1
|
<?xml version="1.0" encoding="UTF-8"?>
|
2
|
<?eclipse version="3.4"?>
|
3
|
<plugin>
|
4
|
<extension
|
5
|
point="org.eclipse.ui.editors">
|
6
|
<editor
|
7
|
class="eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor"
|
8
|
default="false"
|
9
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"
|
10
|
name="%editor.ALIGNMENT_EDITOR">
|
11
|
</editor>
|
12
|
</extension>
|
13
|
<extension
|
14
|
point="org.eclipse.ui.views">
|
15
|
<view
|
16
|
allowMultiple="true"
|
17
|
class="eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart"
|
18
|
id="eu.etaxonomy.taxeditor.molecular.PherogramView"
|
19
|
name="%view.PHEROGRAM_VIEW"
|
20
|
restorable="true">
|
21
|
</view>
|
22
|
</extension>
|
23
|
<extension
|
24
|
point="org.eclipse.ui.commands">
|
25
|
<command
|
26
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
|
27
|
name="%command.name.CUT_PHEROGRAM_LEFT">
|
28
|
</command>
|
29
|
<command
|
30
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
|
31
|
name="%command.name.CUT_PHEROGRAM_RIGHT">
|
32
|
</command>
|
33
|
<command
|
34
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
|
35
|
name="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS">
|
36
|
</command>
|
37
|
<command
|
38
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
|
39
|
name="%command.name.CREATE_CONSENUS_SEQUENCE">
|
40
|
</command>
|
41
|
<command
|
42
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
|
43
|
name="%command.name.UPDATE_CONSENSUS_SEQUENCE">
|
44
|
</command>
|
45
|
<command
|
46
|
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
|
47
|
name="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES">
|
48
|
</command>
|
49
|
<command
|
50
|
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
|
51
|
name="%command.name.TOGGLE_SHOW_BASE_CALL_LINES">
|
52
|
</command>
|
53
|
<command
|
54
|
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
|
55
|
name="%command.name.CHANGE_QUALITY_OUTPUT">
|
56
|
</command>
|
57
|
<command
|
58
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
59
|
name="%command.name.LOAD_PHEROGRAM">
|
60
|
</command>
|
61
|
<command
|
62
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
|
63
|
name="%command.name.TOGGLE_INSERT_OVERWRITE">
|
64
|
</command>
|
65
|
<command
|
66
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
|
67
|
name="%command.name.TOGGLE_LEFT_RIGHT_INSERTION">
|
68
|
</command>
|
69
|
</extension>
|
70
|
<extension
|
71
|
point="org.eclipse.ui.menus">
|
72
|
<menuContribution
|
73
|
locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
|
74
|
<toolbar
|
75
|
id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
|
76
|
<command
|
77
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
|
78
|
label="%command.TOGGLE_INSERT_OVERWRITE"
|
79
|
style="push">
|
80
|
<visibleWhen
|
81
|
checkEnabled="true">
|
82
|
<with
|
83
|
variable="activePartId">
|
84
|
<equals
|
85
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
86
|
</equals>
|
87
|
</with>
|
88
|
</visibleWhen>
|
89
|
</command>
|
90
|
<command
|
91
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
|
92
|
icon="icons/pherogram-insert-left-16x16.png"
|
93
|
style="push">
|
94
|
<visibleWhen
|
95
|
checkEnabled="true">
|
96
|
<with
|
97
|
variable="activePartId">
|
98
|
<equals
|
99
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
100
|
</equals>
|
101
|
</with>
|
102
|
</visibleWhen>
|
103
|
</command>
|
104
|
</toolbar>
|
105
|
</menuContribution>
|
106
|
<menuContribution
|
107
|
allPopups="false"
|
108
|
locationURI="menu:org.eclipse.ui.main.menu">
|
109
|
<menu
|
110
|
label="%menu.ALIGNMENT_EDITOR">
|
111
|
<command
|
112
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
113
|
style="push">
|
114
|
</command>
|
115
|
<command
|
116
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
|
117
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
|
118
|
name="Cut pherogram left">
|
119
|
</command>
|
120
|
<command
|
121
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
|
122
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
|
123
|
style="push">
|
124
|
</command>
|
125
|
<command
|
126
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
|
127
|
mnemonic="r"
|
128
|
style="push">
|
129
|
</command>
|
130
|
<command
|
131
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
|
132
|
style="push">
|
133
|
</command>
|
134
|
<command
|
135
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
|
136
|
style="push">
|
137
|
</command>
|
138
|
<visibleWhen
|
139
|
checkEnabled="true">
|
140
|
<with
|
141
|
variable="activePartId">
|
142
|
<equals
|
143
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
144
|
</equals>
|
145
|
</with>
|
146
|
</visibleWhen>
|
147
|
</menu>
|
148
|
<menu
|
149
|
label="%menu.label.PHEROGRAM_VIEW">
|
150
|
<command
|
151
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
|
152
|
style="push">
|
153
|
</command>
|
154
|
<command
|
155
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
|
156
|
style="push">
|
157
|
</command>
|
158
|
<command
|
159
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
|
160
|
style="push">
|
161
|
</command>
|
162
|
<visibleWhen
|
163
|
checkEnabled="true">
|
164
|
<with
|
165
|
variable="activePartId">
|
166
|
<equals
|
167
|
value="eu.etaxonomy.taxeditor.molecular.PherogramView">
|
168
|
</equals>
|
169
|
</with>
|
170
|
</visibleWhen>
|
171
|
</menu>
|
172
|
</menuContribution>
|
173
|
</extension>
|
174
|
<extension
|
175
|
point="org.eclipse.ui.handlers">
|
176
|
<handler
|
177
|
class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
|
178
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
|
179
|
<activeWhen>
|
180
|
<with
|
181
|
variable="activePartId">
|
182
|
<equals
|
183
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
184
|
</equals>
|
185
|
</with>
|
186
|
</activeWhen>
|
187
|
</handler>
|
188
|
<handler
|
189
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
|
190
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
|
191
|
</handler>
|
192
|
<handler
|
193
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
|
194
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
|
195
|
</handler>
|
196
|
<handler
|
197
|
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
|
198
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
|
199
|
</handler>
|
200
|
<handler
|
201
|
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
|
202
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
|
203
|
</handler>
|
204
|
<handler
|
205
|
class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
|
206
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
|
207
|
</handler>
|
208
|
<handler
|
209
|
class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
|
210
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
|
211
|
</handler>
|
212
|
<handler
|
213
|
class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
|
214
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
|
215
|
</handler>
|
216
|
<handler
|
217
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
|
218
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
|
219
|
</handler>
|
220
|
<handler
|
221
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
|
222
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
|
223
|
</handler>
|
224
|
<handler
|
225
|
class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
|
226
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
|
227
|
</handler>
|
228
|
<handler
|
229
|
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
|
230
|
commandId="org.eclipse.ui.edit.copy">
|
231
|
<activeWhen>
|
232
|
<with
|
233
|
variable="activePartId">
|
234
|
<equals
|
235
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
236
|
</equals>
|
237
|
</with>
|
238
|
</activeWhen>
|
239
|
</handler>
|
240
|
<handler
|
241
|
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler"
|
242
|
commandId="org.eclipse.ui.edit.cut">
|
243
|
<activeWhen>
|
244
|
<with
|
245
|
variable="activePartId">
|
246
|
<equals
|
247
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
248
|
</equals>
|
249
|
</with>
|
250
|
</activeWhen>
|
251
|
</handler>
|
252
|
<handler
|
253
|
class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"
|
254
|
commandId="org.eclipse.ui.edit.paste">
|
255
|
<activeWhen>
|
256
|
<with
|
257
|
variable="activePartId">
|
258
|
<equals
|
259
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
260
|
</equals>
|
261
|
</with>
|
262
|
</activeWhen>
|
263
|
</handler>
|
264
|
</extension>
|
265
|
<extension
|
266
|
point="org.eclipse.ui.bindings">
|
267
|
<scheme
|
268
|
description="%scheme.description"
|
269
|
id="eu.etaxonomy.taxeditor.bindings.scheme.default"
|
270
|
name="%scheme.name">
|
271
|
</scheme>
|
272
|
<key
|
273
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
274
|
schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
|
275
|
sequence="M1+O">
|
276
|
</key>
|
277
|
</extension>
|
278
|
<extension
|
279
|
id="id1"
|
280
|
point="org.eclipse.e4.workbench.model">
|
281
|
<fragment
|
282
|
apply="always"
|
283
|
uri="fragment.e4xmi">
|
284
|
</fragment>
|
285
|
</extension>
|
286
|
|
287
|
</plugin>
|