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="%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                defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler"
  27                id="eu.etaxonomy.taxeditor.molecular.editSequence"
  28                name="%command.EDIT_SEQUENCE">
  29          </command>
  30          <command
  31                defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
  32                id="eu.etaxonomy.taxeditor.molecular.showPherogram"
  33                name="%command.name.SHOW_PHEROGRAM">
  34          </command>
  35          <command
  36                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
  37                name="%command.name.CUT_PHEROGRAM_LEFT">
  38          </command>
  39          <command
  40                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
  41                name="%command.name.CUT_PHEROGRAM_RIGHT">
  42          </command>
  43          <command
  44                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
  45                name="%command.name.REVERSE_COMPLEMENT_SELECTED_ROWS">
  46          </command>
  47          <command
  48                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
  49                name="%command.name.CREATE_CONSENUS_SEQUENCE">
  50          </command>
  51          <command
  52                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
  53                name="%command.name.UPDATE_CONSENSUS_SEQUENCE">
  54          </command>
  55          <command
  56                id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
  57                name="%command.name.TOGGLE_SHOW_PROBABILITY_VALUES">
  58          </command>
  59          <command
  60                id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
  61                name="%command.name.TOGGLE_SHOW_BASE_CALL_LINES">
  62          </command>
  63          <command
  64                id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
  65                name="%command.name.CHANGE_QUALITY_OUTPUT">
  66          </command>
  67          <command
  68                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
  69                name="%command.name.LOAD_PHEROGRAM">
  70          </command>
  71          <command
  72                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
  73                name="%command.name.TOGGLE_INSERT_OVERWRITE">
  74          </command>
  75          <command
  76                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
  77                name="%command.name.TOGGLE_LEFT_RIGHT_INSERTION">
  78          </command>
  79          <command
  80                defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler"
  81                id="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"
  82                name="%command.name.EXPORT_SEQUENCE_TO_FILE">
  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="%command.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="true">
 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="%menu.ALIGNMENT_EDITOR">
 126                <command
 127                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
 128                      style="push">
 129                </command>
 130                <command
 131                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
 132                      id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
 133                      name="Cut pherogram left">
 134                </command>
 135                <command
 136                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
 137                      id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
 138                      style="push">
 139                </command>
 140                <command
 141                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
 142                      mnemonic="r"
 143                      style="push">
 144                </command>
 145                <command
 146                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
 147                      style="push">
 148                </command>
 149                <command
 150                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
 151                      style="push">
 152                </command>
 153                <visibleWhen
 154                      checkEnabled="true">
 155                   <with
 156                         variable="activePartId">
 157                      <equals
 158                            value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 159                      </equals>
 160                   </with>
 161                </visibleWhen>
 162             </menu>
 163             <menu
 164                   label="%menu.label.PHEROGRAM_VIEW">
 165                <command
 166                      commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
 167                      style="push">
 168                </command>
 169                <command
 170                      commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
 171                      style="push">
 172                </command>
 173                <command
 174                      commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
 175                      style="push">
 176                </command>
 177                <visibleWhen
 178                      checkEnabled="true">
 179                   <with
 180                         variable="activePartId">
 181                      <equals
 182                            value="eu.etaxonomy.taxeditor.molecular.PherogramView">
 183                      </equals>
 184                   </with>
 185                </visibleWhen>
 186             </menu>
 187          </menuContribution>
 188          <menuContribution
 189                locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.derivative.reuseSingleReadMenuItem">
 190             <separator
 191                   name="eu.etaxonomy.taxeditor.molecular.separator5"
 192                   visible="true">
 193             </separator>
 194             <command
 195                   commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
 196                   label="%command.label.EDIT_SEQUENCE"
 197                   style="push">
 198                <visibleWhen
 199                      checkEnabled="true">
 200                   <reference
 201                         definitionId="isSequence">
 202                   </reference>
 203                </visibleWhen>
 204             </command>
 205             <command
 206                   commandId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"
 207                   label="%command.label.EXPORT_SEQUENCE_TO_FILE"
 208                   style="push">
 209                <visibleWhen
 210                      checkEnabled="true">
 211                   <reference
 212                         definitionId="isSequence">
 213                   </reference>
 214                </visibleWhen>
 215             </command>
 216             <command
 217                   commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
 218                   label="%command.label.SHOW_PHEROGRAM"
 219                   style="push">
 220                <visibleWhen
 221                      checkEnabled="true">
 222                   <reference
 223                         definitionId="isSingleRead">
 224                   </reference>
 225                </visibleWhen>
 226             </command>
 227          </menuContribution>
 228       </extension>
 229       <extension
 230             point="org.eclipse.ui.handlers">
 231          <handler
 232                class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
 233                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
 234             <activeWhen>
 235                <with
 236                      variable="activePartId">
 237                   <equals
 238                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 239                   </equals>
 240                </with>
 241             </activeWhen>
 242          </handler>
 243          <handler
 244                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
 245                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
 246          </handler>
 247          <handler
 248                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
 249                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
 250          </handler>
 251          <handler
 252                class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
 253                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
 254          </handler>
 255          <handler
 256                class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
 257                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
 258          </handler>
 259          <handler
 260                class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
 261                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
 262          </handler>
 263          <handler
 264                class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
 265                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
 266          </handler>
 267          <handler
 268                class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
 269                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
 270          </handler>
 271          <handler
 272                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
 273                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
 274          </handler>
 275          <handler
 276                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
 277                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
 278          </handler>
 279          <handler
 280                class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
 281                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
 282          </handler>
 283          <handler
 284                class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
 285                commandId="org.eclipse.ui.edit.copy">
 286             <activeWhen>
 287                <with
 288                      variable="activePartId">
 289                   <equals
 290                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 291                   </equals>
 292                </with>
 293             </activeWhen>
 294          </handler>
 295          <handler
 296                class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler"
 297                commandId="org.eclipse.ui.edit.cut">
 298             <activeWhen>
 299                <with
 300                      variable="activePartId">
 301                   <equals
 302                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 303                   </equals>
 304                </with>
 305             </activeWhen>
 306          </handler>
 307          <handler
 308                class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"
 309                commandId="org.eclipse.ui.edit.paste">
 310             <activeWhen>
 311                <with
 312                      variable="activePartId">
 313                   <equals
 314                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 315                   </equals>
 316                </with>
 317             </activeWhen>
 318          </handler>
 319       </extension>
 320       <extension
 321             point="org.eclipse.ui.bindings">
 322          <scheme
 323                description="%scheme.description"
 324                id="eu.etaxonomy.taxeditor.bindings.scheme.default"
 325                name="%scheme.name">
 326          </scheme>
 327          <key
 328                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
 329                schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
 330                sequence="M1+O">
 331          </key>
 332       </extension>
 333
 334 </plugin>