Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MsaWSClient	49	50	21	0.026315792.6%	Show methods

Class MsaWSClient

Class MsaWSClient	Line # 49	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)	7474	9.09	3.03	0.0 0.00%
MsaWSClient()   MsaWSClient()	108108	1.01	1.01	1.0 1.0100%
startMsaWSClient(String,AlignmentView,boolean,boolean,AlignmentI) : void   startMsaWSClient(String,AlignmentView,boolean,boolean,AlignmentI) : void	114114	13.013	8.08	0.0 0.00%
locateWebService() : boolean   locateWebService() : boolean	157157	10.010	2.02	0.0 0.00%
getServiceActionKey() : String   getServiceActionKey() : String	183183	1.01	1.01	0.0 0.00%
getServiceActionDescription() : String   getServiceActionDescription() : String	188188	1.01	1.01	0.0 0.00%
canSubmitGaps() : boolean   canSubmitGaps() : boolean	199199	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	215215	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	236236	2.02	1.01	0.0 0.00%
attachWSMenuEntry(JMenu,ServiceHandle,AlignFrame) : void   attachWSMenuEntry(JMenu,ServiceHandle,AlignFrame) : void	206206	10.010	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.02631579	jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges	1PASS
	0.02631579	jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest	1PASS
	0.02631579	jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest	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 java.util.Locale;
24
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.AlignmentView;
27		import jalview.gui.AlignFrame;
28		import jalview.gui.Desktop;
29		import jalview.gui.JvOptionPane;
30		import jalview.gui.WebserviceInfo;
31		import jalview.util.MessageManager;
32
33		import java.awt.event.ActionEvent;
34		import java.awt.event.ActionListener;
35
36		import javax.swing.JMenu;
37		import javax.swing.JMenuItem;
38
39		import ext.vamsas.MuscleWSServiceLocator;
40		import ext.vamsas.MuscleWSSoapBindingStub;
41		import ext.vamsas.ServiceHandle;
42
43		/**
44		* DOCUMENT ME!
45		*
46		* @author $author$
47		* @version $Revision$
48		*/
		2.6% Uncovered Elements: 74 (76) Complexity: 21 Complexity Density: 0.42
49		public class MsaWSClient extends WS1Client
50		{
51		/**
52		* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
53		*/
54		ext.vamsas.MuscleWS server;
55
56		AlignFrame alignFrame;
57
58		/**
59		* Creates a new MsaWSClient object that uses a service given by an externally
60		* retrieved ServiceHandle
61		*
62		* @param sh
63		* service handle of type AbstractName(MsaWS)
64		* @param altitle
65		* DOCUMENT ME!
66		* @param msa
67		* DOCUMENT ME!
68		* @param submitGaps
69		* DOCUMENT ME!
70		* @param preserveOrder
71		* DOCUMENT ME!
72		*/
73
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.33
74	0	public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,...
75		jalview.datamodel.AlignmentView msa, boolean submitGaps,
76		boolean preserveOrder, AlignmentI seqdataset,
77		AlignFrame _alignFrame)
78		{
79	0	super();
80	0	alignFrame = _alignFrame;
81	0	if (!sh.getAbstractName().equals("MsaWS"))
82		{
83	0	JvOptionPane.showMessageDialog(Desktop.desktop,
84		MessageManager.formatMessage(
85		"label.service_called_is_not_msa_service",
86		new String[]
87		{ sh.getName() }),
88		MessageManager.getString("label.internal_jalview_error"),
89		JvOptionPane.WARNING_MESSAGE);
90
91	0	return;
92		}
93
94	0	if ((wsInfo = setWebService(sh)) == null)
95		{
96	0	JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
97		.formatMessage("label.msa_service_is_unknown", new String[]
98		{ sh.getName() }),
99		MessageManager.getString("label.internal_jalview_error"),
100		JvOptionPane.WARNING_MESSAGE);
101
102	0	return;
103		}
104	0	startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
105
106		}
107
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
108	6	public MsaWSClient()...
109		{
110	6	super();
111		// add a class reference to the list
112		}
113
		0% Uncovered Elements: 23 (23) Complexity: 8 Complexity Density: 0.62
114	0	private void startMsaWSClient(String altitle, AlignmentView msa,...
115		boolean submitGaps, boolean preserveOrder, AlignmentI seqdataset)
116		{
117	0	if (!locateWebService())
118		{
119	0	return;
120		}
121
122	0	wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
123		+ " of " + altitle + "\nJob details\n");
124	0	String jobtitle = WebServiceName.toLowerCase(Locale.ROOT);
125	0	if (jobtitle.endsWith("alignment"))
126		{
127	0	if (submitGaps && (!jobtitle.endsWith("realignment")
128		|| jobtitle.indexOf("profile") == -1))
129		{
130	0	int pos = jobtitle.indexOf("alignment");
131	0	jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
132		+ altitle;
133		}
134		else
135		{
136	0	jobtitle = WebServiceName + " of " + altitle;
137		}
138		}
139		else
140		{
141	0	jobtitle = WebServiceName + (submitGaps ? " re" : " ")
142		+ "alignment of " + altitle;
143		}
144
145	0	MsaWSThread msathread = new MsaWSThread(server, WsURL, wsInfo,
146		alignFrame, WebServiceName, jobtitle, msa, submitGaps,
147		preserveOrder, seqdataset);
148	0	wsInfo.setthisService(msathread);
149	0	msathread.start();
150		}
151
152		/**
153		* Initializes the server field with a valid service implementation.
154		*
155		* @return true if service was located.
156		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.2
157	0	private boolean locateWebService()...
158		{
159		// TODO: MuscleWS transmuted to generic MsaWS client
160	0	MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
161
162	0	try
163		{
164	0	this.server = loc.getMuscleWS(new java.net.URL(WsURL));
165	0	((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute
166		// timeout
167		} catch (Exception ex)
168		{
169	0	wsInfo.setProgressText("Serious! " + WebServiceName
170		+ " Service location failed\nfor URL :" + WsURL + "\n"
171		+ ex.getMessage());
172	0	wsInfo.setStatus(WebserviceInfo.ERROR);
173	0	ex.printStackTrace();
174
175	0	return false;
176		}
177
178	0	loc.getEngine().setOption("axis", "1");
179
180	0	return true;
181		}
182
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
183	0	protected String getServiceActionKey()...
184		{
185	0	return "MsaWS";
186		}
187
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
188	0	protected String getServiceActionDescription()...
189		{
190	0	return "Multiple Sequence Alignment";
191		}
192
193		/**
194		* look at ourselves and work out if we are a service that can take a profile
195		* and align to it
196		*
197		* @return true if we can send gapped sequences to the alignment service
198		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
199	0	private boolean canSubmitGaps()...
200		{
201		// TODO: query service or extract service handle props to check if we can
202		// realign
203	0	return (WebServiceName.indexOf("lustal") > -1); // cheat!
204		}
205
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
206	0	@Override...
207		public void attachWSMenuEntry(JMenu msawsmenu,
208		final ServiceHandle serviceHandle, final AlignFrame alignFrame)
209		{
210	0	setWebService(serviceHandle, true); // headless
211	0	JMenuItem method = new JMenuItem(WebServiceName);
212	0	method.setToolTipText(WsURL);
213	0	method.addActionListener(new ActionListener()
214		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
215	0	@Override...
216		public void actionPerformed(ActionEvent e)
217		{
218	0	AlignmentView msa = alignFrame.gatherSequencesForAlignment();
219	0	new jalview.ws.jws1.MsaWSClient(serviceHandle,
220		alignFrame.getTitle(), msa, false, true,
221		alignFrame.getViewport().getAlignment().getDataset(),
222		alignFrame);
223
224		}
225
226		});
227	0	msawsmenu.add(method);
228	0	if (canSubmitGaps())
229		{
230		// We know that ClustalWS can accept partial alignments for refinement.
231	0	final JMenuItem methodR = new JMenuItem(
232		serviceHandle.getName() + " Realign");
233	0	methodR.setToolTipText(WsURL);
234	0	methodR.addActionListener(new ActionListener()
235		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
236	0	@Override...
237		public void actionPerformed(ActionEvent e)
238		{
239	0	AlignmentView msa = alignFrame.gatherSequencesForAlignment();
240	0	new jalview.ws.jws1.MsaWSClient(serviceHandle,
241		alignFrame.getTitle(), msa, true, true,
242		alignFrame.getViewport().getAlignment().getDataset(),
243		alignFrame);
244
245		}
246
247		});
248	0	msawsmenu.add(methodR);
249
250		}
251
252		}
253		}