1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
|
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
|
15 |
|
|
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
|
21 |
|
package jalview.ws.jws2; |
22 |
|
|
23 |
|
import jalview.api.AlignCalcWorkerI; |
24 |
|
import jalview.gui.AlignFrame; |
25 |
|
import jalview.gui.Desktop; |
26 |
|
import jalview.gui.JvSwingUtils; |
27 |
|
import jalview.util.MessageManager; |
28 |
|
import jalview.ws.jws2.dm.AAConSettings; |
29 |
|
import jalview.ws.jws2.jabaws2.Jws2Instance; |
30 |
|
import jalview.ws.params.WsParamSetI; |
31 |
|
import jalview.ws.uimodel.AlignAnalysisUIText; |
32 |
|
|
33 |
|
import java.awt.event.ActionEvent; |
34 |
|
import java.awt.event.ActionListener; |
35 |
|
import java.util.List; |
36 |
|
|
37 |
|
import javax.swing.JMenu; |
38 |
|
import javax.swing.JMenuItem; |
39 |
|
|
40 |
|
|
41 |
|
@author |
42 |
|
|
43 |
|
|
|
|
| 29% |
Uncovered Elements: 66 (93) |
Complexity: 24 |
Complexity Density: 0.4 |
|
44 |
|
public class SequenceAnnotationWSClient extends Jws2Client |
45 |
|
{ |
46 |
|
|
47 |
|
|
48 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
49 |
2804 |
public SequenceAnnotationWSClient()... |
50 |
|
{ |
51 |
|
|
52 |
|
} |
53 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
54 |
0 |
public SequenceAnnotationWSClient(final Jws2Instance sh,... |
55 |
|
AlignFrame alignFrame, WsParamSetI preset, boolean editParams) |
56 |
|
{ |
57 |
0 |
super(alignFrame, preset, null); |
58 |
0 |
initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams); |
59 |
|
} |
60 |
|
|
61 |
|
|
62 |
|
|
63 |
|
|
|
|
| 0% |
Uncovered Elements: 40 (40) |
Complexity: 10 |
Complexity Density: 0.38 |
|
64 |
0 |
public void initSequenceAnnotationWSClient(final Jws2Instance sh,... |
65 |
|
AlignFrame alignFrame, WsParamSetI preset, boolean editParams) |
66 |
|
{ |
67 |
|
|
68 |
|
|
69 |
|
|
70 |
|
|
71 |
|
|
72 |
|
|
73 |
|
|
74 |
|
|
75 |
|
|
76 |
0 |
AlignAnalysisUIText aaui = sh.getAlignAnalysisUI(); |
77 |
0 |
if (aaui != null) |
78 |
|
{ |
79 |
0 |
Class clientClass = aaui.getClient(); |
80 |
|
|
81 |
|
|
82 |
|
|
83 |
|
|
84 |
0 |
List<AlignCalcWorkerI> clnts = alignFrame.getViewport() |
85 |
|
.getCalcManager().getRegisteredWorkersOfClass(clientClass); |
86 |
0 |
AbstractJabaCalcWorker worker; |
87 |
0 |
if (clnts == null || clnts.size() == 0) |
88 |
|
{ |
89 |
0 |
if (!processParams(sh, editParams)) |
90 |
|
{ |
91 |
0 |
return; |
92 |
|
} |
93 |
0 |
try |
94 |
|
{ |
95 |
0 |
worker = (AbstractJabaCalcWorker) (clientClass |
96 |
|
.getConstructor(new Class[] |
97 |
|
{ Jws2Instance.class, AlignFrame.class, WsParamSetI.class, |
98 |
|
List.class }) |
99 |
|
.newInstance(new Object[] |
100 |
|
{ sh, alignFrame, this.preset, paramset })); |
101 |
|
} catch (Exception x) |
102 |
|
{ |
103 |
0 |
x.printStackTrace(); |
104 |
0 |
throw new Error( |
105 |
|
MessageManager.getString("error.implementation_error"), |
106 |
|
x); |
107 |
|
} |
108 |
0 |
alignFrame.getViewport().getCalcManager().registerWorker(worker); |
109 |
0 |
alignFrame.getViewport().getCalcManager().startWorker(worker); |
110 |
|
|
111 |
|
} |
112 |
|
else |
113 |
|
{ |
114 |
0 |
worker = (AbstractJabaCalcWorker) clnts.get(0); |
115 |
0 |
if (editParams) |
116 |
|
{ |
117 |
0 |
paramset = worker.getArguments(); |
118 |
0 |
preset = worker.getPreset(); |
119 |
|
} |
120 |
|
|
121 |
0 |
if (!processParams(sh, editParams, true)) |
122 |
|
{ |
123 |
0 |
return; |
124 |
|
} |
125 |
|
|
126 |
|
|
127 |
0 |
alignFrame.getViewport().getCalcManager().enableWorker(worker); |
128 |
0 |
worker.updateParameters(this.preset, paramset); |
129 |
|
} |
130 |
|
} |
131 |
0 |
if (sh.action.toLowerCase().contains("disorder")) |
132 |
|
{ |
133 |
|
|
134 |
|
|
135 |
0 |
if (!processParams(sh, editParams)) |
136 |
|
{ |
137 |
0 |
return; |
138 |
|
} |
139 |
|
|
140 |
0 |
alignFrame.getViewport().getCalcManager().startWorker( |
141 |
|
new AADisorderClient(sh, alignFrame, preset, paramset)); |
142 |
|
} |
143 |
|
} |
144 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
145 |
0 |
public SequenceAnnotationWSClient(AAConSettings fave,... |
146 |
|
AlignFrame alignFrame, boolean b) |
147 |
|
{ |
148 |
0 |
super(alignFrame, fave.getPreset(), fave.getJobArgset()); |
149 |
0 |
initSequenceAnnotationWSClient(fave.getService(), alignFrame, |
150 |
|
fave.getPreset(), b); |
151 |
|
} |
152 |
|
|
153 |
|
|
154 |
|
|
155 |
|
|
156 |
|
@see |
157 |
|
|
158 |
|
|
|
|
| 69.4% |
Uncovered Elements: 11 (36) |
Complexity: 7 |
Complexity Density: 0.27 |
|
159 |
2804 |
public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,... |
160 |
|
final AlignFrame alignFrame) |
161 |
|
{ |
162 |
2796 |
if (registerAAConWSInstance(wsmenu, service, alignFrame)) |
163 |
|
{ |
164 |
|
|
165 |
932 |
return; |
166 |
|
} |
167 |
1864 |
boolean hasparams = service.hasParameters(); |
168 |
|
|
169 |
1864 |
String calcName = service.serviceType.substring(0, |
170 |
|
service.serviceType.length() - 2); |
171 |
|
|
172 |
1864 |
JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage( |
173 |
|
"label.calcname_with_default_settings", new String[] |
174 |
|
{ calcName })); |
175 |
1864 |
annotservice.addActionListener(new ActionListener() |
176 |
|
{ |
177 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
178 |
0 |
@Override... |
179 |
|
public void actionPerformed(ActionEvent e) |
180 |
|
{ |
181 |
0 |
new SequenceAnnotationWSClient(service, alignFrame, null, false); |
182 |
|
} |
183 |
|
}); |
184 |
1864 |
wsmenu.add(annotservice); |
185 |
1864 |
if (hasparams) |
186 |
|
{ |
187 |
|
|
188 |
|
|
189 |
466 |
annotservice = new JMenuItem( |
190 |
|
MessageManager.getString("label.edit_settings_and_run")); |
191 |
466 |
annotservice.setToolTipText(MessageManager.getString( |
192 |
|
"label.view_and_change_parameters_before_running_calculation")); |
193 |
|
|
194 |
466 |
annotservice.addActionListener(new ActionListener() |
195 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
196 |
0 |
public void actionPerformed(ActionEvent e)... |
197 |
|
{ |
198 |
0 |
new SequenceAnnotationWSClient(service, alignFrame, null, true); |
199 |
|
} |
200 |
|
}); |
201 |
466 |
wsmenu.add(annotservice); |
202 |
466 |
List<WsParamSetI> presets = service.getParamStore().getPresets(); |
203 |
466 |
if (presets != null && presets.size() > 0) |
204 |
|
{ |
205 |
0 |
JMenu presetlist = new JMenu(MessageManager |
206 |
|
.formatMessage("label.run_with_preset", new String[] |
207 |
|
{ calcName })); |
208 |
|
|
209 |
0 |
for (final WsParamSetI preset : presets) |
210 |
|
{ |
211 |
0 |
final JMenuItem methodR = new JMenuItem(preset.getName()); |
212 |
0 |
methodR.setToolTipText(JvSwingUtils.wrapTooltip(true, "<strong>" |
213 |
0 |
+ (preset.isModifiable() |
214 |
|
? MessageManager.getString("label.user_preset") |
215 |
|
: MessageManager |
216 |
|
.getString("label.service_preset")) |
217 |
|
+ "</strong><br/>" + preset.getDescription())); |
218 |
0 |
methodR.addActionListener(new ActionListener() |
219 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
220 |
0 |
public void actionPerformed(ActionEvent e)... |
221 |
|
{ |
222 |
0 |
new SequenceAnnotationWSClient(service, alignFrame, preset, |
223 |
|
false); |
224 |
|
} |
225 |
|
|
226 |
|
}); |
227 |
0 |
presetlist.add(methodR); |
228 |
|
} |
229 |
0 |
wsmenu.add(presetlist); |
230 |
|
} |
231 |
|
|
232 |
|
} |
233 |
|
else |
234 |
|
{ |
235 |
1398 |
annotservice = new JMenuItem( |
236 |
|
MessageManager.getString("label.view_documentation")); |
237 |
1398 |
if (service.docUrl != null) |
238 |
|
{ |
239 |
1398 |
annotservice.addActionListener(new ActionListener() |
240 |
|
{ |
241 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
242 |
0 |
@Override... |
243 |
|
public void actionPerformed(ActionEvent arg0) |
244 |
|
{ |
245 |
0 |
Desktop.instance.showUrl(service.docUrl); |
246 |
|
} |
247 |
|
}); |
248 |
1398 |
annotservice.setToolTipText( |
249 |
|
JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( |
250 |
|
"label.view_service_doc_url", new String[] |
251 |
|
{ service.docUrl, service.docUrl }))); |
252 |
1398 |
wsmenu.add(annotservice); |
253 |
|
} |
254 |
|
} |
255 |
|
} |
256 |
|
} |