merge-update from trunk

diff --combined eu.etaxonomy.taxeditor.cdmlib/.classpath
index 41a7f1b3198fd75534a726f2f07c06b691d9056c,2cc9dede15dde187a6a1e10e15c6b450c1fc5311..e84b6d824a49f00a18bb2db11832690054f0988f
--- 1/eu.etaxonomy.taxeditor.cdmlib/.classpath
--- 2/eu.etaxonomy.taxeditor.cdmlib/.classpath
+++ b/eu.etaxonomy.taxeditor.cdmlib/.classpath
@@@ -194,22 -194,22 +194,22 @@@
        <classpathentry exported="true" kind="lib" path="lib/spring-security-remoting-3.1.3.RELEASE.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/jena-core-2.11.2.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/jena-iri-1.0.2.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.4.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.4.1-SNAPSHOT.jar" sourcepath="lib/cdmlib-model-3.4.1-SNAPSHOT-sources.jar"/>
 -      <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.4.1-SNAPSHOT.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.4.1-SNAPSHOT-sources.jar"/>
--      <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.4.1-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.5.0-SNAPSHOT.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.5.0-SNAPSHOT-sources.jar"/>
++      <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.5.0-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/poi-3.10-FINAL.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/poi-ooxml-3.10-FINAL.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/xmlbeans-2.3.0.jar"/>

diff --combined eu.etaxonomy.taxeditor.editor/plugin.xml
index 8a8db7b123c02af2a53921708cb07ad606358933,83b8d25e3ccb2ddc25bbb73242bd2ae515a7cfd4..5775ab4f5454f4e3388492e3e735ad6e8a2cb88c
--- 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"
@@@ -159,15 -152,9 +159,15 @@@
                 id="eu.etaxonomy.taxeditor.editor.view.validation.problems"
                 name="%view.name.6">
           </view>
 +         <view
 +               allowMultiple="true"
 +               class="eu.etaxonomy.taxeditor.editor.molecular.PherogramViewPart"
 +               id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
 +               name="PherogramView"
 +               restorable="true">
 +         </view>
        </extension>
 -      
 -      <!-- VALIDATION RELATED STUFF -->
 +      <!-- VALIDATION RELATED STUFF -->
        <extension point="org.eclipse.core.resources.markers" name="Validation Error" id="eu.etaxonomy.taxeditor.markers.validationerror">
                <super type="org.eclipse.core.resources.problemmarker"/>
                <attribute name="databaseId"/>
@@@ -239,7 -226,8 +239,7 @@@
                        name="%marker.field.7">
                </markerField>
        </extension>
 -      
 -  <extension
 +   <extension
           point="org.eclipse.ui.elementFactories">
        <factory
              class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
@@@ -337,11 -325,6 +337,11 @@@
                 </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">
@@@ -717,10 -700,6 +717,6 @@@
        </menuContribution>
        <menuContribution
              locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView">
-          <dynamic
-                class="eu.etaxonomy.taxeditor.editor.view.derivate.contextMenu.DerivateViewContextMenu"
-                id="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
-          </dynamic>
           <command
                 commandId="org.eclipse.ui.edit.delete"
                 label="Delete"
@@@ -737,28 -716,10 +733,32 @@@
                 label="Delete (with children)"
                 style="push">
           </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.editSequence"
 +               label="Edit Sequence"
 +               style="push">
 +            <visibleWhen
 +                  checkEnabled="true">
 +               <reference
 +                     definitionId="isSequence">
 +               </reference>
 +            </visibleWhen>
 +         </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.showPherogram"
 +               label="Show Pherogram"
 +               style="push">
 +            <visibleWhen
 +                  checkEnabled="true">
 +               <reference
 +                     definitionId="isSingleRead">
 +               </reference>
 +            </visibleWhen>
 +         </command>
+          <dynamic
+                class="eu.etaxonomy.taxeditor.editor.view.derivate.contextMenu.DerivateViewContextMenu"
+                id="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
+          </dynamic>
        </menuContribution>
        <menuContribution
              locationURI="popup:eu.etaxonomy.taxeditor.editor.view.dataimport.SpecimenImportEditor">
@@@ -972,62 -933,6 +972,62 @@@
              </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">
 +            <command
 +                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite"
 +                  label="Toggle insert/overwrite"
 +                  style="push">
 +               <visibleWhen
 +                     checkEnabled="true">
 +                  <with
 +                        variable="activePartId">
 +                     <equals
 +                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                     </equals>
 +                  </with>
 +               </visibleWhen>
 +            </command>
 +            <command
 +                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion"
 +                  label="Toggle left/right insertion"
 +                  style="push">
 +               <visibleWhen
 +                     checkEnabled="true">
 +                  <with
 +                        variable="activePartId">
 +                     <equals
 +                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                     </equals>
 +                  </with>
 +               </visibleWhen>
 +            </command>
 +         </toolbar>
 +      </menuContribution>
 +      
        <menuContribution
              allPopups="false"
              locationURI="toolbar:eu.etaxonomy.taxeditor.editor.view.descriptive">
@@@ -1169,18 -1074,6 +1169,18 @@@
        <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"
@@@ -1214,14 -1107,6 +1214,14 @@@
              class="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler"
              commandId="eu.etaxonomy.taxeditor.editor.handler.FixClassificationHierarchyHandler">
        </handler>
 +      <handler
 +            class="eu.etaxonomy.taxeditor.editor.handler.ToggleInsertOverwriteHandler"
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite">
 +      </handler>
 +      <handler
 +            class="eu.etaxonomy.taxeditor.editor.handler.ToggleLeftRightInsertionHandler"
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion">
 +      </handler>
     </extension>
     <extension
           name="%extension.name"
@@@ -1494,34 -1379,17 +1494,34 @@@
               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.OpenAlignmentEditorHandler"
 +            id="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +            name="Open Alignment Editor">
 +      </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>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite"
 +            name="Toggle insert/overwrite">
 +      </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion"
 +            name="Toggle left/right insertion in base call sequence">
 +      </command>
        <command
              defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenTaxonEditorHandler"
              id="eu.etaxonomy.taxeditor.editor.openTaxonEditor"
@@@ -1553,16 -1421,6 +1553,16 @@@
              id="eu.etaxonomy.taxeditor.editor.handler.OpenFixClassificationHierarchyHandler"
              name="Fix Classification Hierarchy">
        </command>
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.EditSequenceHandler"
 +            id="eu.etaxonomy.taxeditor.editor.editSequence"
 +            name="Edit Sequence">
 +      </command>
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.ShowPherogramHandler"
 +            id="eu.etaxonomy.taxeditor.editor.showPherogram"
 +            name="Show Pherogram">
 +      </command>
     </extension>
     <extension
           point="org.eclipse.core.expressions.definitions">
@@@ -1719,24 -1577,6 +1719,24 @@@
              </test>
           </with>
        </definition>
 +      <definition
 +            id="isSequence">
 +         <with
 +               variable="selection">
 +            <test
 +                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSequence">
 +            </test>
 +         </with>
 +      </definition>
 +      <definition
 +            id="isSingleRead">
 +         <with
 +               variable="selection">
 +            <test
 +                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSingleRead">
 +            </test>
 +         </with>
 +      </definition>
     </extension>
     <extension
           point="org.eclipse.core.expressions.propertyTesters">
@@@ -1761,13 -1601,6 +1761,13 @@@
              properties="isGroup"
              type="eu.etaxonomy.taxeditor.bulkeditor.BulkEditor">
        </propertyTester>
 +      <propertyTester
 +            class="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
 +            id="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
 +            namespace="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
 +            properties="isSequence,isSingleRead"
 +            type="org.eclipse.jface.viewers.IStructuredSelection">
 +      </propertyTester>
     </extension>
     <extension
           point="org.eclipse.ui.bindings">   
@@@ -1776,11 -1609,6 +1776,11 @@@
              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">