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="View">
 121                <menu
 122                      label="Pherogram">
 123                   <command
 124                         commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
 125                         style="push">
 126                   </command>
 127                   <command
 128                         commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
 129                         style="push">
 130                   </command>
 131                   <command
 132                         commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
 133                         style="push">
 134                   </command>
 135                   <visibleWhen
 136                         checkEnabled="true">
 137                      <with
 138                            variable="activePartId">
 139                         <or>
 140                            <equals
 141                                  value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 142                            </equals>
 143                            <equals
 144                                  value="eu.etaxonomy.taxeditor.molecular.PherogramView">
 145                            </equals>
 146                         </or>
 147                      </with>
 148                   </visibleWhen>
 149                </menu>
 150             </menu>
 151             <menu
 152                   label="Alignment Editor">
 153                <command
 154                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
 155                      style="push">
 156                </command>
 157                <command
 158                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
 159                      id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
 160                      name="Cut pherogram left">
 161                </command>
 162                <command
 163                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
 164                      id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
 165                      style="push">
 166                </command>
 167                <command
 168                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
 169                      mnemonic="r"
 170                      style="push">
 171                </command>
 172                <command
 173                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
 174                      style="push">
 175                </command>
 176                <command
 177                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
 178                      style="push">
 179                </command>
 180                <!--visibleWhen
 181                      checkEnabled="true">
 182                   <with
 183                         variable="activePartId">
 184                      <equals
 185                            value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 186                      </equals>
 187                   </with>
 188                </visibleWhen-->
 189             </menu>
 190          </menuContribution>
 191          <menuContribution
 192                locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
 193             <command
 194                   commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
 195                   label="Edit Sequence"
 196                   style="push">
 197                <visibleWhen
 198                      checkEnabled="true">
 199                   <reference
 200                         definitionId="isSequence">
 201                   </reference>
 202                </visibleWhen>
 203             </command>
 204             <command
 205                   commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
 206                   label="Show Pherogram"
 207                   style="push">
 208                <visibleWhen
 209                      checkEnabled="true">
 210                   <reference
 211                         definitionId="isSingleRead">
 212                   </reference>
 213                </visibleWhen>
 214             </command>
 215          </menuContribution>
 216       </extension>
 217       <extension
 218             point="org.eclipse.ui.handlers">
 219          <handler
 220                class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
 221                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
 222             <activeWhen>
 223                <with
 224                      variable="activePartId">
 225                   <equals
 226                         value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
 227                   </equals>
 228                </with>
 229             </activeWhen>
 230          </handler>
 231          <handler
 232                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
 233                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
 234          </handler>
 235          <handler
 236                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
 237                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
 238          </handler>
 239          <handler
 240                class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
 241                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
 242          </handler>
 243          <handler
 244                class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
 245                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
 246          </handler>
 247          <handler
 248                class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
 249                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
 250          </handler>
 251          <handler
 252                class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
 253                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
 254          </handler>
 255          <handler
 256                class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
 257                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
 258          </handler>
 259          <handler
 260                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
 261                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
 262          </handler>
 263          <handler
 264                class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
 265                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
 266          </handler>
 267          <handler
 268                class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
 269                commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
 270          </handler>
 271       </extension>
 272       <extension
 273             point="org.eclipse.core.expressions.definitions">
 274          <definition
 275                id="isSequence">
 276             <with
 277                   variable="selection">
 278                <test
 279                      property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
 280                </test>
 281             </with>
 282          </definition>
 283          <definition
 284                id="isSingleRead">
 285             <with
 286                   variable="selection">
 287                <test
 288                      property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
 289                </test>
 290             </with>
 291          </definition>
 292       </extension>
 293       <extension
 294             point="org.eclipse.core.expressions.propertyTesters">
 295          <propertyTester
 296                class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
 297                id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
 298                namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
 299                properties="isSequence,isSingleRead"
 300                type="org.eclipse.jface.viewers.IStructuredSelection">
 301          </propertyTester>
 302       </extension>
 303       <extension
 304             point="org.eclipse.ui.bindings">
 305          <scheme
 306                description="%scheme.description"
 307                id="eu.etaxonomy.taxeditor.bindings.scheme.default"
 308                name="%scheme.name">
 309          </scheme>
 310          <key
 311                commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
 312                schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
 313                sequence="M1+O">
 314          </key>
 315       </extension>
 316
 317 </plugin>