- moved "Add..." menu item to the bottom to avoid other items not to be drawn
[taxeditor.git] / eu.etaxonomy.taxeditor.molecular / plugin.xml
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 defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.OpenAlignmentEditorHandler"
69 id="eu.etaxonomy.taxeditor.molecular.OpenAlignmentEditor"
70 name="Open Alignment Editor">
71 </command>
72 <command
73 id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
74 name="Load Pherogram">
75 </command>
76 <command
77 id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
78 name="Toggle insert/overwrite">
79 </command>
80 <command
81 id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
82 name="Toggle left/right insertion in base call sequence">
83 </command>
84 </extension>
85 <extension
86 point="org.eclipse.ui.menus">
87 <menuContribution
88 locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
89 <toolbar
90 id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
91 <command
92 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
93 label="Toggle insert/overwrite"
94 style="push">
95 <visibleWhen
96 checkEnabled="true">
97 <with
98 variable="activePartId">
99 <equals
100 value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
101 </equals>
102 </with>
103 </visibleWhen>
104 </command>
105 <command
106 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
107 icon="icons/pherogram-insert-left-16x16.png"
108 style="push">
109 <visibleWhen
110 checkEnabled="false">
111 <with
112 variable="activePartId">
113 <equals
114 value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
115 </equals>
116 </with>
117 </visibleWhen>
118 </command>
119 </toolbar>
120 </menuContribution>
121 <menuContribution
122 allPopups="false"
123 locationURI="menu:org.eclipse.ui.main.menu">
124 <menu
125 label="View">
126 <menu
127 label="Pherogram">
128 <command
129 commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
130 style="push">
131 </command>
132 <command
133 commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
134 style="push">
135 </command>
136 <command
137 commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
138 style="push">
139 </command>
140 <visibleWhen
141 checkEnabled="true">
142 <with
143 variable="activePartId">
144 <or>
145 <equals
146 value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
147 </equals>
148 <equals
149 value="eu.etaxonomy.taxeditor.molecular.PherogramView">
150 </equals>
151 </or>
152 </with>
153 </visibleWhen>
154 </menu>
155 </menu>
156 <menu
157 label="Alignment Editor">
158 <command
159 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
160 style="push">
161 </command>
162 <command
163 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
164 id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
165 name="Cut pherogram left">
166 </command>
167 <command
168 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
169 id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
170 style="push">
171 </command>
172 <command
173 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
174 mnemonic="r"
175 style="push">
176 </command>
177 <command
178 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
179 style="push">
180 </command>
181 <command
182 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
183 style="push">
184 </command>
185 <visibleWhen
186 checkEnabled="true">
187 <with
188 variable="activePartId">
189 <equals
190 value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
191 </equals>
192 </with>
193 </visibleWhen>
194 </menu>
195 </menuContribution>
196 <menuContribution
197 locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
198 <command
199 commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
200 label="Edit Sequence"
201 style="push">
202 <visibleWhen
203 checkEnabled="true">
204 <reference
205 definitionId="isSequence">
206 </reference>
207 </visibleWhen>
208 </command>
209 <command
210 commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
211 label="Show Pherogram"
212 style="push">
213 <visibleWhen
214 checkEnabled="true">
215 <reference
216 definitionId="isSingleRead">
217 </reference>
218 </visibleWhen>
219 </command>
220 </menuContribution>
221 </extension>
222 <extension
223 point="org.eclipse.ui.handlers">
224 <handler
225 class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
226 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
227 <activeWhen>
228 <with
229 variable="activePartId">
230 <equals
231 value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
232 </equals>
233 </with>
234 </activeWhen>
235 </handler>
236 <handler
237 class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
238 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
239 </handler>
240 <handler
241 class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
242 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
243 </handler>
244 <handler
245 class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
246 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
247 </handler>
248 <handler
249 class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
250 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
251 </handler>
252 <handler
253 class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
254 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
255 </handler>
256 <handler
257 class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
258 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
259 </handler>
260 <handler
261 class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
262 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
263 </handler>
264 <handler
265 class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
266 commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
267 </handler>
268 <handler
269 class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
270 commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
271 </handler>
272 <handler
273 class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
274 commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
275 </handler>
276 </extension>
277 <extension
278 point="org.eclipse.core.expressions.definitions">
279 <definition
280 id="isSequence">
281 <with
282 variable="selection">
283 <test
284 property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
285 </test>
286 </with>
287 </definition>
288 <definition
289 id="isSingleRead">
290 <with
291 variable="selection">
292 <test
293 property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
294 </test>
295 </with>
296 </definition>
297 </extension>
298 <extension
299 point="org.eclipse.core.expressions.propertyTesters">
300 <propertyTester
301 class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
302 id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
303 namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
304 properties="isSequence,isSingleRead"
305 type="org.eclipse.jface.viewers.IStructuredSelection">
306 </propertyTester>
307 </extension>
308 <extension
309 point="org.eclipse.ui.bindings">
310 <scheme
311 description="%scheme.description"
312 id="eu.etaxonomy.taxeditor.bindings.scheme.default"
313 name="%scheme.name">
314 </scheme>
315 <key
316 commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
317 schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
318 sequence="M1+O">
319 </key>
320 </extension>
321
322 </plugin>