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       </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="%command.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="%menu.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="%menu.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.derivative.reuseSingleReadMenuItem">
 185             <separator
 186                   name="eu.etaxonomy.taxeditor.molecular.separator5"
 187                   visible="true">
 188             </separator>
 189             <command
 190                   commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
 191                   label="%command.label.EDIT_SEQUENCE"
 192                   style="push">
 193                <visibleWhen
 194                      checkEnabled="true">
 195                   <reference
 196                         definitionId="isSequence">
 197                   </reference>
 198                </visibleWhen>
 199             </command>
 200             <command
 201                   commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
 202                   label="%command.label.SHOW_PHEROGRAM"
 203                   style="push">
 204                <visibleWhen
 205                      checkEnabled="true">
 206                   <reference
 207                         definitionId="isSingleRead">
 208                   </reference>
 209                </visibleWhen>
 210             </command>
 211          </menuContribution>
 212       </extension>
 213       <extension
 214             point="org.eclipse.ui.handlers">
 215          <handler
 216                class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
 217                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
 218             <activeWhen>
 219                <with
 220                      variable="activePartId">
 221                   <equals
 222                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 223                   </equals>
 224                </with>
 225             </activeWhen>
 226          </handler>
 227          <handler
 228                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
 229                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
 230          </handler>
 231          <handler
 232                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
 233                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
 234          </handler>
 235          <handler
 236                class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
 237                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
 238          </handler>
 239          <handler
 240                class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
 241                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
 242          </handler>
 243          <handler
 244                class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
 245                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
 246          </handler>
 247          <handler
 248                class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
 249                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
 250          </handler>
 251          <handler
 252                class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
 253                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
 254          </handler>
 255          <handler
 256                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
 257                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
 258          </handler>
 259          <handler
 260                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
 261                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
 262          </handler>
 263          <handler
 264                class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
 265                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
 266          </handler>
 267          <handler
 268                class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
 269                commandId="org.eclipse.ui.edit.copy">
 270             <activeWhen>
 271                <with
 272                      variable="activePartId">
 273                   <equals
 274                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 275                   </equals>
 276                </with>
 277             </activeWhen>
 278          </handler>
 279          <handler
 280                class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler"
 281                commandId="org.eclipse.ui.edit.cut">
 282             <activeWhen>
 283                <with
 284                      variable="activePartId">
 285                   <equals
 286                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 287                   </equals>
 288                </with>
 289             </activeWhen>
 290          </handler>
 291          <handler
 292                class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"
 293                commandId="org.eclipse.ui.edit.paste">
 294             <activeWhen>
 295                <with
 296                      variable="activePartId">
 297                   <equals
 298                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 299                   </equals>
 300                </with>
 301             </activeWhen>
 302          </handler>
 303       </extension>
 304       <extension
 305             point="org.eclipse.ui.bindings">
 306          <scheme
 307                description="%scheme.description"
 308                id="eu.etaxonomy.taxeditor.bindings.scheme.default"
 309                name="%scheme.name">
 310          </scheme>
 311          <key
 312                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
 313                schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
 314                sequence="M1+O">
 315          </key>
 316       </extension>
 317
 318 </plugin>