|
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="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="PherogramView"
|
|
20
|
restorable="true">
|
|
21
|
</view>
|
|
22
|
</extension>
|
|
23
|
<extension
|
|
24
|
point="org.eclipse.ui.commands">
|
|
25
|
<command
|
|
26
|
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler"
|
|
27
|
id="eu.etaxonomy.taxeditor.molecular.editSequence"
|
|
28
|
name="Edit Sequence">
|
|
29
|
</command>
|
|
30
|
<command
|
|
31
|
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
|
|
32
|
id="eu.etaxonomy.taxeditor.molecular.showPherogram"
|
|
33
|
name="Show Pherogram">
|
|
34
|
</command>
|
|
35
|
<command
|
|
36
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
|
|
37
|
name="Cut pherogram left">
|
|
38
|
</command>
|
|
39
|
<command
|
|
40
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
|
|
41
|
name="Cut pherogram right">
|
|
42
|
</command>
|
|
43
|
<command
|
|
44
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
|
|
45
|
name="Reverse complement selected rows">
|
|
46
|
</command>
|
|
47
|
<command
|
|
48
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
|
|
49
|
name="(Re)create consensus sequence">
|
|
50
|
</command>
|
|
51
|
<command
|
|
52
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
|
|
53
|
name="Update consensus sequence">
|
|
54
|
</command>
|
|
55
|
<command
|
|
56
|
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
|
|
57
|
name="Toggle show probability values">
|
|
58
|
</command>
|
|
59
|
<command
|
|
60
|
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
|
|
61
|
name="Toggle show base call lines">
|
|
62
|
</command>
|
|
63
|
<command
|
|
64
|
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
|
|
65
|
name="Change quality output">
|
|
66
|
</command>
|
|
67
|
<command
|
|
68
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
|
69
|
name="Load Pherogram">
|
|
70
|
</command>
|
|
71
|
<command
|
|
72
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
|
|
73
|
name="Toggle insert/overwrite">
|
|
74
|
</command>
|
|
75
|
<command
|
|
76
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
|
|
77
|
name="Toggle left/right insertion in base call sequence">
|
|
78
|
</command>
|
|
79
|
</extension>
|
|
80
|
<extension
|
|
81
|
point="org.eclipse.ui.menus">
|
|
82
|
<menuContribution
|
|
83
|
locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
|
|
84
|
<toolbar
|
|
85
|
id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
|
|
86
|
<command
|
|
87
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
|
|
88
|
label="Toggle insert/overwrite"
|
|
89
|
style="push">
|
|
90
|
<visibleWhen
|
|
91
|
checkEnabled="true">
|
|
92
|
<with
|
|
93
|
variable="activePartId">
|
|
94
|
<equals
|
|
95
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
|
96
|
</equals>
|
|
97
|
</with>
|
|
98
|
</visibleWhen>
|
|
99
|
</command>
|
|
100
|
<command
|
|
101
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
|
|
102
|
icon="icons/pherogram-insert-left-16x16.png"
|
|
103
|
style="push">
|
|
104
|
<visibleWhen
|
|
105
|
checkEnabled="true">
|
|
106
|
<with
|
|
107
|
variable="activePartId">
|
|
108
|
<equals
|
|
109
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
|
110
|
</equals>
|
|
111
|
</with>
|
|
112
|
</visibleWhen>
|
|
113
|
</command>
|
|
114
|
</toolbar>
|
|
115
|
</menuContribution>
|
|
116
|
<menuContribution
|
|
117
|
allPopups="false"
|
|
118
|
locationURI="menu:org.eclipse.ui.main.menu">
|
|
119
|
<menu
|
|
120
|
label="Alignment Editor">
|
|
121
|
<command
|
|
122
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
|
123
|
style="push">
|
|
124
|
</command>
|
|
125
|
<command
|
|
126
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
|
|
127
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
|
|
128
|
name="Cut pherogram left">
|
|
129
|
</command>
|
|
130
|
<command
|
|
131
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
|
|
132
|
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
|
|
133
|
style="push">
|
|
134
|
</command>
|
|
135
|
<command
|
|
136
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
|
|
137
|
mnemonic="r"
|
|
138
|
style="push">
|
|
139
|
</command>
|
|
140
|
<command
|
|
141
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
|
|
142
|
style="push">
|
|
143
|
</command>
|
|
144
|
<command
|
|
145
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
|
|
146
|
style="push">
|
|
147
|
</command>
|
|
148
|
<visibleWhen
|
|
149
|
checkEnabled="true">
|
|
150
|
<with
|
|
151
|
variable="activePartId">
|
|
152
|
<equals
|
|
153
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
|
154
|
</equals>
|
|
155
|
</with>
|
|
156
|
</visibleWhen>
|
|
157
|
</menu>
|
|
158
|
<menu
|
|
159
|
label="Pherogram View">
|
|
160
|
<command
|
|
161
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
|
|
162
|
style="push">
|
|
163
|
</command>
|
|
164
|
<command
|
|
165
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
|
|
166
|
style="push">
|
|
167
|
</command>
|
|
168
|
<command
|
|
169
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
|
|
170
|
style="push">
|
|
171
|
</command>
|
|
172
|
<visibleWhen
|
|
173
|
checkEnabled="true">
|
|
174
|
<with
|
|
175
|
variable="activePartId">
|
|
176
|
<equals
|
|
177
|
value="eu.etaxonomy.taxeditor.molecular.PherogramView">
|
|
178
|
</equals>
|
|
179
|
</with>
|
|
180
|
</visibleWhen>
|
|
181
|
</menu>
|
|
182
|
</menuContribution>
|
|
183
|
<menuContribution
|
|
184
|
locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
|
|
185
|
<command
|
|
186
|
commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
|
|
187
|
label="Edit Sequence"
|
|
188
|
style="push">
|
|
189
|
<visibleWhen
|
|
190
|
checkEnabled="true">
|
|
191
|
<reference
|
|
192
|
definitionId="isSequence">
|
|
193
|
</reference>
|
|
194
|
</visibleWhen>
|
|
195
|
</command>
|
|
196
|
<command
|
|
197
|
commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
|
|
198
|
label="Show Pherogram"
|
|
199
|
style="push">
|
|
200
|
<visibleWhen
|
|
201
|
checkEnabled="true">
|
|
202
|
<reference
|
|
203
|
definitionId="isSingleRead">
|
|
204
|
</reference>
|
|
205
|
</visibleWhen>
|
|
206
|
</command>
|
|
207
|
</menuContribution>
|
|
208
|
</extension>
|
|
209
|
<extension
|
|
210
|
point="org.eclipse.ui.handlers">
|
|
211
|
<handler
|
|
212
|
class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
|
|
213
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
|
|
214
|
<activeWhen>
|
|
215
|
<with
|
|
216
|
variable="activePartId">
|
|
217
|
<equals
|
|
218
|
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
|
|
219
|
</equals>
|
|
220
|
</with>
|
|
221
|
</activeWhen>
|
|
222
|
</handler>
|
|
223
|
<handler
|
|
224
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
|
|
225
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
|
|
226
|
</handler>
|
|
227
|
<handler
|
|
228
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
|
|
229
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
|
|
230
|
</handler>
|
|
231
|
<handler
|
|
232
|
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
|
|
233
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
|
|
234
|
</handler>
|
|
235
|
<handler
|
|
236
|
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
|
|
237
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
|
|
238
|
</handler>
|
|
239
|
<handler
|
|
240
|
class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
|
|
241
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
|
|
242
|
</handler>
|
|
243
|
<handler
|
|
244
|
class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
|
|
245
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
|
|
246
|
</handler>
|
|
247
|
<handler
|
|
248
|
class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
|
|
249
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
|
|
250
|
</handler>
|
|
251
|
<handler
|
|
252
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
|
|
253
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
|
|
254
|
</handler>
|
|
255
|
<handler
|
|
256
|
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
|
|
257
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
|
|
258
|
</handler>
|
|
259
|
<handler
|
|
260
|
class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
|
|
261
|
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
|
|
262
|
</handler>
|
|
263
|
</extension>
|
|
264
|
<extension
|
|
265
|
point="org.eclipse.ui.bindings">
|
|
266
|
<scheme
|
|
267
|
description="%scheme.description"
|
|
268
|
id="eu.etaxonomy.taxeditor.bindings.scheme.default"
|
|
269
|
name="%scheme.name">
|
|
270
|
</scheme>
|
|
271
|
<key
|
|
272
|
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
|
|
273
|
schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
|
|
274
|
sequence="M1+O">
|
|
275
|
</key>
|
|
276
|
</extension>
|
|
277
|
|
|
278
|
</plugin>
|