Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceAnnotationWSClient	46	60	24	0.00%	Show methods

Class SequenceAnnotationWSClient

Class SequenceAnnotationWSClient	Line # 46	Total Statements 60	Complexity 24	TOTAL Coverage 0.00%
SequenceAnnotationWSClient()   SequenceAnnotationWSClient()	5151	0.00	1.01	-1.0 -1.0 -
SequenceAnnotationWSClient(Jws2Instance,AlignFrame,WsParamSetI,boolean)   SequenceAnnotationWSClient(Jws2Instance,AlignFrame,WsParamSetI,boolean)	5656	2.02	1.01	0.0 0.00%
initSequenceAnnotationWSClient(Jws2Instance,AlignFrame,WsParamSetI,boolean) : void   initSequenceAnnotationWSClient(Jws2Instance,AlignFrame,WsParamSetI,boolean) : void	6666	26.026	10.010	0.0 0.00%
SequenceAnnotationWSClient(AAConSettings,AlignFrame,boolean)   SequenceAnnotationWSClient(AAConSettings,AlignFrame,boolean)	147147	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	180180	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	198198	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	222222	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	244244	1.01	1.01	0.0 0.00%
attachWSMenuEntry(JMenu,Jws2Instance,AlignFrame) : void   attachWSMenuEntry(JMenu,Jws2Instance,AlignFrame) : void	161161	26.026	7.07	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;
22
23		import java.util.Locale;
24
25		import jalview.api.AlignCalcWorkerI;
26		import jalview.gui.AlignFrame;
27		import jalview.gui.Desktop;
28		import jalview.gui.JvSwingUtils;
29		import jalview.util.MessageManager;
30		import jalview.ws.jws2.dm.AAConSettings;
31		import jalview.ws.jws2.jabaws2.Jws2Instance;
32		import jalview.ws.params.WsParamSetI;
33		import jalview.ws.uimodel.AlignAnalysisUIText;
34
35		import java.awt.event.ActionEvent;
36		import java.awt.event.ActionListener;
37		import java.util.List;
38
39		import javax.swing.JMenu;
40		import javax.swing.JMenuItem;
41
42		/**
43		* @author jprocter
44		*
45		*/
		0% Uncovered Elements: 93 (93) Complexity: 24 Complexity Density: 0.4
46		public class SequenceAnnotationWSClient extends Jws2Client
47		{
48		/**
49		* initialise a client so its attachWSMenuEntry method can be called.
50		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
51	0	public SequenceAnnotationWSClient()...
52		{
53		// TODO Auto-generated constructor stub
54		}
55
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
56	0	public SequenceAnnotationWSClient(final Jws2Instance sh,...
57		AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
58		{
59	0	super(alignFrame, preset, null);
60	0	initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
61		}
62
63		// dan think. Do I need to change this method to run RNAalifold through the
64		// GUI
65
		0% Uncovered Elements: 40 (40) Complexity: 10 Complexity Density: 0.38
66	0	public void initSequenceAnnotationWSClient(final Jws2Instance sh,...
67		AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
68		{
69		// dan changed! dan test. comment out if conditional
70		// if (alignFrame.getViewport().getAlignment().isNucleotide())
71		// {
72		// JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
73		// + " can only be used\nfor amino acid alignments.",
74		// "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
75		// return;
76		//
77		// }
78	0	AlignAnalysisUIText aaui = sh.getAlignAnalysisUI();
79	0	if (aaui != null)
80		{
81	0	Class clientClass = aaui.getClient();
82
83		// Build an AACon style client - take alignment, return annotation for
84		// columns
85
86	0	List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
87		.getCalcManager().getRegisteredWorkersOfClass(clientClass);
88	0	AbstractJabaCalcWorker worker;
89	0	if (clnts == null || clnts.size() == 0)
90		{
91	0	if (!processParams(sh, editParams))
92		{
93	0	return;
94		}
95	0	try
96		{
97	0	worker = (AbstractJabaCalcWorker) (clientClass
98		.getConstructor(new Class[]
99		{ Jws2Instance.class, AlignFrame.class, WsParamSetI.class,
100		List.class })
101		.newInstance(new Object[]
102		{ sh, alignFrame, this.preset, paramset }));
103		} catch (Exception x)
104		{
105	0	x.printStackTrace();
106	0	throw new Error(
107		MessageManager.getString("error.implementation_error"),
108		x);
109		}
110	0	alignFrame.getViewport().getCalcManager().registerWorker(worker);
111	0	alignFrame.getViewport().getCalcManager().startWorker(worker);
112
113		}
114		else
115		{
116	0	worker = (AbstractJabaCalcWorker) clnts.get(0);
117	0	if (editParams)
118		{
119	0	paramset = worker.getArguments();
120	0	preset = worker.getPreset();
121		}
122
123	0	if (!processParams(sh, editParams, true))
124		{
125	0	return;
126		}
127		// reinstate worker if it was blacklisted (might have happened due to
128		// invalid parameters)
129	0	alignFrame.getViewport().getCalcManager().enableWorker(worker);
130	0	worker.updateParameters(this.preset, paramset);
131		}
132		}
133	0	if (sh.action.toLowerCase(Locale.ROOT).contains("disorder"))
134		{
135		// build IUPred style client. take sequences, returns annotation per
136		// sequence.
137	0	if (!processParams(sh, editParams))
138		{
139	0	return;
140		}
141
142	0	alignFrame.getViewport().getCalcManager().startWorker(
143		new AADisorderClient(sh, alignFrame, preset, paramset));
144		}
145		}
146
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
147	0	public SequenceAnnotationWSClient(AAConSettings fave,...
148		AlignFrame alignFrame, boolean b)
149		{
150	0	super(alignFrame, fave.getPreset(), fave.getJobArgset());
151	0	initSequenceAnnotationWSClient(fave.getService(), alignFrame,
152		fave.getPreset(), b);
153		}
154
155		/*
156		* (non-Javadoc)
157		*
158		* @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu,
159		* jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame)
160		*/
		0% Uncovered Elements: 36 (36) Complexity: 7 Complexity Density: 0.27
161	0	public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,...
162		final AlignFrame alignFrame)
163		{
164	0	if (registerAAConWSInstance(wsmenu, service, alignFrame))
165		{
166		// Alignment dependent analysis calculation WS gui
167	0	return;
168		}
169	0	boolean hasparams = service.hasParameters();
170		// Assume name ends in WS
171	0	String calcName = service.serviceType.substring(0,
172		service.serviceType.length() - 2);
173
174	0	JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage(
175		"label.calcname_with_default_settings", new String[]
176		{ calcName }));
177	0	annotservice.addActionListener(new ActionListener()
178		{
179
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public void actionPerformed(ActionEvent e)
182		{
183	0	new SequenceAnnotationWSClient(service, alignFrame, null, false);
184		}
185		});
186	0	wsmenu.add(annotservice);
187	0	if (hasparams)
188		{
189		// only add these menu options if the service has user-modifiable
190		// arguments
191	0	annotservice = new JMenuItem(
192		MessageManager.getString("label.edit_settings_and_run"));
193	0	annotservice.setToolTipText(MessageManager.getString(
194		"label.view_and_change_parameters_before_running_calculation"));
195
196	0	annotservice.addActionListener(new ActionListener()
197		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
198	0	public void actionPerformed(ActionEvent e)...
199		{
200	0	new SequenceAnnotationWSClient(service, alignFrame, null, true);
201		}
202		});
203	0	wsmenu.add(annotservice);
204	0	List<WsParamSetI> presets = service.getParamStore().getPresets();
205	0	if (presets != null && presets.size() > 0)
206		{
207	0	JMenu presetlist = new JMenu(MessageManager
208		.formatMessage("label.run_with_preset", new String[]
209		{ calcName }));
210
211	0	for (final WsParamSetI preset : presets)
212		{
213	0	final JMenuItem methodR = new JMenuItem(preset.getName());
214	0	methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>"
215	0	+ (preset.isModifiable()
216		? MessageManager.getString("label.user_preset")
217		: MessageManager
218		.getString("label.service_preset"))
219		+ "</strong><br/>" + preset.getDescription()));
220	0	methodR.addActionListener(new ActionListener()
221		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
222	0	public void actionPerformed(ActionEvent e)...
223		{
224	0	new SequenceAnnotationWSClient(service, alignFrame, preset,
225		false);
226		}
227
228		});
229	0	presetlist.add(methodR);
230		}
231	0	wsmenu.add(presetlist);
232		}
233
234		}
235		else
236		{
237	0	annotservice = new JMenuItem(
238		MessageManager.getString("label.view_documentation"));
239	0	if (service.docUrl != null)
240		{
241	0	annotservice.addActionListener(new ActionListener()
242		{
243
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
244	0	@Override...
245		public void actionPerformed(ActionEvent arg0)
246		{
247	0	Desktop.instance.showUrl(service.docUrl);
248		}
249		});
250	0	annotservice.setToolTipText(
251		JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage(
252		"label.view_service_doc_url", new String[]
253		{ service.docUrl, service.docUrl })));
254	0	wsmenu.add(annotservice);
255		}
256		}
257		}
258		}