : vamsas.objects.simple.WsJobId	422422	17.017	4.04	21.021	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 ext.vamsas;
22
		0% Uncovered Elements: 249 (249) Complexity: 33 Complexity Density: 0.16
23		public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
24		implements ext.vamsas.MuscleWS
25		{
26		static org.apache.axis.description.OperationDesc[] _operations;
27
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
28	0	static...
29		{
30	0	_operations = new org.apache.axis.description.OperationDesc[4];
31	0	_initOperationDesc1();
32		}
33
34		private java.util.Vector cachedSerClasses = new java.util.Vector();
35
36		private java.util.Vector cachedSerQNames = new java.util.Vector();
37
38		private java.util.Vector cachedSerFactories = new java.util.Vector();
39
40		private java.util.Vector cachedDeserFactories = new java.util.Vector();
41
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
42	0	public MuscleWSSoapBindingStub() throws org.apache.axis.AxisFault...
43		{
44	0	this(null);
45		}
46
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
47	0	public MuscleWSSoapBindingStub(java.net.URL endpointURL,...
48		javax.xml.rpc.Service service) throws org.apache.axis.AxisFault
49		{
50	0	this(service);
51	0	super.cachedEndpoint = endpointURL;
52		}
53
		0% Uncovered Elements: 65 (65) Complexity: 2 Complexity Density: 0.03
54	0	public MuscleWSSoapBindingStub(javax.xml.rpc.Service service)...
55		throws org.apache.axis.AxisFault
56		{
57	0	if (service == null)
58		{
59	0	super.service = new org.apache.axis.client.Service();
60		}
61		else
62		{
63	0	super.service = service;
64		}
65
66	0	java.lang.Class cls;
67	0	javax.xml.namespace.QName qName;
68	0	java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
69	0	java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
70		// java.lang.Class enumsf =
71		// org.apache.axis.encoding.ser.EnumSerializerFactory.class;
72		// java.lang.Class enumdf =
73		// org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
74	0	java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
75	0	java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
76		// java.lang.Class simplesf =
77		// org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
78		// java.lang.Class simpledf =
79		// org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
80		// java.lang.Class simplelistsf =
81		// org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
82		// java.lang.Class simplelistdf =
83		// org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
84	0	qName = new javax.xml.namespace.QName("simple.objects.vamsas",
85		"Sequence");
86	0	cachedSerQNames.add(qName);
87	0	cls = vamsas.objects.simple.Sequence.class;
88	0	cachedSerClasses.add(cls);
89	0	cachedSerFactories.add(beansf);
90	0	cachedDeserFactories.add(beandf);
91
92	0	qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
93	0	cachedSerQNames.add(qName);
94	0	cls = vamsas.objects.simple.Sequence[].class;
95	0	cachedSerClasses.add(cls);
96	0	cachedSerFactories.add(arraysf);
97	0	cachedDeserFactories.add(arraydf);
98
99	0	qName = new javax.xml.namespace.QName("simple.objects.vamsas",
100		"MsaResult");
101	0	cachedSerQNames.add(qName);
102	0	cls = vamsas.objects.simple.MsaResult.class;
103	0	cachedSerClasses.add(cls);
104	0	cachedSerFactories.add(beansf);
105	0	cachedDeserFactories.add(beandf);
106
107	0	qName = new javax.xml.namespace.QName("simple.objects.vamsas",
108		"SequenceSet");
109	0	cachedSerQNames.add(qName);
110	0	cls = vamsas.objects.simple.SequenceSet.class;
111	0	cachedSerClasses.add(cls);
112	0	cachedSerFactories.add(beansf);
113	0	cachedDeserFactories.add(beandf);
114
115	0	qName = new javax.xml.namespace.QName("http://simple.objects.vamsas",
116		"Object");
117	0	cachedSerQNames.add(qName);
118	0	cls = vamsas.objects.simple.Object.class;
119	0	cachedSerClasses.add(cls);
120	0	cachedSerFactories.add(beansf);
121	0	cachedDeserFactories.add(beandf);
122
123	0	qName = new javax.xml.namespace.QName("simple.objects.vamsas",
124		"Alignment");
125	0	cachedSerQNames.add(qName);
126	0	cls = vamsas.objects.simple.Alignment.class;
127	0	cachedSerClasses.add(cls);
128	0	cachedSerFactories.add(beansf);
129	0	cachedDeserFactories.add(beandf);
130
131	0	qName = new javax.xml.namespace.QName("simple.objects.vamsas",
132		"WsJobId");
133	0	cachedSerQNames.add(qName);
134	0	cls = vamsas.objects.simple.WsJobId.class;
135	0	cachedSerClasses.add(cls);
136	0	cachedSerFactories.add(beansf);
137	0	cachedDeserFactories.add(beandf);
138
139	0	qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_xsd_string");
140	0	cachedSerQNames.add(qName);
141	0	cls = java.lang.String[].class;
142	0	cachedSerClasses.add(cls);
143	0	cachedSerFactories.add(arraysf);
144	0	cachedDeserFactories.add(arraydf);
145
146	0	qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
147	0	cachedSerQNames.add(qName);
148	0	cls = vamsas.objects.simple.Result.class;
149	0	cachedSerClasses.add(cls);
150	0	cachedSerFactories.add(beansf);
151	0	cachedDeserFactories.add(beandf);
152		}
153
		0% Uncovered Elements: 37 (37) Complexity: 1 Complexity Density: 0.03
154	0	private static void _initOperationDesc1()...
155		{
156	0	org.apache.axis.description.OperationDesc oper;
157	0	oper = new org.apache.axis.description.OperationDesc();
158	0	oper.setName("align");
159	0	oper.addParameter(new javax.xml.namespace.QName("", "seqSet"),
160		new javax.xml.namespace.QName("simple.objects.vamsas",
161		"SequenceSet"),
162		vamsas.objects.simple.SequenceSet.class,
163		org.apache.axis.description.ParameterDesc.IN, false, false);
164	0	oper.setReturnType(new javax.xml.namespace.QName(
165		"simple.objects.vamsas", "WsJobId"));
166	0	oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
167	0	oper.setReturnQName(new javax.xml.namespace.QName("", "alignReturn"));
168	0	oper.setStyle(org.apache.axis.constants.Style.RPC);
169	0	oper.setUse(org.apache.axis.constants.Use.ENCODED);
170	0	_operations[0] = oper;
171
172	0	oper = new org.apache.axis.description.OperationDesc();
173	0	oper.setName("getalign");
174	0	oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
175		new javax.xml.namespace.QName(
176		"http://www.w3.org/2001/XMLSchema", "string"),
177		java.lang.String.class,
178		org.apache.axis.description.ParameterDesc.IN, false, false);
179	0	oper.setReturnType(new javax.xml.namespace.QName(
180		"simple.objects.vamsas", "Alignment"));
181	0	oper.setReturnClass(vamsas.objects.simple.Alignment.class);
182	0	oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));
183	0	oper.setStyle(org.apache.axis.constants.Style.RPC);
184	0	oper.setUse(org.apache.axis.constants.Use.ENCODED);
185	0	_operations[1] = oper;
186
187	0	oper = new org.apache.axis.description.OperationDesc();
188	0	oper.setName("getResult");
189	0	oper.addParameter(new javax.xml.namespace.QName("", "job_id"),
190		new javax.xml.namespace.QName(
191		"http://www.w3.org/2001/XMLSchema", "string"),
192		java.lang.String.class,
193		org.apache.axis.description.ParameterDesc.IN, false, false);
194	0	oper.setReturnType(new javax.xml.namespace.QName(
195		"simple.objects.vamsas", "MsaResult"));
196	0	oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
197	0	oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
198	0	oper.setStyle(org.apache.axis.constants.Style.RPC);
199	0	oper.setUse(org.apache.axis.constants.Use.ENCODED);
200	0	_operations[2] = oper;
201
202	0	oper = new org.apache.axis.description.OperationDesc();
203	0	oper.setName("cancel");
204	0	oper.addParameter(new javax.xml.namespace.QName("", "jobId"),
205		new javax.xml.namespace.QName(
206		"http://www.w3.org/2001/XMLSchema", "string"),
207		java.lang.String.class,
208		org.apache.axis.description.ParameterDesc.IN, false, false);
209	0	oper.setReturnType(new javax.xml.namespace.QName(
210		"simple.objects.vamsas", "WsJobId"));
211	0	oper.setReturnClass(vamsas.objects.simple.WsJobId.class);
212	0	oper.setReturnQName(new javax.xml.namespace.QName("", "cancelReturn"));
213	0	oper.setStyle(org.apache.axis.constants.Style.RPC);
214	0	oper.setUse(org.apache.axis.constants.Use.ENCODED);
215	0	_operations[3] = oper;
216		}
217
		0% Uncovered Elements: 48 (48) Complexity: 11 Complexity Density: 0.37
218	0	protected org.apache.axis.client.Call createCall()...
219		throws java.rmi.RemoteException
220		{
221	0	try
222		{
223	0	org.apache.axis.client.Call _call = (org.apache.axis.client.Call) super.service
224		.createCall();
225
226	0	if (super.maintainSessionSet)
227		{
228	0	_call.setMaintainSession(super.maintainSession);
229		}
230
231	0	if (super.cachedUsername != null)
232		{
233	0	_call.setUsername(super.cachedUsername);
234		}
235
236	0	if (super.cachedPassword != null)
237		{
238	0	_call.setPassword(super.cachedPassword);
239		}
240
241	0	if (super.cachedEndpoint != null)
242		{
243	0	_call.setTargetEndpointAddress(super.cachedEndpoint);
244		}
245
246	0	if (super.cachedTimeout != null)
247		{
248	0	_call.setTimeout(super.cachedTimeout);
249		}
250
251	0	if (super.cachedPortName != null)
252		{
253	0	_call.setPortName(super.cachedPortName);
254		}
255
256	0	java.util.Enumeration keys = super.cachedProperties.keys();
257
258	0	while (keys.hasMoreElements())
259		{
260	0	java.lang.String key = (java.lang.String) keys.nextElement();
261	0	_call.setProperty(key, super.cachedProperties.get(key));
262		}
263
264		// All the type mapping information is registered
265		// when the first call is made.
266		// The type mapping information is actually registered in
267		// the TypeMappingRegistry of the service, which
268		// is the reason why registration is only needed for the first call.
269	0	synchronized (this)
270		{
271	0	if (firstCall())
272		{
273		// must set encoding style before registering serializers
274	0	_call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
275	0	_call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
276
277	0	for (int i = 0; i < cachedSerFactories.size(); ++i)
278		{
279	0	java.lang.Class cls = (java.lang.Class) cachedSerClasses.get(i);
280	0	javax.xml.namespace.QName qName = (javax.xml.namespace.QName) cachedSerQNames
281		.get(i);
282	0	java.lang.Class sf = (java.lang.Class) cachedSerFactories
283		.get(i);
284	0	java.lang.Class df = (java.lang.Class) cachedDeserFactories
285		.get(i);
286	0	_call.registerTypeMapping(cls, qName, sf, df, false);
287		}
288		}
289		}
290
291	0	return _call;
292		} catch (java.lang.Throwable _t)
293		{
294	0	throw new org.apache.axis.AxisFault(
295		"Failure trying to get the Call object", _t);
296		}
297		}
298
		0% Uncovered Elements: 21 (21) Complexity: 4 Complexity Density: 0.24
299	0	public vamsas.objects.simple.WsJobId align(...
300		vamsas.objects.simple.SequenceSet seqSet)
301		throws java.rmi.RemoteException
302		{
303	0	if (super.cachedEndpoint == null)
304		{
305	0	throw new org.apache.axis.NoEndPointException();
306		}
307
308	0	org.apache.axis.client.Call _call = createCall();
309	0	_call.setOperation(_operations[0]);
310	0	_call.setUseSOAPAction(true);
311	0	_call.setSOAPActionURI("");
312	0	_call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
313	0	_call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));
314
315	0	setRequestHeaders(_call);
316	0	setAttachments(_call);
317
318	0	java.lang.Object _resp = _call
319		.invoke(new java.lang.Object[] { seqSet });
320
321	0	if (_resp instanceof java.rmi.RemoteException)
322		{
323	0	throw (java.rmi.RemoteException) _resp;
324		}
325		else
326		{
327	0	extractAttachments(_call);
328
329	0	try
330		{
331	0	return (vamsas.objects.simple.WsJobId) _resp;
332		} catch (java.lang.Exception _exception)
333		{
334	0	return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
335		.convert(_resp, vamsas.objects.simple.WsJobId.class);
336		}
337		}
338		}
339
		0% Uncovered Elements: 21 (21) Complexity: 4 Complexity Density: 0.24
340	0	public vamsas.objects.simple.Alignment getalign(java.lang.String job_id)...
341		throws java.rmi.RemoteException
342		{
343	0	if (super.cachedEndpoint == null)
344		{
345	0	throw new org.apache.axis.NoEndPointException();
346		}
347
348	0	org.apache.axis.client.Call _call = createCall();
349	0	_call.setOperation(_operations[1]);
350	0	_call.setUseSOAPAction(true);
351	0	_call.setSOAPActionURI("");
352	0	_call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
353	0	_call.setOperationName(new javax.xml.namespace.QName("vamsas",
354		"getalign"));
355
356	0	setRequestHeaders(_call);
357	0	setAttachments(_call);
358
359	0	java.lang.Object _resp = _call
360		.invoke(new java.lang.Object[] { job_id });
361
362	0	if (_resp instanceof java.rmi.RemoteException)
363		{
364	0	throw (java.rmi.RemoteException) _resp;
365		}
366		else
367		{
368	0	extractAttachments(_call);
369
370	0	try
371		{
372	0	return (vamsas.objects.simple.Alignment) _resp;
373		} catch (java.lang.Exception _exception)
374		{
375	0	return (vamsas.objects.simple.Alignment) org.apache.axis.utils.JavaUtils
376		.convert(_resp, vamsas.objects.simple.Alignment.class);
377		}
378		}
379		}
380
		0% Uncovered Elements: 21 (21) Complexity: 4 Complexity Density: 0.24
381	0	public vamsas.objects.simple.MsaResult getResult(java.lang.String job_id)...
382		throws java.rmi.RemoteException
383		{
384	0	if (super.cachedEndpoint == null)
385		{
386	0	throw new org.apache.axis.NoEndPointException();
387		}
388
389	0	org.apache.axis.client.Call _call = createCall();
390	0	_call.setOperation(_operations[2]);
391	0	_call.setUseSOAPAction(true);
392	0	_call.setSOAPActionURI("");
393	0	_call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
394	0	_call.setOperationName(new javax.xml.namespace.QName("vamsas",
395		"getResult"));
396
397	0	setRequestHeaders(_call);
398	0	setAttachments(_call);
399
400	0	java.lang.Object _resp = _call
401		.invoke(new java.lang.Object[] { job_id });
402
403	0	if (_resp instanceof java.rmi.RemoteException)
404		{
405	0	throw (java.rmi.RemoteException) _resp;
406		}
407		else
408		{
409	0	extractAttachments(_call);
410
411	0	try
412		{
413	0	return (vamsas.objects.simple.MsaResult) _resp;
414		} catch (java.lang.Exception _exception)
415		{
416	0	return (vamsas.objects.simple.MsaResult) org.apache.axis.utils.JavaUtils
417		.convert(_resp, vamsas.objects.simple.MsaResult.class);
418		}
419		}
420		}
421
		0% Uncovered Elements: 21 (21) Complexity: 4 Complexity Density: 0.24
422	0	public vamsas.objects.simple.WsJobId cancel(java.lang.String jobId)...
423		throws java.rmi.RemoteException
424		{
425	0	if (super.cachedEndpoint == null)
426		{
427	0	throw new org.apache.axis.NoEndPointException();
428		}
429
430	0	org.apache.axis.client.Call _call = createCall();
431	0	_call.setOperation(_operations[3]);
432	0	_call.setUseSOAPAction(true);
433	0	_call.setSOAPActionURI("");
434	0	_call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
435	0	_call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
436
437	0	setRequestHeaders(_call);
438	0	setAttachments(_call);
439
440	0	java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobId });
441
442	0	if (_resp instanceof java.rmi.RemoteException)
443		{
444	0	throw (java.rmi.RemoteException) _resp;
445		}
446		else
447		{
448	0	extractAttachments(_call);
449
450	0	try
451		{
452	0	return (vamsas.objects.simple.WsJobId) _resp;
453		} catch (java.lang.Exception _exception)
454		{
455	0	return (vamsas.objects.simple.WsJobId) org.apache.axis.utils.JavaUtils
456		.convert(_resp, vamsas.objects.simple.WsJobId.class);
457		}
458		}
459		}
460		}