Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MsaWSClient	47	50	21	0.026315792.6%	Show methods

Class MsaWSClient

Class MsaWSClient	Line # 47	Total Statements 50	Complexity 21	TOTAL Coverage 0.026315792.6%
MsaWSClient(ext.vamsas.ServiceHandle,String,jalview.datamodel.AlignmentView,boolean,boolean,AlignmentI,AlignFrame)   MsaWSClient(ext.vamsas.ServiceHandle,String,jalview.datamodel.AlignmentView,boolean,boolean,AlignmentI,AlignFrame)	7272	9.09	3.03	0.0 0.00%
MsaWSClient()   MsaWSClient()	106106	1.01	1.01	1.0 1.0100%
startMsaWSClient(String,AlignmentView,boolean,boolean,AlignmentI) : void   startMsaWSClient(String,AlignmentView,boolean,boolean,AlignmentI) : void	112112	13.013	8.08	0.0 0.00%
locateWebService() : boolean   locateWebService() : boolean	155155	10.010	2.02	0.0 0.00%
getServiceActionKey() : String   getServiceActionKey() : String	181181	1.01	1.01	0.0 0.00%
getServiceActionDescription() : String   getServiceActionDescription() : String	186186	1.01	1.01	0.0 0.00%
canSubmitGaps() : boolean   canSubmitGaps() : boolean	197197	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	213213	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	234234	2.02	1.01	0.0 0.00%
attachWSMenuEntry(JMenu,ServiceHandle,AlignFrame) : void   attachWSMenuEntry(JMenu,ServiceHandle,AlignFrame) : void	204204	10.010	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.02631579	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS

 

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.jws1;
22
23		import jalview.datamodel.AlignmentI;
24		import jalview.datamodel.AlignmentView;
25		import jalview.gui.AlignFrame;
26		import jalview.gui.Desktop;
27		import jalview.gui.JvOptionPane;
28		import jalview.gui.WebserviceInfo;
29		import jalview.util.MessageManager;
30
31		import java.awt.event.ActionEvent;
32		import java.awt.event.ActionListener;
33
34		import javax.swing.JMenu;
35		import javax.swing.JMenuItem;
36
37		import ext.vamsas.MuscleWSServiceLocator;
38		import ext.vamsas.MuscleWSSoapBindingStub;
39		import ext.vamsas.ServiceHandle;
40
41		/**
42		* DOCUMENT ME!
43		*
44		* @author $author$
45		* @version $Revision$
46		*/
		2.6% Uncovered Elements: 74 (76) Complexity: 21 Complexity Density: 0.42
47		public class MsaWSClient extends WS1Client
48		{
49		/**
50		* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
51		*/
52		ext.vamsas.MuscleWS server;
53
54		AlignFrame alignFrame;
55
56		/**
57		* Creates a new MsaWSClient object that uses a service given by an externally
58		* retrieved ServiceHandle
59		*
60		* @param sh
61		* service handle of type AbstractName(MsaWS)
62		* @param altitle
63		* DOCUMENT ME!
64		* @param msa
65		* DOCUMENT ME!
66		* @param submitGaps
67		* DOCUMENT ME!
68		* @param preserveOrder
69		* DOCUMENT ME!
70		*/
71
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.33
72	0	public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,...
73		jalview.datamodel.AlignmentView msa, boolean submitGaps,
74		boolean preserveOrder, AlignmentI seqdataset,
75		AlignFrame _alignFrame)
76		{
77	0	super();
78	0	alignFrame = _alignFrame;
79	0	if (!sh.getAbstractName().equals("MsaWS"))
80		{
81	0	JvOptionPane.showMessageDialog(Desktop.desktop,
82		MessageManager.formatMessage(
83		"label.service_called_is_not_msa_service",
84		new String[]
85		{ sh.getName() }),
86		MessageManager.getString("label.internal_jalview_error"),
87		JvOptionPane.WARNING_MESSAGE);
88
89	0	return;
90		}
91
92	0	if ((wsInfo = setWebService(sh)) == null)
93		{
94	0	JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
95		.formatMessage("label.msa_service_is_unknown", new String[]
96		{ sh.getName() }),
97		MessageManager.getString("label.internal_jalview_error"),
98		JvOptionPane.WARNING_MESSAGE);
99
100	0	return;
101		}
102	0	startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
103
104		}
105
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
106	1	public MsaWSClient()...
107		{
108	1	super();
109		// add a class reference to the list
110		}
111
		0% Uncovered Elements: 23 (23) Complexity: 8 Complexity Density: 0.62
112	0	private void startMsaWSClient(String altitle, AlignmentView msa,...
113		boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
114		{
115	0	if (!locateWebService())
116		{
117	0	return;
118		}
119
120	0	wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
121		+ " of " + altitle + "\nJob details\n");
122	0	String jobtitle = WebServiceName.toLowerCase();
123	0	if (jobtitle.endsWith("alignment"))
124		{
125	0	if (submitGaps && (!jobtitle.endsWith("realignment")
126		|| jobtitle.indexOf("profile") == -1))
127		{
128	0	int pos = jobtitle.indexOf("alignment");
129	0	jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
130		+ altitle;
131		}
132		else
133		{
134	0	jobtitle = WebServiceName + " of " + altitle;
135		}
136		}
137		else
138		{
139	0	jobtitle = WebServiceName + (submitGaps ? " re" : " ")
140		+ "alignment of " + altitle;
141		}
142
143	0	MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo,
144		alignFrame, WebServiceName, jobtitle, msa, submitGaps,
145		preserveOrder, seqdataset);
146	0	wsInfo.setthisService(msathread);
147	0	msathread.start();
148		}
149
150		/**
151		* Initializes the server field with a valid service implementation.
152		*
153		* @return true if service was located.
154		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.2
155	0	private boolean locateWebService()...
156		{
157		// TODO: MuscleWS transmuted to generic MsaWS client
158	0	MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
159
160	0	try
161		{
162	0	this.server = loc.getMuscleWS(new java.net.URL(WsURL));
163	0	((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
164		// timeout
165		} catch (Exception ex)
166		{
167	0	wsInfo.setProgressText("Serious! " + WebServiceName
168		+ " Service location failed\nfor URL :" + WsURL + "\n"
169		+ ex.getMessage());
170	0	wsInfo.setStatus(WebserviceInfo.ERROR);
171	0	ex.printStackTrace();
172
173	0	return false;
174		}
175
176	0	loc.getEngine().setOption("axis", "1");
177
178	0	return true;
179		}
180
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
181	0	protected String getServiceActionKey()...
182		{
183	0	return "MsaWS";
184		}
185
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
186	0	protected String getServiceActionDescription()...
187		{
188	0	return "Multiple Sequence Alignment";
189		}
190
191		/**
192		* look at ourselves and work out if we are a service that can take a profile
193		* and align to it
194		*
195		* @return true if we can send gapped sequences to the alignment service
196		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
197	0	private boolean canSubmitGaps()...
198		{
199		// TODO: query service or extract service handle props to check if we can
200		// realign
201	0	return (WebServiceName.indexOf("lustal") > -1); // cheat!
202		}
203
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
204	0	@Override...
205		public void attachWSMenuEntry(JMenu msawsmenu,
206		final ServiceHandle serviceHandle, final AlignFrame alignFrame)
207		{
208	0	setWebService(serviceHandle, true); // headless
209	0	JMenuItem method = new JMenuItem(WebServiceName);
210	0	method.setToolTipText(WsURL);
211	0	method.addActionListener(new ActionListener()
212		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
213	0	@Override...
214		public void actionPerformed(ActionEvent e)
215		{
216	0	AlignmentView msa = alignFrame.gatherSequencesForAlignment();
217	0	new jalview.ws.jws1.MsaWSClient(serviceHandle,
218		alignFrame.getTitle(), msa, false, true,
219		alignFrame.getViewport().getAlignment().getDataset(),
220		alignFrame);
221
222		}
223
224		});
225	0	msawsmenu.add(method);
226	0	if (canSubmitGaps())
227		{
228		// We know that ClustalWS can accept partial alignments for refinement.
229	0	final JMenuItem methodR = new JMenuItem(
230		serviceHandle.getName() + " Realign");
231	0	methodR.setToolTipText(WsURL);
232	0	methodR.addActionListener(new ActionListener()
233		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
234	0	@Override...
235		public void actionPerformed(ActionEvent e)
236		{
237	0	AlignmentView msa = alignFrame.gatherSequencesForAlignment();
238	0	new jalview.ws.jws1.MsaWSClient(serviceHandle,
239		alignFrame.getTitle(), msa, true, true,
240		alignFrame.getViewport().getAlignment().getDataset(),
241		alignFrame);
242
243		}
244
245		});
246	0	msawsmenu.add(methodR);
247
248		}
249
250		}
251		}