merge-update from trunk

diff --combined .gitattributes
index 8022fc5c55944043c09384f2ed723cd2036a2825,03a3a308100b889127190287cd83520083fb5dc7..52d0b6230dc9d1703b5fb68943c2edd563d9a6e8
--- 1/.gitattributes
--- 2/.gitattributes
+++ b/.gitattributes
@@@ -357,12 -357,8 +357,13 @@@ eu.etaxonomy.taxeditor.editor/icons/der
  eu.etaxonomy.taxeditor.editor/icons/edit_16x16.gif -text
  eu.etaxonomy.taxeditor.editor/icons/emblem-photos.png -text
  eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
+ eu.etaxonomy.taxeditor.editor/icons/link_obj.gif -text
  eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text
  eu.etaxonomy.taxeditor.editor/p2.inf -text
  eu.etaxonomy.taxeditor.editor/plugin.xml -text
  eu.etaxonomy.taxeditor.editor/pom.xml -text
@@@ -387,8 -383,6 +388,8 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditor.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenDerivateViewHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenParentHandler.java -text
@@@ -421,14 -415,6 +422,14 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/CreateNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramView.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ToggleInsertOverwriteButton.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ToggleLeftRightInsertionButton.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text
@@@ -552,7 -538,9 +553,9 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/DerivateViewContextMenu.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/SingleReadSequenceContextMenu.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/handler/DeleteDerivateHandler.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/handler/OpenDerivateEditorForTaxonHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/operation/DeleteDerivateOperation.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/operation/MoveDerivateOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementDragListener.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementDropAdapter.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementTransfer.java -text
@@@ -567,6 -555,7 +570,7 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/handler/DynamicFeatureMenu.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/handler/MoveDescriptionElementsHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/handler/MoveDescriptionToOtherTaxonHandler.java -text
+ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/handler/ToggleShowOnlyIndividualAssociationsHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/operation/AddDerivedUnitFacadeMediaOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/operation/CreateDescriptionElementOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/operation/CreateSpecimenDescriptionOperation.java -text
@@@ -600,10 -589,7 +604,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateTaxonUseOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseRecordOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseSummaryOperation.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text
@@@ -1246,6 -1232,7 +1250,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/AbstractExcelImportWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/AbstractExportWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/AbstractImportWizard.java -text
+ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/CsvExportWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/DarwinCoreArchiveExportWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/EndnoteImportWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/wizard/ExcelNormalExplicitTaxaImportWizard.java -text
@@@ -1305,7 -1292,6 +1310,6 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AmplificationCloningWizardPage.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AmplificationGelPhotoWizardPage.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AmplificationGeneralWizardPage.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AmplificationPrimerWizardPage.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/ExternalReferenceServiceWizardPage.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewAmplificationWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewClassificationWizard.java -text
@@@ -1681,12 -1667,8 +1685,8 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SingleReadPherogramCollectionDetailSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/TissueSampleGeneralDetailElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/TissueSampleGeneralDetailSection.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/LivingPlantPhotoGeneralDetailElement.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/LivingPlantPhotoGeneralDetailSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/MediaSpecimenGeneralDetailElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/MediaSpecimenGeneralDetailSection.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/SpecimenScanGeneralDetailElement.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/SpecimenScanGeneralDetailSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/reference/NomenclaturalReferenceDetailElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/reference/NomenclaturalReferenceDetailSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/reference/ReferenceDetailElement.java -text

diff --combined eu.etaxonomy.taxeditor.editor/plugin.xml
index c139ebbe59d5a5d44e011397a7b226c5555780b1,e0dc27452a6e82856dd48cd39980258a16e69300..1fdf2b517425979d001b956dc22b96ef267e501e
--- 1/eu.etaxonomy.taxeditor.editor/plugin.xml
--- 2/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@@ -83,15 -83,8 +83,15 @@@
              id="eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditor"
              name="%editor.name.8">
        </editor>
 +      <editor
 +            class="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"
 +            default="false"
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"
 +            name="Alignment Editor">
 +      </editor>
     </extension>
        <extension
 +            id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
              point="org.eclipse.ui.views">
           <view
                 allowMultiple="false"
@@@ -151,13 -144,6 +151,13 @@@
                 id="eu.etaxonomy.taxeditor.editor.view.dataimport.GbifResponseImportView"
                 name="%view.name.5">
           </view>
 +         <view
 +               allowMultiple="true"
 +               class="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
 +               id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
 +               name="PherogramView"
 +               restorable="true">
 +         </view>
        </extension>
     <extension
           point="org.eclipse.ui.elementFactories">
@@@ -257,11 -243,6 +257,11 @@@
                 </reference>
              </visibleWhen>
           </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +               label="Alignment Editor"
 +               style="push">
 +         </command>
        </menuContribution>
        <menuContribution
              locationURI="menu:org.eclipse.ui.main.menu.navigate">
@@@ -842,57 -823,29 +842,81 @@@
              </visibleWhen>
           </command>
        </menuContribution>
 +      <menuContribution
 +            allPopups="false"
 +            locationURI="menu:org.eclipse.ui.main.menu">
 +         <menu
 +               label="Alignment Editor">
 +            <command
 +                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
 +                  label="Load Pherogram"
 +                  style="push">
 +            </command>
 +            <visibleWhen
 +                  checkEnabled="true">
 +               <with
 +                     variable="activePartId">
 +                  <equals
 +                        value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                  </equals>
 +               </with>
 +            </visibleWhen>
 +         </menu>
 +      </menuContribution>
 +      <menuContribution
 +            locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
 +         <toolbar
 +               id="eu.etaxonomy.taxeditor.editor.alignmentToolbar">
 +            <control
 +                  class="eu.etaxonomy.taxeditor.editor.molecular.ToggleLeftRightInsertionButton">
 +               <visibleWhen
 +                     checkEnabled="true">
 +                  <with
 +                        variable="activePartId">
 +                     <equals
 +                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                     </equals>
 +                  </with>
 +               </visibleWhen>
 +            </control>
 +            <control
 +                  class="eu.etaxonomy.taxeditor.editor.molecular.ToggleInsertOverwriteButton">
 +               <visibleWhen
 +                     checkEnabled="true">
 +                  <with
 +                        variable="activePartId">
 +                     <equals
 +                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                     </equals>
 +                  </with>
 +               </visibleWhen>
 +            </control>
 +         </toolbar>
 +      </menuContribution>
++      
+       <menuContribution
+             allPopups="false"
+             locationURI="toolbar:eu.etaxonomy.taxeditor.editor.view.descriptive">
+          <command
+                commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations"
+                icon="icons/link_obj.gif"
+                style="toggle"
+                tooltip="Show Only Individuals Associations">
+          </command>
+       </menuContribution>
+       <menuContribution
+             allPopups="false"
+             locationURI="popup:eu.etaxonomy.taxeditor.navigation.navigatorpopup?after=taxeditor-navigation.separator2">
+          <command
+                commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView"
+                label="Open Associated Derivates"
+                style="push">
+          </command>
+          <separator
+                name="eu.etaxonomy.taxeditor.editor.separator1"
+                visible="true">
+          </separator>
+       </menuContribution>
     </extension>
     <extension
           point="org.eclipse.ui.handlers">
@@@ -984,18 -937,6 +1008,18 @@@
        <handler
              class="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
              commandId="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler">
 +      </handler>
 +            <handler
 +            class="eu.etaxonomy.taxeditor.editor.handler.LoadPherogramHandler"
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram">
 +         <activeWhen>
 +            <with
 +                  variable="activePartId">
 +               <equals
 +                     value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +               </equals>
 +            </with>
 +         </activeWhen>
        </handler>
        <handler
              class="eu.etaxonomy.taxeditor.editor.view.derivate.handler.DeleteDerivateHandler"
@@@ -1009,6 -950,22 +1033,22 @@@
              </with>
           </activeWhen>
        </handler>
+       <handler
+             class="eu.etaxonomy.taxeditor.editor.view.derivate.handler.OpenDerivateEditorForTaxonHandler"
+             commandId="eu.etaxonomy.taxeditor.editor.handler.openDerivateView">
+          <activeWhen>
+             <with
+                   variable="activePartId">
+                <equals
+                      value="eu.etaxonomy.taxeditor.navigation.navigator">
+                </equals>
+             </with>
+          </activeWhen>
+       </handler>
+       <handler
+             class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.ToggleShowOnlyIndividualAssociationsHandler"
+             commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations">
+       </handler>
     </extension>
     <extension
           name="%extension.name"
@@@ -1281,27 -1238,17 +1321,31 @@@
               defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
               id="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistViewHandler"
               name="%command.name.38">
 -       </command>
 +      </command>
        <command
              categoryId="eu.etaxonomy.taxeditor.editor.new.category"
              defaultHandler="eu.etaxonomy.taxeditor.view.datasource.handler.CreateDataSourceHandler"
              id="eu.etaxonomy.taxeditor.editor.command.new.datasource"
              name="%command.name.39">
        </command>
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +            id="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +            name="Open Alignment Editor">
 +      </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.addA"
 +            name="Add A">
 +      </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
 +            name="Load Pherogram">
 +      </command>
+       <command
+             id="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations"
+             name="Show Only Individual Associations">
+       </command>
 +
     </extension>
     <extension
           point="org.eclipse.core.expressions.definitions">
@@@ -1490,11 -1437,6 +1534,11 @@@
              id="eu.etaxonomy.taxeditor.bindings.scheme.default"
              name="%scheme.name">
        </scheme>
 +      <key
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
 +            schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
 +            sequence="M1+O">
 +      </key>
     </extension>
      <extension
           point="org.eclipse.ui.importWizards">