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                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.core.expressions.definitions">
 266          <definition
 267                id="isSequence">
 268             <with
 269                   variable="selection">
 270                <test
 271                      property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
 272                </test>
 273             </with>
 274          </definition>
 275          <definition
 276                id="isSingleRead">
 277             <with
 278                   variable="selection">
 279                <test
 280                      property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
 281                </test>
 282             </with>
 283          </definition>
 284       </extension>
 285       <extension
 286             point="org.eclipse.core.expressions.propertyTesters">
 287          <propertyTester
 288                class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
 289                id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
 290                namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
 291                properties="isSequence,isSingleRead"
 292                type="org.eclipse.jface.viewers.IStructuredSelection">
 293          </propertyTester>
 294       </extension>
 295       <extension
 296             point="org.eclipse.ui.bindings">
 297          <scheme
 298                description="%scheme.description"
 299                id="eu.etaxonomy.taxeditor.bindings.scheme.default"
 300                name="%scheme.name">
 301          </scheme>
 302          <key
 303                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
 304                schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
 305                sequence="M1+O">
 306          </key>
 307       </extension>
 308
 309 </plugin>