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">
 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>