import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.NullProgressMonitor;
import org.eclipse.core.runtime.OperationCanceledException;
import org.eclipse.core.runtime.Status;
import org.eclipse.core.runtime.jobs.IJobChangeEvent;
import org.eclipse.equinox.internal.p2.ui.ProvUI;
import org.eclipse.equinox.internal.p2.ui.model.ElementUtils;
import org.eclipse.equinox.internal.p2.ui.model.MetadataRepositoryElement;
+import org.eclipse.equinox.p2.repository.IRepository;
+import org.eclipse.equinox.p2.repository.IRepositoryManager;
+import org.eclipse.equinox.p2.repository.metadata.IMetadataRepository;
+import org.eclipse.equinox.p2.repository.metadata.IMetadataRepositoryManager;
import org.eclipse.equinox.p2.core.IProvisioningAgent;
import org.eclipse.equinox.p2.core.ProvisionException;
import org.eclipse.equinox.p2.operations.ProvisioningJob;
import org.eclipse.equinox.p2.operations.ProvisioningSession;
+import org.eclipse.equinox.p2.operations.RepositoryTracker;
import org.eclipse.equinox.p2.operations.Update;
import org.eclipse.equinox.p2.operations.UpdateOperation;
-import org.eclipse.equinox.p2.repository.IRepository;
-import org.eclipse.equinox.p2.repository.IRepositoryManager;
-import org.eclipse.equinox.p2.repository.metadata.IMetadataRepositoryManager;
import org.eclipse.equinox.p2.ui.ProvisioningUI;
import org.eclipse.swt.widgets.Display;
import org.eclipse.ui.PlatformUI;
*
*/
public static void checkForUpdates() {
-
+ // the main job which performs the update
Job updateJob = new Job("Update Job") {
@Override
public IStatus run(IProgressMonitor monitor) {
*/
private static IStatus doCheckForUpdates(IProgressMonitor monitor) {
- // force refresh all the caches before
- IMetadataRepositoryManager metaManager = ProvUI.getMetadataRepositoryManager(ProvisioningUI.getDefaultUI().getSession());
- URI[] repos = metaManager.getKnownRepositories(IRepositoryManager.REPOSITORIES_ALL);
- for(URI repo : repos) {
- try {
- metaManager.refreshRepository(repo, monitor);
- } catch (ProvisionException pe) {
- IStatus errorStatus = new Status(IStatus.ERROR, TaxonomicEditorPlugin.PLUGIN_ID,
- "Error occured while reloading cache.", pe);
-
- } catch (OperationCanceledException oce) {
- IStatus errorStatus = new Status(IStatus.ERROR, TaxonomicEditorPlugin.PLUGIN_ID,
- "Error occured while reloading cache.", oce);
- }
- }
BundleContext bundleContext = TaxonomicEditorPlugin.getContext();
ServiceReference reference = bundleContext.getServiceReference(IProvisioningAgent.SERVICE_NAME);
if (reference == null) {
import org.eclipse.ui.handlers.HandlerUtil;
import org.eclipse.ui.texteditor.IDocumentProvider;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.strategy.merge.MergeException;
import eu.etaxonomy.taxeditor.annotatedlineeditor.IEntityContainer;
import eu.etaxonomy.taxeditor.annotatedlineeditor.LineAnnotation;
import eu.etaxonomy.taxeditor.annotatedlineeditor.LineAnnotationModel;
import eu.etaxonomy.taxeditor.bulkeditor.BulkEditor;
import eu.etaxonomy.taxeditor.bulkeditor.IBulkEditorConstants;
import eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput;
+import eu.etaxonomy.taxeditor.store.CdmStore;
/**
* <p>MergeGroupHandler class.</p>
}
Object targetEntity = ((IEntityContainer<?>) targetAnnotation).getEntity();
+ TeamOrPersonBase teamOrPerson = null;
+ Reference ref = null;
+ if (targetEntity instanceof TeamOrPersonBase){
+ teamOrPerson = HibernateProxyHelper.deproxy(targetEntity, TeamOrPersonBase.class);
+ } else if(targetEntity instanceof Reference){
+ ref = HibernateProxyHelper.deproxy(targetEntity, Reference.class);
+ }
logger.info("Merging group");
// model.printAnnotations();
for (LineAnnotation annotation : candidateAnnotations) {
+ //first check whether entities are mergeable
+
+ try{
+ if (ref != null){
+ Reference ref2 = HibernateProxyHelper.deproxy(annotation.getEntity(), Reference.class);
+
+ if (!CdmStore.getCommonService().isMergeable(ref, ref2, null)){
+ MessageDialog.openWarning(HandlerUtil.getActiveShell(event),
+ "No merge possible", "A merge of " + ref.getTitleCache() + " and " + ref2.getTitleCache() + " is not possible.");
+ return null;
+ }
+ }
+ if (teamOrPerson != null){
+ TeamOrPersonBase teamOrPerson2 = HibernateProxyHelper.deproxy(annotation.getEntity(), TeamOrPersonBase.class);
+
+ if (!CdmStore.getCommonService().isMergeable(teamOrPerson, teamOrPerson2, null)){
+ MessageDialog.openWarning(HandlerUtil.getActiveShell(event),
+ "No merge possible", "A merge of " + teamOrPerson.getTitleCache() + " and " + teamOrPerson2.getTitleCache() + " is not possible.");
+ return null;
+ }
+ }
+ }catch(MergeException e){
+
+ }
((BulkEditor) editor).removeAnnotatedLine(annotation);
// Mark entity container for merging with target entity
marker.field.3 = Problematischer Wert
marker.field.4 = Problembeschreibung
marker.field.5 = Validierer
-marker.field.6 = Entit\u00e4tsklasse
-marker.field.7 = Entit\u00e4ts ID
+marker.field.6 = Entit�tsklasse
+marker.field.7 = Entit�ts ID
extension.name.0 = Validierungs-Fehler
command.label.51 = \u00d6ffne Specimen-Editor
command.label.52 = L\u00f6schen
commandId="eu.etaxonomy.taxeditor.editor.command.new.name"
label="%command.label.46"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="eu.etaxonomy.taxeditor.editor.command.new.reference"
label="%command.label.47"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="eu.etaxonomy.taxeditor.editor.command.new.team"
label="%command.label.1"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="eu.etaxonomy.taxeditor.editor.command.new.person"
label="%command.label.2"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<separator
name="eu.etaxonomy.navigation.menu.new.separator2"
commandId="eu.etaxonomy.taxeditor.editor.command.new.specimen"
label="%command.label.3"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<separator
name="eu.etaxonomy.navigation.menu.new.separator3"
commandId="eu.etaxonomy.taxeditor.editor.command.new.datasource"
label="%command.label.48"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
</menuContribution>
<menuContribution
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.editor.view.descriptive">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="org.eclipse.ui.views.showView"
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.editor.view.media">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="org.eclipse.ui.views.showView"
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.editor.view.concept">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="org.eclipse.ui.views.showView"
value="eu.etaxonomy.taxeditor.editor.view.concept.graph">
</parameter>
<visibleWhen
- checkEnabled="true">
- <and>
- <reference
- definitionId="isShowExperimentalFeatures">
- </reference>
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </and>
+ checkEnabled="false">
+ <reference
+ definitionId="isShowExperimentalFeatures">
+ </reference>
</visibleWhen>
</command>
</menuContribution>
commandId="eu.etaxonomy.taxeditor.editor.command.openParent"
label="%command.label.8"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
</menuContribution>
<menuContribution
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.editor.view.validation.problems">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
</menuContribution>
</extension>
</description>
</wizard>
</extension>
+ <extension
+ point="eu.etaxonomy.taxeditor.store.cdmViewer">
+ <cdmViewer
+ class="eu.etaxonomy.taxeditor.editor.EditorCdmViewer">
+ </cdmViewer>
+ </extension>
</plugin>
@Override
public void setFocus() {
+ getConversationHolder().commit(true);
getConversationHolder().bind();
super.setFocus();
}
import org.eclipse.ui.handlers.HandlerUtil;
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
+import eu.etaxonomy.cdm.api.service.DeleteResult;
import eu.etaxonomy.cdm.api.service.IPolytomousKeyNodeService;
import eu.etaxonomy.cdm.api.service.ITaxonService;
import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
+import eu.etaxonomy.taxeditor.bulkeditor.internal.TaxeditorBulkeditorPlugin;
+import eu.etaxonomy.taxeditor.model.MessagingUtils;
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
import eu.etaxonomy.taxeditor.store.CdmStore;
controller = (ICdmApplicationConfiguration) CdmStore.getCurrentApplicationConfiguration();
IPolytomousKeyNodeService service = controller.getPolytomousKeyNodeService();
-
+ DeleteResult result;
if (node.getChildren().size()>0){
if(! MessageDialog.openQuestion(null, "Confirm deletion of children", "The selected node has children, do you want to delete them, too?")) {
- service.delete(node.getUuid(), false);
+ result = service.delete(node.getUuid(), false);
} else{
- service.delete(node.getUuid(), true);
+ result = service.delete(node.getUuid(), true);
}
} else{
- service.delete(node.getUuid(), true);
+ result = service.delete(node.getUuid(), true);
+ }
+
+ if (!result.isOk() || result.getExceptions().size() > 0){
+ Exception t = new Exception();
+ if (result.getExceptions().size() >1){
+ for (Exception e:result.getExceptions()){
+ t.addSuppressed(e);
+ }
+ }else {
+ t = result.getExceptions().iterator().next();
+ }
+ MessagingUtils.errorDialog("Exception occured. Delete not possible", getClass(),null, TaxeditorBulkeditorPlugin.PLUGIN_ID, t, true);
}
return postExecute(null);
}
return defaultService.merge(arg0);
}
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(java.util.UUID, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
- */
- @Override
- public DeleteResult deleteDerivateHierarchy(UUID arg0, SpecimenDeleteConfigurator arg1) {
- return defaultService.deleteDerivateHierarchy(arg0, arg1);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteSingleRead(java.util.UUID, java.util.UUID)
- */
- @Override
- public DeleteResult deleteSingleRead(UUID arg0, UUID arg1) {
- return defaultService.deleteSingleRead(arg0, arg1);
- }
-
}
* {@inheritDoc}
*/
@Override
- public UpdateResult moveSynonymToAnotherTaxon(
+ public SynonymRelationship moveSynonymToAnotherTaxon(
SynonymRelationship oldSynonymRelation, UUID newTaxonUUID,
boolean moveHomotypicGroup,
SynonymRelationshipType newSynonymRelationshipType,
public DeleteResult deleteSynonym(UUID arg0, SynonymDeletionConfigurator arg1) {
return defaultService.deleteSynonym(arg0, arg1);
}
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#changeRelatedTaxonToSynonym(java.util.UUID, java.util.UUID, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)
- */
- @Override
- public UpdateResult changeRelatedTaxonToSynonym(UUID arg0, UUID arg1, TaxonRelationshipType arg2,
- SynonymRelationshipType arg3) throws DataChangeNoRollbackException {
- return defaultService.changeRelatedTaxonToSynonym(arg0, arg1, arg2, arg3);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(java.util.UUID, java.util.UUID, boolean, boolean, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)
- */
- @Override
- public Taxon changeSynonymToAcceptedTaxon(UUID arg0, UUID arg1, boolean arg2, boolean arg3, Reference arg4,
- String arg5) throws HomotypicalGroupChangeException {
- return defaultService.changeSynonymToAcceptedTaxon(arg0, arg1, arg2, arg3, arg4, arg5);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToRelatedTaxon(java.util.UUID, java.util.UUID, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)
- */
- @Override
- public UpdateResult changeSynonymToRelatedTaxon(UUID arg0, UUID arg1, TaxonRelationshipType arg2, Reference arg3,
- String arg4) {
- return defaultService.changeSynonymToRelatedTaxon(arg0, arg1, arg2, arg3, arg4);
- }
}
version="0.0.0"
unpack="false"/>
- <plugin
- id="eu.etaxonomy.taxeditor.molecular"
- download-size="0"
- install-size="0"
- version="0.0.0"
- unpack="false"/>
-
- <plugin
- id="eu.etaxonomy.taxeditor.molecular.lib"
- download-size="0"
- install-size="0"
- version="0.0.0"
- unpack="false"/>
-
</feature>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
- <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swt-2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/core-1.9.2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/libralign-core-0-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/libralign-swt-0-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/tic-core-2-SNAPSHOT.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/tic-swt-2-SNAPSHOT.jar"/>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+++ /dev/null
-/target
-.settings/
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>eu.etaxonomy.taxeditor.molecular.lib</name>
- <comment>The Taxonomic Editor for EDIT's platform for
- cybertaxonomy. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.pde.ManifestBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.pde.SchemaBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.pde.PluginNature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
-</projectDescription>
+++ /dev/null
-Manifest-Version: 1.0
-Bundle-ManifestVersion: 2
-Bundle-Name: eu.etaxonomy.taxeditor.molecular.lib
-Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
-Bundle-Version: 3.8.0.qualifier
-Bundle-ClassPath: .,
- lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
- lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
- lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,
- lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,
- lib/core-1.9.2-SNAPSHOT.jar,
- lib/libralign-biojava1-0-SNAPSHOT.jar,
- lib/libralign-core-0-SNAPSHOT.jar,
- lib/libralign-swt-0-SNAPSHOT.jar,
- lib/sequencing-1.9.2-SNAPSHOT.jar,
- lib/tic-core-2-SNAPSHOT.jar,
- lib/tic-swt-2-SNAPSHOT.jar
-Export-Package: info.bioinfweb.commons,
- info.bioinfweb.commons.appversion,
- info.bioinfweb.commons.beans,
- info.bioinfweb.commons.bio,
- info.bioinfweb.commons.changemonitor,
- info.bioinfweb.commons.collections,
- info.bioinfweb.commons.collections.observable,
- info.bioinfweb.commons.graphics,
- info.bioinfweb.commons.io,
- info.bioinfweb.commons.log,
- info.bioinfweb.commons.progress,
- info.bioinfweb.commons.swing,
- info.bioinfweb.commons.swing.scrollpaneselector,
- info.bioinfweb.commons.swt,
- info.bioinfweb.commons.text,
- info.bioinfweb.libralign,
- info.bioinfweb.libralign.actions,
- info.bioinfweb.libralign.alignmentarea,
- info.bioinfweb.libralign.alignmentarea.content,
- info.bioinfweb.libralign.alignmentarea.label,
- info.bioinfweb.libralign.alignmentarea.order,
- info.bioinfweb.libralign.alignmentarea.paintsettings,
- info.bioinfweb.libralign.alignmentarea.rowsarea,
- info.bioinfweb.libralign.alignmentarea.selection,
- info.bioinfweb.libralign.alignmentarea.tokenpainter,
- info.bioinfweb.libralign.dataarea,
- info.bioinfweb.libralign.dataarea.implementations,
- info.bioinfweb.libralign.dataarea.implementations.charset,
- info.bioinfweb.libralign.dataarea.implementations.pherogram,
- info.bioinfweb.libralign.editsettings,
- info.bioinfweb.libralign.model,
- info.bioinfweb.libralign.model.adapters,
- info.bioinfweb.libralign.model.concatenated,
- info.bioinfweb.libralign.model.data,
- info.bioinfweb.libralign.model.events,
- info.bioinfweb.libralign.model.exception,
- info.bioinfweb.libralign.model.factory,
- info.bioinfweb.libralign.model.factory.continuous,
- info.bioinfweb.libralign.model.implementations,
- info.bioinfweb.libralign.model.implementations.swingundo,
- info.bioinfweb.libralign.model.implementations.swingundo.edits,
- info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence,
- info.bioinfweb.libralign.model.implementations.swingundo.edits.token,
- info.bioinfweb.libralign.model.implementations.translation,
- info.bioinfweb.libralign.model.tokenset,
- info.bioinfweb.libralign.model.tokenset.continuous,
- info.bioinfweb.libralign.multiplealignments,
- info.bioinfweb.libralign.pherogram,
- info.bioinfweb.libralign.pherogram.distortion,
- info.bioinfweb.libralign.pherogram.model,
- info.bioinfweb.libralign.pherogram.provider,
- info.bioinfweb.libralign.pherogram.view,
- info.bioinfweb.tic,
- info.bioinfweb.tic.exception,
- info.bioinfweb.tic.input,
- info.bioinfweb.tic.toolkit,
- info.bioinfweb.tic.toolkit.layoutdata,
- org.biojava.bibliography,
- org.biojava.bio,
- org.biojava.bio.alignment,
- org.biojava.bio.annodb,
- org.biojava.bio.chromatogram,
- org.biojava.bio.chromatogram.graphic,
- org.biojava.bio.dist,
- org.biojava.bio.dp,
- org.biojava.bio.dp.onehead,
- org.biojava.bio.dp.twohead,
- org.biojava.bio.molbio,
- org.biojava.bio.program,
- org.biojava.bio.program.abi,
- org.biojava.bio.program.blast2html,
- org.biojava.bio.program.fastq,
- org.biojava.bio.program.formats,
- org.biojava.bio.program.gff,
- org.biojava.bio.program.gff3,
- org.biojava.bio.program.hmmer,
- org.biojava.bio.program.homologene,
- org.biojava.bio.program.indexdb,
- org.biojava.bio.program.phred,
- org.biojava.bio.program.scf,
- org.biojava.bio.program.ssaha,
- org.biojava.bio.program.ssbind,
- org.biojava.bio.program.tagvalue,
- org.biojava.bio.program.unigene,
- org.biojava.bio.program.xff,
- org.biojava.bio.program.xml,
- org.biojava.bio.proteomics,
- org.biojava.bio.proteomics.aaindex,
- org.biojava.bio.search,
- org.biojava.bio.seq,
- org.biojava.bio.seq.db,
- org.biojava.bio.seq.db.biofetch,
- org.biojava.bio.seq.db.emblcd,
- org.biojava.bio.seq.db.flat,
- org.biojava.bio.seq.distributed,
- org.biojava.bio.seq.filter,
- org.biojava.bio.seq.homol,
- org.biojava.bio.seq.impl,
- org.biojava.bio.seq.io,
- org.biojava.bio.seq.io.agave,
- org.biojava.bio.seq.io.filterxml,
- org.biojava.bio.seq.io.game,
- org.biojava.bio.seq.io.game12,
- org.biojava.bio.seq.projection,
- org.biojava.bio.symbol,
- org.biojava.bio.taxa,
- org.biojava.directory,
- org.biojava.naming,
- org.biojava.ontology,
- org.biojava.ontology.io,
- org.biojava.ontology.obo,
- org.biojava.stats.svm,
- org.biojava.stats.svm.tools,
- org.biojava.utils,
- org.biojava.utils.automata,
- org.biojava.utils.cache,
- org.biojava.utils.candy,
- org.biojava.utils.io,
- org.biojava.utils.lsid,
- org.biojava.utils.math,
- org.biojava.utils.net,
- org.biojava.utils.process,
- org.biojava.utils.regex,
- org.biojava.utils.stax,
- org.biojava.utils.walker,
- org.biojava.utils.xml,
- org.biojavax,
- org.biojavax.bio,
- org.biojavax.bio.alignment,
- org.biojavax.bio.alignment.blast,
- org.biojavax.bio.db,
- org.biojavax.bio.db.ncbi,
- org.biojavax.bio.seq,
- org.biojavax.bio.seq.io,
- org.biojavax.bio.taxa,
- org.biojavax.bio.taxa.io,
- org.biojavax.ga,
- org.biojavax.ga.exception,
- org.biojavax.ga.functions,
- org.biojavax.ga.impl,
- org.biojavax.ga.util,
- org.biojavax.ontology,
- org.biojavax.utils,
- org.jdesktop.swingx.scrollpaneselector
-Bundle-ActivationPolicy: lazy
-Import-Package: javax.swing
-Require-Bundle: org.eclipse.swt
+++ /dev/null
-bin.includes = META-INF/,\
- lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,\
- lib/bioinfweb-commons-core-2-SNAPSHOT.jar,\
- lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,\
- lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,\
- lib/core-1.9.2-SNAPSHOT.jar,\
- lib/libralign-biojava1-0-SNAPSHOT.jar,\
- lib/libralign-core-0-SNAPSHOT.jar,\
- lib/libralign-swt-0-SNAPSHOT.jar,\
- lib/sequencing-1.9.2-SNAPSHOT.jar,\
- lib/tic-core-2-SNAPSHOT.jar,\
- lib/tic-swt-2-SNAPSHOT.jar
+++ /dev/null
-<project>
- <modelVersion>4.0.0</modelVersion>
- <groupId>eu.etaxonomy.taxeditor</groupId>
- <artifactId>eu.etaxonomy.taxeditor.molecular.lib</artifactId>
- <packaging>eclipse-plugin</packaging>
-
- <parent>
- <groupId>eu.etaxonomy</groupId>
- <artifactId>taxeditor-parent</artifactId>
- <version>3.8.0-SNAPSHOT</version>
- </parent>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-dependency-plugin</artifactId>
- <version>2.4</version>
- <executions>
- <execution>
- <id>copy-dependencies</id>
- <phase>validate</phase>
- <goals>
- <goal>copy-dependencies</goal>
- </goals>
- <configuration>
- <includeArtifactIds>libralign-swt, libralign-core,
- bioinfweb-commons-swt, bioinfweb-commons-core,
- bioinfweb-commons-bio, bioinfweb-commons-swing,
- tic-core, libralign-biojava1, core, sequencing, tic-swt</includeArtifactIds>
- <outputDirectory>lib</outputDirectory>
- <overWriteReleases>true</overWriteReleases>
- <overWriteSnapshots>true</overWriteSnapshots>
- <excludeTransitive>true</excludeTransitive>
- </configuration>
- </execution>
- <!-- <execution> -->
- <!-- <id>copy-dependencies-sources</id> -->
- <!-- <phase>validate</phase> -->
- <!-- <goals> -->
- <!-- <goal>copy-dependencies</goal> -->
- <!-- </goals> -->
- <!-- <configuration> -->
- <!-- <classifier>sources</classifier> -->
- <!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> -->
- <!-- <outputDirectory>lib</outputDirectory> -->
- <!-- <overWriteReleases>true</overWriteReleases> -->
- <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
- <!-- <excludeTransitive>true</excludeTransitive> -->
- <!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> -->
- <!-- </configuration> -->
- <!-- </execution> -->
- </executions>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-antrun-plugin</artifactId>
- <version>1.7</version>
- <executions>
- <execution>
- <id>remove-existing-jars</id>
- <phase>clean</phase>
- <goals>
- <goal>run</goal>
- </goals>
- <configuration>
- <target>
- <echo>Remove all jars</echo>
- <delete>
- <fileset dir="./lib" includes="*" />
- </delete>
- </target>
- </configuration>
- </execution>
- <execution>
- <id>update-snapshot-jar-names</id>
- <phase>validate</phase>
- <goals>
- <goal>run</goal>
- </goals>
- <configuration>
- <target>
- <echo>Update jars to SNAPSHOT when build with
- timestamp</echo>
- <move todir="./lib">
- <fileset dir="./lib" />
- <mapper type="regexp"
- from="(^bioinfweb\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
- </move>
- <move todir="./lib">
- <fileset dir="./lib" />
- <mapper type="regexp"
- from="(^libralign\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
- </move>
- <move todir="./lib">
- <fileset dir="./lib" />
- <mapper type="regexp"
- from="(^tic\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
- </move>
- <move todir="./lib">
- <fileset dir="./lib" />
- <mapper type="regexp"
- from="(^core\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
- </move>
- <move todir="./lib">
- <fileset dir="./lib" />
- <mapper type="regexp"
- from="(^sequencing\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
- </move>
- </target>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
-
- <dependencies>
- <!-- LibrAling -->
- <dependency>
- <groupId>info.bioinfweb.libralign</groupId>
- <artifactId>libralign-core</artifactId>
- <version>0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>info.bioinfweb.libralign</groupId>
- <artifactId>libralign-swt</artifactId>
- <version>0-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>info.bioinfweb.libralign</groupId>
- <artifactId>libralign-biojava1</artifactId>
- <version>0-SNAPSHOT</version>
- </dependency>
- <!-- commons -->
- <dependency>
- <groupId>info.bioinfweb.commons.java</groupId>
- <artifactId>bioinfweb-commons-swt</artifactId>
- <version>2-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>info.bioinfweb.commons.java</groupId>
- <artifactId>bioinfweb-commons-core</artifactId>
- <version>2-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>info.bioinfweb.commons.java</groupId>
- <artifactId>bioinfweb-commons-bio</artifactId>
- <version>2-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>info.bioinfweb.commons.java</groupId>
- <artifactId>bioinfweb-commons-swing</artifactId>
- <version>2-SNAPSHOT</version>
- </dependency>
- <!-- tic -->
- <dependency>
- <groupId>info.bioinfweb.tic</groupId>
- <artifactId>tic-core</artifactId>
- <version>2-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>info.bioinfweb.tic</groupId>
- <artifactId>tic-swt</artifactId>
- <version>2-SNAPSHOT</version>
- </dependency>
- <!-- biojava -->
- <dependency>
- <groupId>org.biojava</groupId>
- <artifactId>core</artifactId>
- <version>1.9.2</version>
- </dependency>
- <dependency>
- <groupId>org.biojava</groupId>
- <artifactId>sequencing</artifactId>
- <version>1.9.2</version>
- </dependency>
- </dependencies>
-
- <repositories>
- <repository>
- <id>bioinfweb-maven-repo</id>
- <name>bioinfweb repository</name>
- <url>http://bioinfweb.info/MavenRepository/</url>
- </repository>
- </repositories>
-
-</project>
-
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
- <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
- <classpathentry including="**/*.java" kind="src" path="src/main/java"/>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
+++ /dev/null
-/target
-.settings/
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>eu.etaxonomy.taxeditor.molecular</name>
- <comment>Provides editors, views and operations for handling molecular data and alignments. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.pde.ManifestBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.pde.SchemaBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.pde.PluginNature</nature>
- </natures>
-</projectDescription>
+++ /dev/null
-Manifest-Version: 1.0
-Bundle-ManifestVersion: 2
-Bundle-Name: Molecular Bundle
-Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular;singleton:=true
-Bundle-Version: 3.8.0.qualifier
-Bundle-Activator: eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin
-Require-Bundle: org.eclipse.ui,
- org.eclipse.core.runtime,
- org.eclipse.core.expressions,
- org.eclipse.ui.ide,
- eu.etaxonomy.taxeditor.bulkeditor,
- eu.etaxonomy.taxeditor.cdmlib,
- eu.etaxonomy.taxeditor.editor,
- eu.etaxonomy.taxeditor.store,
- eu.etaxonomy.taxeditor.molecular.lib
-Bundle-RequiredExecutionEnvironment: JavaSE-1.6
-Bundle-ActivationPolicy: lazy
-Bundle-Vendor: EDIT
+++ /dev/null
-#Properties file for taxeditor-editor
-Bundle-Vendor.0 = EDIT
-Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle
-command.name.17 = Set Basionym
-command.name.18 = Remove Basionym
-editor.name = Multipage Taxon Editor
-editor.name.0 = Taxon Name Editor
-editor.name.1 = Key
-editor.name.2 = Polytomous Key Graph Editor
-editor.name.3 = Polytomous Key List Editor
-editor.name.4 = Cdm Authority Editor
-editor.name.5 = Derivative View
-view.name = Factual Data
-view.name.0 = Uses
-view.name.1 = Media
-view.name.2 = Concept Relations
-view.name.3 = Concept Graph
-category.name = Taxonomic Editor
-command.label = Reference
-command.label.0 = Name
-command.label.1 = Team
-command.label.2 = Person
-command.label.3 = Specimen
-command.label.4 = Factual Data
-command.label.5 = Media
-command.label.6 = Concept
-command.label.7 = Concept Graph
-command.label.8 = Open Parent
-menu.label = New
-command.label.9 = Heterotypic Synonym
-command.label.10 = Homotypic Synonym
-command.label.11 = Synonym In Homotypical Group
-menu.label.0 = Change To
-command.label.12 = Accepted Taxon
-command.label.13 = Synonym
-command.label.14 = Misapplication
-command.label.15 = Delete
-command.label.16 = Delete All Empty Names
-command.label.17 = Swap Synonym With Accepted
-command.label.18 = Show Details
-command.label.19 = Save
-command.label.20 = New Node
-command.label.21 = Delete
-command.label.22 = Apply Layout
-command.label.23 = New Key Number
-command.label.24 = New Alternative
-command.label.25 = Refresh Nodes
-command.label.26 = Delete
-command.label.27 = New Factual Data
-menu.label.1 = New
-command.label.28 = Move Description to Taxon
-command.label.29 = Move Elements to Taxon
-command.label.30 = Delete
-command.label.31 = Save
-menu.label.2 = New Derivative
-command.label.32 = New Use
-command.label.33 = New Use Summary
-command.label.34 = New Use Record
-command.label.35 = Delete
-command.label.36 = Save
-command.label.37 = New Image Gallery
-command.label.38 = New Image
-command.label.39 = Move Image Up In List
-command.label.40 = Move Image Down In List
-command.label.41 = Delete
-command.label.42 = Save
-menu.label.3 = New
-command.label.43 = Open Related Concept
-command.label.44 = Delete
-command.label.45 = Edit Authorities
-extension.name = Name Commands
-category.name.0 = -- Name Editor
-command.name = Open Parent
-command.name.0 = Create Homotypic Synonym
-command.name.1 = Create Heterotypic Synonym
-command.name.2 = Create Synonym In Homotypical Group
-command.name.3 = Change To Synonym
-command.name.4 = Change To Accepted Taxon
-command.name.5 = Change To Misapplication
-command.name.6 = Swap Synonym With Accepted
-
-command.name.7 = Set Basionym / Original Combination
-command.name.8 = Remove Basionym / Original Combination
-command.name.9 = Delete All Empty Names
-category.name.1 = -- Factual
-command.name.10 = Create Description Element
-command.name.11 = New Description
-command.name.12 = Move Description Elements to Taxon
-command.name.13 = Move Description to Taxon
-category.name.2 = -- New Uses
-command.name.14 = New Use
-command.name.15 = New Use Summary
-command.name.16 = New Use Record
-category.name.3 = -- Media
-command.name.19 = Move Image Down In List
-command.name.20 = New Image Gallery
-command.name.21 = New Image
-command.name.22 = Move Image Up In List
-category.name.4 = -- New Entity
-command.name.23 = New Reference
-command.name.24 = New Name
-command.name.25 = New Team
-command.name.26 = New Person
-command.name.27 = New Specimen
-category.name.5 = -- Polytomous Keys
-command.name.28 = New Child Node
-command.name.29 = New Sibling Node
-command.name.30 = Refresh Node Numbering
-command.name.31 = Apply Layout
-category.name.6 = -- Concept Relations
-command.name.32 = Create Concept Relation
-command.name.33 = Open Related Concept
-category.name.7 = -- Group
-command.name.34 = Edit CDM Authorities
-command.name.35 = Open Derivative View
-scheme.description = The default key binding scheme for the Taxonomic Editor
-scheme.name = Taxonomic Editor Default Key Bindings
-editor.name.6 = Specimen Import Editor
-editor.name.7 = Gbif Import Editor
-editor.name.8 = Checklist Editor
-view.name.4 = Specimen Import
-view.name.5 = GBIF Specimen Import
-command.label.46 = Name
-command.label.47 = Reference
-command.label.48 = Datasource
-command.label.49 = Misapplication
-command.label.50 = Use Existing Image
-command.name.36 = Create Misapplication
-command.name.37 = Use Existing Image
-command.name.38 = Open Checklist Editor
-command.name.39 = New Datasource
-wizard.name = Specimen Search/Import
-wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100.
-command.name.40 = Validation
-view.name.6 = Validation
-marker.field.0 = Object Type
-marker.field.1 = Object
-marker.field.2 = Attribute
-marker.field.3 = Problematic Value
-marker.field.4 = Problem description
-marker.field.5 = Validator
-marker.field.6 = Entity Class
-marker.field.7 = Entity Id
-extension.name.0 = Validation Error
-command.label.51 = Open in Specimen Editor
-command.label.52 = Delete
-command.label.53 = Create Field Unit
-command.label.54 = Delete (with children)
-command.tooltip = Show Only Individuals Associations
-command.label.55 = Open Associated Specimens
-command.name.41 = Show Only Individual Associations
-command.name.42 = Open Taxon Editor
-command.name.43 = Create Field Unit
-command.name.44 = Deep Delete
-command.name.46 = Move Synonym (Homotypical Group) to another Accepted Taxon
-command.label.56 = Move Synonym (Homotypical Group) to another Accepted Taxon
-markerContentGenerator.name = Validation Problems Marker Generator
-command.name.45 = Delete
-command.name.47 = Delete
-commandParameter.name = taxonUUID
-Bundle-Name = Editor Bundle
-command.name.48 = delete
-command.name.49 = delete
-command.name.50 = delete
\ No newline at end of file
+++ /dev/null
-# Properties file for taxeditor-editor
-Bundle-Vendor.0 = EDIT
-Bundle-Name.0 = EDIT Taxonomischer Editor - Editor Bundle
-command.name.17 = Setze Basionym
-command.name.18 = Entferne Basionym
-editor.name = Multipage Taxon Editor
-editor.name.0 = Editor Taxonname
-editor.name.1 = Bestimmungsschl\u00fcssel
-editor.name.2 = Polytomer Bestimmungsschl\u00fcssel Graph Editor
-editor.name.3 = Polytomer Bestimmungsschl\u00fcssel List Editor
-editor.name.4 = CDM Rechtemanagement
-editor.name.5 = Ansicht Derivate
-view.name = Faktendaten
-view.name.0 = Nutzung
-view.name.1 = Medien
-view.name.2 = Konzeptrelationen
-view.name.3 = Konzeptgraph
-category.name = Taxonomischer Editor
-command.label = Referenz
-command.label.0 = Name
-command.label.1 = Team
-command.label.2 = Person
-command.label.3 = Beleg
-command.label.4 = Faktendaten
-command.label.5 = Medien
-command.label.6 = Konzeptrelationen
-command.label.7 = Konzeptgraph
-command.label.8 = \u00d6ffne Parent
-menu.label = Neue
-command.label.9 = Heterotypisches Synonym
-command.label.10 = Homotypisches Synonym
-command.label.11 = Synonym in Homotypischer Gruppe
-menu.label.0 = \u00c4ndere zu
-command.label.12 = Akzeptiertes Taxon
-command.label.13 = Synonym
-command.label.14 = Misapplication
-command.label.15 = L\u00f6schen
-command.label.16 = L\u00f6sche alle leeren Namen
-command.label.17 = Tausche Synonym mit akzeptiertem Namen
-command.label.18 = Zeige Details
-command.label.19 = Speichern
-command.label.20 = Neue Knoten
-command.label.21 = L\u00f6schen
-command.label.22 = Wende Layout an
-command.label.23 = Neue Bestimmungsschl\u00fcsselnummer
-command.label.24 = Neue Alternative
-command.label.25 = Erneuere Knoten
-command.label.26 = L\u00f6schen
-command.label.27 = Neue Faktendaten
-menu.label.1 = Neue
-command.label.28 = Verschiebe Eigenschaften zu Taxon
-command.label.29 = Verschiebe Elemente zu Taxon
-command.label.30 = L\u00f6schen
-command.label.31 = Speichern
-menu.label.2 = Neue Derivate
-command.label.32 = Neue Nutzung
-command.label.33 = Neue Zusammenfassung
-command.label.34 = Neuer Nutzungsdatensatz
-command.label.35 = L\u00f6schen
-command.label.36 = Speichern
-command.label.37 = Neue Bildergalerie
-command.label.38 = Neues Bild
-command.label.39 = Bild nach oben
-command.label.40 = Bild nach unten
-command.label.41 = L\u00f6schen
-command.label.42 = Speichern
-menu.label.3 = Neue
-command.label.43 = \u00d6ffne verbundenes Konzept
-command.label.44 = L\u00f6schen
-command.label.45 = Bearbeite Rechte
-extension.name = Namensbefehle
-category.name.0 = -- Namenseditor
-command.name = \u00d6ffne Elter
-command.name.0 = Erstelle homotypisches Synonym
-command.name.1 = Erstelle heterotypisches Synonym
-command.name.2 = Erstelle Synonym in homotypischer Gruppe
-command.name.3 = \u00c4ndere zu Synonym
-command.name.4 = \u00c4ndere zu akzeptiertem Taxon
-command.name.5 = \u00c4ndere zu Misapplication
-command.name.6 = Tausche Synonym mit akzeptiertem Namen
-
-command.name.7 = Setze Basionym / Originalkombination
-command.name.8 = Entferne Basionym / Originalkombination
-command.name.9 = L\u00f6sche alle leeren Namen
-category.name.1 = -- Fakten
-command.name.10 = Erstelle Beschreibungselement
-command.name.11 = Neue Beschreibung
-command.name.12 = Bewege Beschreibungselement zu Taxon
-command.name.13 = Bewege Beschreibung zu Taxon
-category.name.2 = -- Neue Nutzung
-command.name.14 = Neue Nutzung
-command.name.15 = Neue Zusammenfassung
-command.name.16 = Neuer Nutzungsdatensatz
-category.name.3 = -- Media
-command.name.19 = Bewege Bild nach unten
-command.name.20 = Neue Bildergalerie
-command.name.21 = Neues Bild
-command.name.22 = Bewege Bild nach oben
-category.name.4 = -- Neue Entit\u00e4t
-command.name.23 = Neue Referenz
-command.name.24 = Neuer Name
-command.name.25 = Neues Team
-command.name.26 = Neue Person
-command.name.27 = Neuer Beleg
-category.name.5 = -- Polytomer Bestimmungsschl\u00fcssel
-command.name.28 = Neue Kinderknoten
-command.name.29 = Neuer Geschwisterknoten
-command.name.30 = Knotennummerierung aktualisieren
-command.name.31 = Layout anwenden
-category.name.6 = -- Konzeptbeziehungen
-command.name.32 = Erstelle Konzeptrelationen
-command.name.33 = \u00d6ffne verbundenes Konzept
-category.name.7 = -- Gruppe
-command.name.34 = Bearbeite CDM Rechte
-command.name.35 = \u00d6ffne Derivate Ansicht
-scheme.description = Die Standard Tastenkombinationsschema f\u00fcr den Taxonomischen Editor
-scheme.name = Taxonomic Editor Standard Tastenkombinationen
-editor.name.6 = Specimen Import Editor
-editor.name.7 = GBIF Import Editor
-editor.name.8 = Checklist Editor
-view.name.4 = Specimen Import
-view.name.5 = GBIF Specimen Import
-command.label.46 = Name
-command.label.47 = Referenz
-command.label.48 = Datenquelle
-command.label.49 = Misapplication
-command.label.50 = Benutze vorhandenes Bild
-command.name.36 = Erstelle Misapplication
-command.name.37 = Benutze vorhandenes Bild
-command.name.38 = \u00d6ffne Checklist Editor
-command.name.39 = Neue Datenquelle
-wizard.name = Specimen Suche/Import
-wizard.description = Sendet eine Anfrage mit den eingegebenen Parametern an den Datenprovider.\nHinweis: Die Anzahl der Anfrageergebnisse sind auf 100 begrenzt.
-command.name.40 = Validierung
-view.name.6 = Validierung
-marker.field.0 = Objekttyp
-marker.field.1 = Objekt
-marker.field.2 = Attribut
-marker.field.3 = Problematischer Wert
-marker.field.4 = Problembeschreibung
-marker.field.5 = Validierer
-marker.field.6 = Entit�tsklasse
-marker.field.7 = Entit�ts ID
-extension.name.0 = Validierungs-Fehler
-command.label.51 = \u00d6ffne Specimen-Editor
-command.label.52 = L\u00f6schen
-command.label.53 = Neue Field Unit
-command.label.54 = L\u00f6schen (mit Kindern)
-command.tooltip = Nur Individuals Associations anzeigen
-command.label.55 = \u00d6ffne zugeh\u00f6rige Specimens
-command.name.41 = Nur Individuals Associations anzeigen
-command.name.42 = \u00d6ffne Taxon Editor
-command.name.43 = Neue Field Unit
-command.name.44 = L\u00f6schen (mit Kindern)
-command.name.46 = Verschiebe Synonym(Homotypische Gruppe) zu neuem Akzeptierten Taxon
-command.label.56 = Verschiebe Synonym(Homotypische Gruppe) zu neuem Akzeptierten Taxon
\ No newline at end of file
+++ /dev/null
-#Properties file for taxeditor-editor
-Bundle-Vendor.0 = EDIT
-Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle
-command.name.17 = Set Basionym
-command.name.18 = Remove Basionym
-editor.name = Multipage Taxon Editor
-editor.name.0 = Taxon Name Editor
-editor.name.1 = Key
-editor.name.2 = Polytomous Key Graph Editor
-editor.name.3 = Polytomous Key List Editor
-editor.name.4 = Cdm Authority Editor
-editor.name.5 = Derivate View
-view.name = Factual Data
-view.name.0 = Uses
-view.name.1 = Media
-view.name.2 = Concept Relations
-view.name.3 = Concept Graph
-category.name = Taxonomic Editor
-command.label = Reference
-command.label.0 = Name
-command.label.1 = Team
-command.label.2 = Person
-command.label.3 = Specimen
-command.label.4 = Factual Data
-command.label.5 = Media
-command.label.6 = Concept
-command.label.7 = Concept Graph
-command.label.8 = Open Parent
-menu.label = New
-command.label.9 = Heterotypic Synonym
-command.label.10 = Homotypic Synonym
-command.label.11 = Synonym In Homotypical Group
-menu.label.0 = Change To
-command.label.12 = Accepted Taxon
-command.label.13 = Synonym
-command.label.14 = Misapplication
-command.label.15 = Delete
-command.label.16 = Delete All Empty Names
-command.label.17 = Swap Synonym With Accepted
-command.label.18 = Show Details
-command.label.19 = Save
-command.label.20 = New Node
-command.label.21 = Delete
-command.label.22 = Apply Layout
-command.label.23 = New Key Number
-command.label.24 = New Alternative
-command.label.25 = Refresh Nodes
-command.label.26 = Delete
-command.label.27 = New Factual Data
-menu.label.1 = New
-command.label.28 = Move Description to Taxon
-command.label.29 = Move Elements to Taxon
-command.label.30 = Delete
-command.label.31 = Save
-menu.label.2 = New Derivate
-command.label.32 = New Use
-command.label.33 = New Use Summary
-command.label.34 = New Use Record
-command.label.35 = Delete
-command.label.36 = Save
-command.label.37 = New Image Gallery
-command.label.38 = New Image
-command.label.39 = Move Image Up In List
-command.label.40 = Move Image Down In List
-command.label.41 = Delete
-command.label.42 = Save
-menu.label.3 = New
-command.label.43 = Open Related Concept
-command.label.44 = Delete
-command.label.45 = Edit Authorities
-extension.name = Name Commands
-category.name.0 = -- Name Editor
-command.name = Open Parent
-command.name.0 = Create Homotypic Synonym
-command.name.1 = Create Heterotypic Synonym
-command.name.2 = Create Synonym In Homotypical Group
-command.name.3 = Change To Synonym
-command.name.4 = Change To Accepted Taxon
-command.name.5 = Change To Misapplication
-command.name.6 = Swap Synonym With Accepted
-command.name.7 = Set Basionym / Original Combination
-command.name.8 = Remove Basionym / Original Combination
-command.name.9 = Delete All Empty Names
-category.name.1 = -- Factual
-command.name.10 = Create Description Element
-command.name.11 = New Description
-command.name.12 = Move Description Elements to Taxon
-command.name.13 = Move Description to Taxon
-category.name.2 = -- New Uses
-command.name.14 = New Use
-command.name.15 = New Use Summary
-command.name.16 = New Use Record
-category.name.3 = -- Media
-command.name.19 = Move Image Down In List
-command.name.20 = New Image Gallery
-command.name.21 = New Image
-command.name.22 = Move Image Up In List
-category.name.4 = -- New Entity
-command.name.23 = New Reference
-command.name.24 = New Name
-command.name.25 = New Team
-command.name.26 = New Person
-command.name.27 = New Specimen
-category.name.5 = -- Polytomous Keys
-command.name.28 = New Child Node
-command.name.29 = New Sibling Node
-command.name.30 = Refresh Node Numbering
-command.name.31 = Apply Layout
-category.name.6 = -- Concept Relations
-command.name.32 = Create Concept Relation
-command.name.33 = Open Related Concept
-category.name.7 = -- Group
-command.name.34 = Edit CDM Authorities
-command.name.35 = Open Derivate View
-scheme.description = The default key binding scheme for the Taxonomic Editor
-scheme.name = Taxonomic Editor Default Key Bindingseditor.name.6 = Specimen Import Editor
-editor.name.7 = Gbif Import Editor
-editor.name.8 = Checklist Editor
-view.name.4 = Specimen Import
-view.name.5 = GBIF Specimen Import
-command.label.46 = Name
-command.label.47 = Reference
-command.label.48 = Datasource
-command.label.49 = Misapplication
-command.label.50 = Use Existing Image
-command.name.36 = Create Misapplication
-command.name.37 = Use Existing Image
-command.name.38 = Open Checklist Editor
-command.name.39 = New Datasource
-wizard.name = Specimen Search/Import
-wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100.
-command.name.40 = Validation
-view.name.6 = Validation
-marker.field.0 = Object Type
-marker.field.1 = Object
-marker.field.2 = Attribute
-marker.field.3 = Problematic Value
-marker.field.4 = Problem description
-marker.field.5 = Validator
-marker.field.6 = Entity Class
-marker.field.7 = Entity Id
\ No newline at end of file
+++ /dev/null
-bin.includes = META-INF/,\
- plugin.xml,\
- icons/,\
- OSGI-INF/
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<?eclipse version="3.4"?>
-<plugin>
- <extension
- point="org.eclipse.ui.editors">
- <editor
- class="eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor"
- default="false"
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"
- name="Alignment Editor">
- </editor>
- </extension>
- <extension
- point="org.eclipse.ui.views">
- <view
- allowMultiple="true"
- class="eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart"
- id="eu.etaxonomy.taxeditor.molecular.PherogramView"
- name="PherogramView"
- restorable="true">
- </view>
- </extension>
- <extension
- point="org.eclipse.ui.commands">
- <command
- defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler"
- id="eu.etaxonomy.taxeditor.molecular.editSequence"
- name="Edit Sequence">
- </command>
- <command
- defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
- id="eu.etaxonomy.taxeditor.molecular.showPherogram"
- name="Show Pherogram">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
- name="Cut pherogram left">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
- name="Cut pherogram right">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
- name="Reverse complement selected rows">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
- name="(Re)create consensus sequence">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
- name="Update consensus sequence">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
- name="Toggle show probability values">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
- name="Toggle show base call lines">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
- name="Change quality output">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
- name="Load Pherogram">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
- name="Toggle insert/overwrite">
- </command>
- <command
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
- name="Toggle left/right insertion in base call sequence">
- </command>
- </extension>
- <extension
- point="org.eclipse.ui.menus">
- <menuContribution
- locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
- <toolbar
- id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
- label="Toggle insert/overwrite"
- style="push">
- <visibleWhen
- checkEnabled="true">
- <with
- variable="activePartId">
- <equals
- value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
- </equals>
- </with>
- </visibleWhen>
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
- icon="icons/pherogram-insert-left-16x16.png"
- style="push">
- <visibleWhen
- checkEnabled="true">
- <with
- variable="activePartId">
- <equals
- value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
- </equals>
- </with>
- </visibleWhen>
- </command>
- </toolbar>
- </menuContribution>
- <menuContribution
- allPopups="false"
- locationURI="menu:org.eclipse.ui.main.menu">
- <menu
- label="Alignment Editor">
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
- style="push">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
- name="Cut pherogram left">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
- id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
- style="push">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
- mnemonic="r"
- style="push">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
- style="push">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
- style="push">
- </command>
- <visibleWhen
- checkEnabled="true">
- <with
- variable="activePartId">
- <equals
- value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
- </equals>
- </with>
- </visibleWhen>
- </menu>
- <menu
- label="Pherogram View">
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
- style="push">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
- style="push">
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
- style="push">
- </command>
- <visibleWhen
- checkEnabled="true">
- <with
- variable="activePartId">
- <equals
- value="eu.etaxonomy.taxeditor.molecular.PherogramView">
- </equals>
- </with>
- </visibleWhen>
- </menu>
- </menuContribution>
- <menuContribution
- locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
- label="Edit Sequence"
- style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isSequence">
- </reference>
- </visibleWhen>
- </command>
- <command
- commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
- label="Show Pherogram"
- style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isSingleRead">
- </reference>
- </visibleWhen>
- </command>
- </menuContribution>
- </extension>
- <extension
- point="org.eclipse.ui.handlers">
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
- <activeWhen>
- <with
- variable="activePartId">
- <equals
- value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
- </equals>
- </with>
- </activeWhen>
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
- commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
- </handler>
- <handler
- class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
- commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
- </handler>
- </extension>
- <extension
- point="org.eclipse.core.expressions.definitions">
- <definition
- id="isSequence">
- <with
- variable="selection">
- <test
- property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
- </test>
- </with>
- </definition>
- <definition
- id="isSingleRead">
- <with
- variable="selection">
- <test
- property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
- </test>
- </with>
- </definition>
- </extension>
- <extension
- point="org.eclipse.core.expressions.propertyTesters">
- <propertyTester
- class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
- id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
- namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
- properties="isSequence,isSingleRead"
- type="org.eclipse.jface.viewers.IStructuredSelection">
- </propertyTester>
- </extension>
- <extension
- point="org.eclipse.ui.bindings">
- <scheme
- description="%scheme.description"
- id="eu.etaxonomy.taxeditor.bindings.scheme.default"
- name="%scheme.name">
- </scheme>
- <key
- commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
- schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
- sequence="M1+O">
- </key>
- </extension>
-
-</plugin>
+++ /dev/null
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-
- <parent>
- <groupId>eu.etaxonomy</groupId>
- <artifactId>taxeditor-parent</artifactId>
- <version>3.8.0-SNAPSHOT</version>
- </parent>
-
- <modelVersion>4.0.0</modelVersion>
- <artifactId>eu.etaxonomy.taxeditor.molecular</artifactId>
- <packaging>eclipse-plugin</packaging>
-
- <name>Molecular Bundle</name>
- <description>Provides editors, views and operations for handling molecular data and alignments</description>
-
-</project>
+++ /dev/null
-package eu.etaxonomy.taxeditor.molecular;
-
-import org.eclipse.ui.plugin.AbstractUIPlugin;
-import org.osgi.framework.BundleContext;
-
-/**
- * The activator class controls the plug-in life cycle
- */
-public class TaxeditorMolecularPlugin extends AbstractUIPlugin {
-
- // The plug-in ID
- public static final String PLUGIN_ID = "eu.etaxonomy.taxeditor.molecular"; //$NON-NLS-1$
-
- // The shared instance
- private static TaxeditorMolecularPlugin plugin;
-
- /**
- * The constructor
- */
- public TaxeditorMolecularPlugin() {
- }
-
- @Override
- public void start(BundleContext context) throws Exception {
- super.start(context);
- plugin = this;
- }
-
- @Override
- public void stop(BundleContext context) throws Exception {
- plugin = null;
- super.stop(context);
- }
-
- /**
- * Returns the shared instance
- *
- * @return the shared instance
- */
- public static TaxeditorMolecularPlugin getDefault() {
- return plugin;
- }
-
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2014 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.editor;
-
-
-import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
-import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
-import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter;
-import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
-import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
-import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent;
-import info.bioinfweb.libralign.editsettings.EditSettingsListener;
-import info.bioinfweb.libralign.model.AlignmentModel;
-import info.bioinfweb.libralign.model.AlignmentModelChangeListener;
-import info.bioinfweb.libralign.model.AlignmentModelUtils;
-import info.bioinfweb.libralign.model.adapters.StringAdapter;
-import info.bioinfweb.libralign.model.events.SequenceChangeEvent;
-import info.bioinfweb.libralign.model.events.SequenceRenamedEvent;
-import info.bioinfweb.libralign.model.events.TokenChangeEvent;
-import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
-import info.bioinfweb.libralign.model.tokenset.CharacterTokenSet;
-import info.bioinfweb.libralign.model.tokenset.TokenSet;
-import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
-import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
-import info.bioinfweb.libralign.pherogram.model.PherogramAreaModel;
-import info.bioinfweb.libralign.pherogram.model.ShiftChange;
-import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider;
-import info.bioinfweb.libralign.pherogram.provider.PherogramProvider;
-import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider;
-import info.bioinfweb.tic.SWTComponentFactory;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.biojava.bio.chromatogram.ChromatogramFactory;
-import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
-import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.widgets.Composite;
-import org.eclipse.ui.IActionBars;
-import org.eclipse.ui.IEditorInput;
-import org.eclipse.ui.IEditorPart;
-import org.eclipse.ui.IEditorSite;
-import org.eclipse.ui.PartInitException;
-import org.eclipse.ui.PlatformUI;
-import org.eclipse.ui.commands.ICommandService;
-import org.eclipse.ui.part.EditorPart;
-
-import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
-import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
-import eu.etaxonomy.cdm.model.media.MediaUtils;
-import eu.etaxonomy.cdm.model.molecular.Sequence;
-import eu.etaxonomy.cdm.model.molecular.SequenceString;
-import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
-import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift;
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler;
-import eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler;
-import eu.etaxonomy.taxeditor.store.CdmStore;
-import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;
-
-
-
-/**
- * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
- * a consensus sequence.
- * <p>
- * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
- *
- * @author Ben Stöver
- * @author pplitzner
- * @date 04.08.2014
- */
-public class AlignmentEditor extends EditorPart {
- public static final String ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor";
-
- public static final int READS_AREA_INDEX = 1;
- public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
- public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1;
- public static final int PHEROGRAM_AREA_INDEX = 0;
- public static final int CONSENSUS_DATA_AREA_INDEX = 0;
- public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
- public static final String CONSENSUS_NAME = "Consensus";
-
-
- private final ConversationHolder conversationHolder;
-
- private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() {
- @Override
- public <T> void afterTokenChange(TokenChangeEvent<T> e) {
- setDirty();
- }
-
- @Override
- public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) {
- setDirty();
- }
-
- @Override
- public <T> void afterSequenceChange(SequenceChangeEvent<T> e) {
- setDirty();
- }
-
- @Override
- public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider,
- AlignmentModel<U> newProvider) { // Not expected.
-
- setDirty();
- }
- };
-
- private MultipleAlignmentsContainer alignmentsContainer = null;
- private final Map<Integer, SingleReadAlignment> cdmMap = new TreeMap<Integer, SingleReadAlignment>(); //TODO Move this to ContigSequenceDataProvider
- private boolean dirty = false;
-
-
- public AlignmentEditor() {
- super();
- conversationHolder = CdmStore.createConversation();
- //conversationHolder = null;
- }
-
-
- private void refreshToolbarElement(String id) {
- ICommandService commandService =
- (ICommandService)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);
- if (commandService != null) {
- commandService.refreshElements(id, Collections.EMPTY_MAP);
- }
- }
-
-
- private void registerEditSettingListener(MultipleAlignmentsContainer container) {
- container.getEditSettings().addListener(new EditSettingsListener() {
- @Override
- public void workingModeChanged(EditSettingsChangeEvent e) {} // Currently nothing to do
-
- @Override
- public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
- updateStatusBar();
- refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
- }
-
- @Override
- public void insertChanged(EditSettingsChangeEvent e) {
- updateStatusBar();
- refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
- }
- });
- }
-
-
- private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {
- AlignmentArea result = new AlignmentArea(container);
- result.setAllowVerticalScrolling(false);
- result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea(), labeledArea));
- return result;
- }
-
-
- private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
- AlignmentArea result = new AlignmentArea(container);
- result.setAllowVerticalScrolling(allowVerticalScrolling);
-
- CharacterTokenSet tokenSet = CharacterTokenSet.newDNAInstance(); //TODO Should NUCLEOTIDE be used instead?
- AlignmentModel<Character> provider = new PackedAlignmentModel<Character>(tokenSet);
- result.setAlignmentModel(provider, false);
- provider.getChangeListeners().add(DIRTY_LISTENER);
- result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter());
-
- return result;
- }
-
-
- private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
- AlignmentArea labeledArea) {
-
- AlignmentArea result = new AlignmentArea(container);
- result.setAllowVerticalScrolling(false);
- result.getDataAreas().getBottomAreas().add(
- new ConsensusSequenceArea(result.getContentArea(), labeledArea));
- return result;
- }
-
-
- private MultipleAlignmentsContainer getAlignmentsContainer() {
- if (alignmentsContainer == null) {
- alignmentsContainer = new MultipleAlignmentsContainer();
-
- AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
- AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
- list.add(createIndexArea(alignmentsContainer, readsArea));
- list.add(readsArea); // Make sure READS_AREA_INDEX is correct.
- list.add(createEditableAlignmentArea(alignmentsContainer, false)); // Make sure COMSENSUS_AREA_INDEX is correct.
- list.add(createConsensusHintArea(alignmentsContainer, readsArea));
-
- registerEditSettingListener(alignmentsContainer);
- }
- return alignmentsContainer;
- }
-
-
- public AlignmentArea getReadsArea() {
- return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);
- }
-
-
- private AlignmentArea getEditableConsensusArea() {
- return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX);
- }
-
-
- public boolean hasPherogram(int sequenceID) {
- return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;
- }
-
-
- public PherogramArea getPherogramArea(int sequenceID) {
- if (hasPherogram(sequenceID)) {
- return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);
- }
- else {
- return null;
- }
- }
-
-
- private ConsensusSequenceArea getConsensusHintDataArea() {
- return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas().
- get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas().
- get(CONSENSUS_DATA_AREA_INDEX);
- }
-
-
- @Deprecated //TODO Remove as soon as testing period is over
- private void createTestContents() {
- // Just for testing:
- try {
- addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI(), false);
- //addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false);
- addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/Test_qualityScore.scf").toURI(), false);
-
- // Add test consensus sequence:
- AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
- int id = consensusModel.addSequence(CONSENSUS_NAME);
- Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token.
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A"));
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G"));
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T"));
- consensusModel.insertTokensAt(id, 0, tokens);
- }
- catch (Exception e) {
- throw new RuntimeException(e);
- }
- }
-
-
- private void readCDMData(Sequence sequenceNode) {
- //TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).
-
- // Add reads:
- for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) {
- try {
- SingleRead pherogramInfo = singleReadAlignment.getSingleRead();
- URI uri = null;
- if (pherogramInfo.getPherogram() != null) {
- uri = MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
- }
- int id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder),
- uri,
- singleReadAlignment.isReverseComplement(),
- singleReadAlignment.getEditedSequence(),
- singleReadAlignment.getFirstSeqPosition(),
- singleReadAlignment.getLeftCutPosition(),
- singleReadAlignment.getRightCutPosition(),
- singleReadAlignment.getShifts());
- cdmMap.put(id, singleReadAlignment);
- }
- catch (Exception e) { // Usually due to an error while trying to read the pherogram (e.g. due to an unsupported format or an invalid URI).
- MessagingUtils.errorDialog("Error", null, "A single read was skipped because of the following error:\n\n" +
- e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
- }
- }
-
- // Set consensus sequence:
- AlignmentModel consensusProvider = getEditableConsensusArea().getAlignmentModel();
- int id = consensusProvider.addSequence(CONSENSUS_NAME);
- consensusProvider.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList(
- sequenceNode.getConsensusSequence().getString(), consensusProvider.getTokenSet()));
- //TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
- */
- @Override
- public void createPartControl(Composite parent) {
- SWTComponentFactory.getInstance().getSWTComponent(getAlignmentsContainer(), parent, SWT.NONE);
- updateStatusBar();
-
- if (getEditorInput() instanceof AlignmentEditorInput) {
- if (((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid() != null) {
- Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
- //re-load into the current session if it is already persisted in the DB
- if(sequenceNode!=null && sequenceNode.getId()!=0){
- sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid());
- }
- readCDMData(sequenceNode);
- }
- else {
- createTestContents(); // This case will removed after the test phase and an exception should probably be thrown.
- }
- }
- else {
- throw new IllegalArgumentException("The editor input must have the type " +
- AlignmentEditorInput.class.getCanonicalName()); //TODO What should be done here?
- }
- }
-
-
- private void updateStatusBar() {
- IActionBars bars = getEditorSite().getActionBars();
- bars.getStatusLineManager().setMessage("Edit mode: " +
- (getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + " " +
- "Insertion in pherogram: " +
- (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
- }
-
-
- private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) {
- Iterator<ShiftChange> iterator = model.shiftChangeIterator();
- List<Shift> shifts = new ArrayList<SingleReadAlignment.Shift>();
- while (iterator.hasNext()) {
- ShiftChange shiftChange = iterator.next();
- shifts.add(new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange()));
- }
- return shifts.toArray(new Shift[]{});
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void doSave(IProgressMonitor monitor) {
- if (getEditorInput() instanceof AlignmentEditorInput) {
- String taskName = "Saving alignment";
- monitor.beginTask(taskName, 3);
-
- //re-loading sequence to avoid session conflicts
- Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
- StringAdapter stringProvider = new StringAdapter(getEditableConsensusArea().getAlignmentModel(), false); // Throws an exception if a token has more than one character.
-
- // Write consensus sequence:
- SequenceString consensusSequenceObj = sequenceNode.getConsensusSequence();
- String newConsensusSequence = stringProvider.getSequence(
- getEditableConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME));
- if (consensusSequenceObj == null) {
- sequenceNode.setConsensusSequence(SequenceString.NewInstance(newConsensusSequence));
- }
- else {
- consensusSequenceObj.setString(newConsensusSequence);
- }
-
- // Write single reads:
- stringProvider.setUnderlyingProvider(getReadsArea().getAlignmentModel());
- sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values()); // Remove all reads that are not in the alignment anymore.
- Iterator<Integer> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
- while (iterator.hasNext()) {
- int id = iterator.next();
- SingleReadAlignment singleRead = cdmMap.get(id);
- if (singleRead == null) {
- throw new InternalError("Creating new reads from AlignmentEditor not implemented.");
- //TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved?
- //singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence);
- }
-
- singleRead.setEditedSequence(stringProvider.getSequence(id));
-
- PherogramArea pherogramArea = getPherogramArea(id);
- if (pherogramArea != null) {
- PherogramAreaModel model = pherogramArea.getModel();
- singleRead.setReverseComplement(model.getPherogramProvider() instanceof ReverseComplementPherogramProvider); // Works only if ReverseComplementPherogramProvider instances are not nested.
- singleRead.setShifts(convertToCDMShifts(getPherogramArea(id).getModel()));
- singleRead.setFirstSeqPosition(model.getFirstSeqPos());
- singleRead.setLeftCutPosition(model.getLeftCutPosition());
- singleRead.setRightCutPosition(model.getRightCutPosition());
- }
- }
-
- if (!conversationHolder.isBound()) {
- conversationHolder.bind();
- }
- monitor.worked(1);
-
- // Commit the conversation and start a new transaction immediately:
- conversationHolder.commit(true);
- monitor.worked(1);
-
- dirty = false;
- monitor.worked(1);
- monitor.done();
- firePropertyChange(PROP_DIRTY);
- }
- else {
- //TODO Throw exception as soon as testing period which allows unlinked AlignmentEditor is over.
- }
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#doSaveAs()
- */
- @Override
- public void doSaveAs() {}
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
- */
- @Override
- public void init(IEditorSite site, IEditorInput input) throws PartInitException {
- setSite(site);
- setInput(input);
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#isDirty()
- */
- @Override
- public boolean isDirty() {
- return dirty;
- }
-
-
- private void setDirty() {
- dirty = true;
- firePropertyChange(IEditorPart.PROP_DIRTY);
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
- */
- @Override
- public boolean isSaveAsAllowed() {
- return false; // "Save as" not allowed.
- }
-
-
- @Override
- public void setFocus() {
- if(conversationHolder!=null){
- conversationHolder.bind();
- }
- }
-
-
- public boolean isInsertMode() {
- return getAlignmentsContainer().getEditSettings().isInsert();
- }
-
-
- public boolean isInsertLeftInPherogram() {
- return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea();
- }
-
-
- public void toggleLeftRightInsertionInPherogram() {
- getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea();
- }
-
-
- public void toggleInsertOverwrite() {
- getAlignmentsContainer().getEditSettings().toggleInsert();
- }
-
-
- private String cutPherogram(boolean left) {
- SelectionModel selection = getReadsArea().getSelection();
- if (selection.getCursorHeight() != 1) {
- return "Cutting pherograms is only possible if exactly one row is selected.";
- }
- else {
- PherogramArea pherogramArea =
- getPherogramArea(getReadsArea().getSequenceOrder().idByIndex(selection.getCursorRow()));
- if (pherogramArea == null) {
- return "There is no pherogram attached to the current sequence.";
- }
- else {
- if (left) {
- if (pherogramArea.setLeftCutPositionBySelection()) {
- return null;
- }
- else {
- return "The left end of the selection lies outside the pherogram attached to this sequence.";
- }
- }
- else {
- if (pherogramArea.setRightCutPositionBySelection()) {
- return null;
- }
- else {
- return "The right end of the selection lies outside the pherogram attached to this sequence.";
- }
- }
- }
- }
- }
-
-
- public String cutPherogramLeft() {
- return cutPherogram(true);
- }
-
-
- public String cutPherogramRight() {
- return cutPherogram(false);
- }
-
-
- public void reverseComplementSelectedSequences() {
- SelectionModel selection = getReadsArea().getSelection();
- AlignmentModel<?> model = getReadsArea().getAlignmentModel();
- for (int row = selection.getFirstRow(); row < selection.getFirstRow() + selection.getCursorHeight(); row++) {
- int sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
- PherogramArea area = getPherogramArea(sequenceID);
- PherogramAreaModel pherogramAlignmentModel = area.getModel();
- AlignmentModelUtils.reverseComplement(model, sequenceID,
- pherogramAlignmentModel.editableIndexByBaseCallIndex(
- pherogramAlignmentModel.getLeftCutPosition()).getBeforeValidIndex(),
- pherogramAlignmentModel.editableIndexByBaseCallIndex(
- pherogramAlignmentModel.getRightCutPosition()).getAfterValidIndex());
- pherogramAlignmentModel.reverseComplement();
- }
- }
-
-
- /**
- * Recreates the whole consensus sequence from all single read sequences. The previous consensus
- * sequence is overwritte.
- */
- @SuppressWarnings("unchecked")
- public <T> void createConsensusSequence() {
- ConsensusSequenceArea area = getConsensusHintDataArea();
- AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
- int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
- int length = getReadsArea().getAlignmentModel().getMaxSequenceLength();
-
- Collection<T> tokens = new ArrayList<T>(length);
- for (int column = 0; column < length; column++) {
- tokens.add(model.getTokenSet().tokenByRepresentation(area.getConsensusToken(column)));
- }
-
- model.removeTokensAt(sequenceID, 0, model.getSequenceLength(sequenceID));
- model.insertTokensAt(sequenceID, 0, tokens);
- }
-
-
- /**
- * Updates the current consensus sequence by replacing gaps by the according consensus tokens
- * calculated from the single read sequences and extends the consensus sequence if necessary.
- */
- @SuppressWarnings("unchecked")
- public <T> void updateConsensusSequence() {
- ConsensusSequenceArea area = getConsensusHintDataArea();
- AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
- TokenSet<T> tokenSet = model.getTokenSet();
- int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
- int currentConsensusLength = model.getSequenceLength(sequenceID);
- int overallLength = getReadsArea().getAlignmentModel().getMaxSequenceLength();
-
- // Replace gaps by new information:
- for (int column = 0; column < currentConsensusLength; column++) {
- if (tokenSet.isGapToken(model.getTokenAt(sequenceID, column))) {
- T newToken = tokenSet.tokenByRepresentation(area.getConsensusToken(column));
- if (!tokenSet.isGapToken(newToken)) {
- model.setTokenAt(sequenceID, column, newToken);
- }
- }
- }
-
- // Append additional tokens:
- if (overallLength > currentConsensusLength) {
- Collection<T> tokens = new ArrayList<T>(overallLength);
- for (int column = currentConsensusLength; column < overallLength; column++) {
- tokens.add(tokenSet.tokenByRepresentation(area.getConsensusToken(column)));
- }
- model.appendTokens(sequenceID, tokens);
- }
- }
-
-
- public static PherogramProvider readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException {
- PherogramProvider result;
- InputStream stream = uri.toURL().openStream();
- try {
- result = new BioJavaPherogramProvider(ChromatogramFactory.create(stream));
- }
- finally {
- stream.close();
- }
- return result;
- }
-
-
- private String newReadName() {
- int index = 1;
- while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index)
- != AlignmentModel.NO_SEQUENCE_FOUND) {
-
- index++;
- }
- return DEFAULT_READ_NAME_PREFIX + index;
- }
-
-
- public void addRead(URI pherogramURI, boolean reverseComplemented) throws IOException, UnsupportedChromatogramFormatException {
- addRead(newReadName(), pherogramURI, reverseComplemented, null, null, null, null, null);
- }
-
-
- /**
- * Adds a new sequence with attached phergram data area to the reads alignment.
- * <p>
- * If {@code null} is specified as {@code editedSequence} the base call sequence from the pherogram will
- * be set as the edited sequence. If {@code null} is specified as {@code shifts} no shifts between the edited
- * and the base calls sequence are assumed.
- *
- * @param name the name of the new sequence
- * @param pherogramURI the URI where the associated pherogram file is located
- * @param reverseComplemented Specify {@code true} here, if the reverse complement of the pherogram data should
- * be added, {@code false} otherwise.
- * @param editedSequence the edited version of the base call sequence (May be {@code null}.)
- * @param shifts the alignment information that links the edited and the base call sequence (May be {@code null}.)
- * @return the sequence ID of the added read
- * @throws IOException if an error occurred when trying to read the pherogram file
- * @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported
- */
- public int addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
- Integer firstSeqPos, Integer leftCutPos, Integer rightCutPos, SingleReadAlignment.Shift[] shifts)
- throws IOException, UnsupportedChromatogramFormatException {
-
- AlignmentModel provider = getReadsArea().getAlignmentModel();
- PherogramProvider pherogramProvider = null;
- if (pherogramURI != null) {
- pherogramProvider = readPherogram(pherogramURI); // Must happen before a sequence is added, because it might throw an exception.
- if (reverseComplemented) {
- pherogramProvider = new ReverseComplementPherogramProvider(pherogramProvider);
- }
- }
-
- // Create sequence:
- provider.addSequence(name);
- int id = provider.sequenceIDByName(name);
-
- // Set edited sequence:
- Collection<Object> tokens = null; // First save tokens in a collection to avoid GUI updated for each token.
- if (editedSequence != null) {
- tokens = AlignmentModelUtils.charSequenceToTokenList(editedSequence, provider.getTokenSet());
- }
- else if (pherogramProvider != null) { // Copy base call sequence into alignment:
- tokens = new ArrayList<Object>();
- for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
- tokens.add(provider.getTokenSet().tokenByRepresentation(
- Character.toString(pherogramProvider.getBaseCall(i))));
- }
- setDirty();
- }
-
- if (tokens != null) { // If either an edited sequence or a pherogram URI was provided.
- provider.insertTokensAt(id, 0, tokens);
- // Create pherogram area:
- PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(),
- new PherogramAreaModel(pherogramProvider));
-
- // Set position properties and shifts:
- PherogramAreaModel model = pherogramArea.getModel();
- if ((firstSeqPos != null) && (leftCutPos != null)) {
- model.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos);
- }
- if (rightCutPos != null) {
- model.setRightCutPosition(rightCutPos);
- }
- if ((shifts != null) && (shifts.length > 0)) {
- for (int i = 0; i < shifts.length; i++) {
- model.addShiftChange(shifts[i].position, shifts[i].shift);
- }
- setDirty();
- }
-
- // Add pherogram area to GUI:
- pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea));
- getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
- }
-
- return id;
- }
-}
\ No newline at end of file
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2014 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.editor;
-
-
-import java.util.UUID;
-
-import org.eclipse.jface.resource.ImageDescriptor;
-import org.eclipse.ui.IEditorInput;
-import org.eclipse.ui.IPersistableElement;
-
-
-
-/**
- * @author pplitzner
- * @author Ben Stöver
- * @date 04.08.2014
- */
-public class AlignmentEditorInput implements IEditorInput {
- private static final String name = "AlignmentEditor";
-
-
- private final UUID sequenceNodeUuid;
-
-
- public AlignmentEditorInput(UUID sequenceNodeUuid) {
- super();
- this.sequenceNodeUuid = sequenceNodeUuid;
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.core.runtime.IAdaptable#getAdapter(java.lang.Class)
- */
- @Override
- public Object getAdapter(Class adapter) {
- // TODO Auto-generated method stub
- return null;
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.IEditorInput#exists()
- */
- @Override
- public boolean exists() {
- // TODO Auto-generated method stub
- return false;
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.IEditorInput#getImageDescriptor()
- */
- @Override
- public ImageDescriptor getImageDescriptor() {
- // TODO Auto-generated method stub
- return null;
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.IEditorInput#getName()
- */
- @Override
- public String getName() {
- return name;
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.IEditorInput#getPersistable()
- */
- @Override
- public IPersistableElement getPersistable() {
- return null;
- }
-
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.IEditorInput#getToolTipText()
- */
- @Override
- public String getToolTipText() {
- return name;
- }
-
-
- /**
- * Returns the {@link UUID} of the sequence CDM node that should be edited by the {@link AlignmentEditor} this object
- * is used with.
- *
- * @return the uuid of the CDM node to work on
- */
- public UUID getSequenceNodeUuid() {
- return sequenceNodeUuid;
- }
-
-
- @Override
- public int hashCode() {
- final int prime = 31;
- int result = 1;
- result = prime * result
- + ((sequenceNodeUuid == null) ? 0 : sequenceNodeUuid.hashCode());
- return result;
- }
-
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj) {
- return true;
- }
- if (obj == null) {
- return false;
- }
- if (getClass() != obj.getClass()) {
- return false;
- }
- AlignmentEditorInput other = (AlignmentEditorInput) obj;
- if (sequenceNodeUuid == null) {
- if (other.sequenceNodeUuid != null) {
- return false;
- }
- } else if (!sequenceNodeUuid.equals(other.sequenceNodeUuid)) {
- return false;
- }
- return true;
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.editor;
-
-
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
-import info.bioinfweb.tic.input.TICMouseAdapter;
-import info.bioinfweb.tic.input.TICMouseEvent;
-
-import org.eclipse.ui.PartInitException;
-
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler;
-
-
-
-/**
- * Listens to mouse events on data areas displaying a pherogram in {@link AlignmentEditor}.
- *
- * @author Ben Stöver
- * @date 25.11.2014
- */
-public class PherogramMouseListener extends TICMouseAdapter {
- private final PherogramArea area;
-
-
- public PherogramMouseListener(PherogramArea area) {
- super();
- this.area = area;
- }
-
-
- @Override
- public boolean mousePressed(TICMouseEvent event) {
- if (event.getClickCount() == 2) { // Double click
- try {
- ShowPherogramHandler.showPherogram(area.getModel());
- }
- catch (PartInitException e) {
- MessagingUtils.errorDialog("Unable to create pherogram view", null, e.getLocalizedMessage(),
- TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
- }
- return true;
- }
- else {
- return false;
- }
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.editor;
-
-
-import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;
-import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
-import info.bioinfweb.libralign.pherogram.view.PherogramView;
-import info.bioinfweb.tic.SWTComponentFactory;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.widgets.Composite;
-import org.eclipse.ui.PartInitException;
-import org.eclipse.ui.PlatformUI;
-import org.eclipse.ui.part.ViewPart;
-
-
-
-/**
- * Component that allows to view a pherogram without the distortion due to aligning it to a sequence as in
- * {@link AlignmentEditor}.
- *
- * @author Ben Stöver
- * @date Nov 20, 2014
- */
-public class PherogramViewPart extends ViewPart {
- public static final String ID = "eu.etaxonomy.taxeditor.molecular.PherogramView";
-
- private PherogramView pherogramView = null;
-
-
- public static PherogramViewPart createView(PherogramComponentModel model) throws PartInitException {
- PherogramViewPart view = (PherogramViewPart)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);
- view.getPherogramView().getTraceCurveView().setModel(model);
- view.getPherogramView().assignSize();
- return view;
- }
-
-
- public PherogramView getPherogramView() {
- if (pherogramView == null) {
- pherogramView = new PherogramView();
- pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(true);
- pherogramView.getTraceCurveView().setHorizontalScale(1);
- pherogramView.getTraceCurveView().setVerticalScale(100);
- pherogramView.getTraceCurveView().getFormats().setQualityOutputType(QualityOutputType.NONE); //TODO Make this user defined
- pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(false);
- }
- return pherogramView;
- }
-
-
- @Override
- public void createPartControl(Composite parent) {
- SWTComponentFactory.getInstance().getSWTComponent(getPherogramView(), parent, SWT.NONE);
- getPherogramView().assignSize();
- }
-
-
- @Override
- public void setFocus() {} // nothing to do
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.ui.IEditorPart;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-
-/**
- * Abstract implementation for all handlers triggering actions in an active instance of
- * {@link AlignmentEditor}.
- *
- * @author Ben Stöver
- * @date 19.06.2015
- */
-public abstract class AbstractAlignmentEditorHandler extends AbstractHandler {
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- doExecute(event, (AlignmentEditor)activeEditor);
- }
- return null;
- }
-
-
- public abstract void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException;
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
-import info.bioinfweb.libralign.pherogram.PherogramComponent;
-
-import java.util.Iterator;
-
-import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.ui.IWorkbenchPart;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
-
-
-
-/**
- * Abstract handler implementation allows to performs the concrete operation either on an instance of
- * {@link PherogramViewPart} or all {@link AlignmentArea}s inside an instance of {@link AlignmentEditor}.
- *
- * @author Ben Stöver
- * @date 23.06.2015
- */
-public abstract class AbstractPherogramComponentHandler extends AbstractHandler {
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
- IWorkbenchPart activePart = AbstractUtility.getActivePart();
-
- if (activePart instanceof AlignmentEditor) {
- AlignmentEditor editor = (AlignmentEditor)activePart;
- Iterator<Integer> idIterator = editor.getReadsArea().getAlignmentModel().sequenceIDIterator();
- while (idIterator.hasNext()) {
- PherogramArea area = editor.getPherogramArea(idIterator.next());
- if (area != null) {
- doExecute(event, area);
- }
- }
- }
- else if (activePart instanceof PherogramViewPart) {
- doExecute(event, ((PherogramViewPart)activePart).getPherogramView().getTraceCurveView());
- }
- return null;
- }
-
-
- public abstract void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException;
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import info.bioinfweb.libralign.pherogram.PherogramComponent;
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-
-
-/**
- * Switches between the quality output types available for components displaying pherograms.
- *
- * @author Ben Stöver
- * @date 19.06.2015
- */
-public class ChangePherogramQualityOutputType extends AbstractPherogramComponentHandler {
- @Override
- public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {
- component.getFormats().changeQualityOutputType();
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-
-/**
- * Handler that creates the consensus sequence from all single read sequences in the active instance
- * of {@link AlignmentEditor}. A previously present consensus sequence will be overwritten.
- *
- * @author Ben Stöver
- * @date 19.06.2015
- * @see UpdateConsensusSequenceHandler
- * @see AlignmentEditor#createConsensusSequence()
- */
-public class CreateConsensusSequenceHandler extends AbstractAlignmentEditorHandler {
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.createConsensusSequence();
- }
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-/**
- * Handler that cuts the base call sequence of a pherogram attached to the current sequence on the left
- * of the current selection or cursor position.
- *
- * @author Ben Stöver
- * @date 15.06.2015
- */
-public class CutPherogramLeftHandler extends AbstractAlignmentEditorHandler {
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- String errorMessage = editor.cutPherogramLeft();
- if (errorMessage != null) {
- MessagingUtils.errorDialog("Unable to cut base call sequence", this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);
- }
- }
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-/**
- * Handler that cuts the base call sequence of a pherogram attached to the current sequence on the right
- * of the current selection or cursor position.
- *
- * @author BenStoever
- * @date 15.06.2015
- */
-public class CutPherogramRightHandler extends AbstractAlignmentEditorHandler {
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- String errorMessage = editor.cutPherogramRight();
- if (errorMessage != null) {
- MessagingUtils.errorDialog("Unable to cut base call sequence", this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);
- }
- }
-}
+++ /dev/null
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.jface.viewers.ISelection;
-import org.eclipse.jface.viewers.TreeNode;
-import org.eclipse.ui.PartInitException;
-import org.eclipse.ui.handlers.HandlerUtil;
-
-import eu.etaxonomy.cdm.model.molecular.Sequence;
-import eu.etaxonomy.taxeditor.editor.EditorUtil;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditorInput;
-
-
-
-/**
- * Opens the alignment editor from the CDM tree.
- *
- * @author Ben Stöver
- * @author pplitzner
- */
-public class EditSequenceHandler extends AbstractHandler {
-
- org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(EditSequenceHandler.class);
-
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
- ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
- TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
- if(treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence){
- AlignmentEditorInput input = new AlignmentEditorInput(((Sequence)treeNodeOfSelection.getValue()).getUuid()); //TODO Should there always be a new instance created here? What if the specified CDM node is already opened in an AlignmentEditor? => Possible create Singleton that keeps instances by sequence objects in a map.
- try {
- TaxeditorMolecularPlugin.getDefault().getWorkbench()
- .getActiveWorkbenchWindow().getActivePage().openEditor(input, AlignmentEditor.ID);
- }
- catch (PartInitException e) {
- logger.error("Could not open AlignmentEditor", e);
- }
- }
- return null;
- }
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import java.net.URL;
-
-import org.eclipse.core.runtime.FileLocator;
-import org.eclipse.core.runtime.Path;
-import org.eclipse.jface.resource.ImageDescriptor;
-
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-
-
-
-/**
- * Implements shared functionality for handler implementations using tool bar icons.
- *
- * @author Ben Stöver
- * @date 15.06.2015
- */
-public class HandlerTools { //TODO Move this class or method somewhere else?
- public static ImageDescriptor createImageDescriptor(String iconName) {
- URL url = FileLocator.find(TaxeditorMolecularPlugin.getDefault().getBundle(),
- new Path("icons/" + iconName), null);
- if (url != null) {
- return ImageDescriptor.createFromURL(url);
- }
- else {
- throw new InternalError("Icon \"" + iconName + "\" could not be loaded."); //TODO Throw other type of exception?
- }
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import java.io.File;
-import java.io.IOException;
-
-import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
-import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.swt.widgets.FileDialog;
-import org.eclipse.ui.IEditorPart;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-/**
- * Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditor}.
- *
- * @author Ben Stöver
- * @author pplitzner
- */
-public class LoadPherogramHandler extends AbstractHandler {
- //TODO Change so that also URIs which do not point to files can be specified.
-
- /* (non-Javadoc)
- * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
- */
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- AlignmentEditor alignmentEditor = (AlignmentEditor)activeEditor;
-
- FileDialog fileDialog = new FileDialog(alignmentEditor.getSite().getShell());
- fileDialog.setText("Import pherogram into contig alignment");
- fileDialog.setFilterNames(new String[]{"All supported formats", "AB1 pherogram files", "SCF pherogram files", "All files"});
- fileDialog.setFilterExtensions(new String[]{"*.ab1;*.scf", "*.ab1", "*.scf", "*.*"});
-
- String path = fileDialog.open();
- if (path != null) {
- try {
- alignmentEditor.addRead(new File(path).toURI(), false);
- }
- catch (UnsupportedChromatogramFormatException e) {
- MessagingUtils.errorDialog("Unsupported format", this, "The format of the pherogram file \"" + path +
- "\" is not supported. (Only AB1 and SCF are supported.)", TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
- }
- catch (IOException e) {
- MessagingUtils.errorDialog("Unsupported format", this,
- "An IO error occurred while trying to read the file \"" + path + "\".",
- TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
- }
- }
- }
- return null;
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-
-/**
- * Reverse complements the single read sequence in an active {@link AlignmentEditor}, where the alignment cursor
- * is currently located.
- *
- * @author Ben Stöver
- */
-public class ReverseComplementHandler extends AbstractAlignmentEditorHandler {
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.reverseComplementSelectedSequences();
- }
-}
+++ /dev/null
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
-
-import java.net.URI;
-
-import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.jface.viewers.ISelection;
-import org.eclipse.jface.viewers.TreeNode;
-import org.eclipse.ui.PartInitException;
-import org.eclipse.ui.handlers.HandlerUtil;
-
-import eu.etaxonomy.cdm.model.media.MediaUtils;
-import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.taxeditor.editor.EditorUtil;
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
-
-
-
-/**
- * Displays an undistorted pherogram with {@link PherogramViewPart}.
- *
- * @author Ben Stöver
- *
- */
-public class ShowPherogramHandler extends AbstractHandler {
- public static void showPherogram(PherogramComponentModel model) throws PartInitException {
- PherogramViewPart.createView(model);
- }
-
-
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
- ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
- TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
- if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {
- //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?
- try {
- SingleRead singleRead = (SingleRead)treeNodeOfSelection.getValue();
- URI uri = null;
- if (singleRead.getPherogram() != null) { // Pherogram objects without URI are possible.
- uri = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri();
- }
-
- if (uri == null) {
- MessagingUtils.messageDialog("No pherogram available", this,
- "The selected read does not have an associated pherogram.");
- }
- else {
- showPherogram(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));
- }
- }
- catch (Exception e) {
- MessagingUtils.errorDialog("Error", null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,
- e, false);
- }
- }
- return null;
- }
-}
+++ /dev/null
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.expressions.PropertyTester;
-import org.eclipse.jface.viewers.IStructuredSelection;
-import org.eclipse.jface.viewers.TreeNode;
-
-import eu.etaxonomy.cdm.model.molecular.Sequence;
-import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.taxeditor.editor.EditorUtil;
-
-
-
-/**
- * Tests types of specimens to add items to the context menu.
- *
- * @author pplitzner
- * @author BenStoever
- */
-public class SpecimenPropertyTester extends PropertyTester {
- private static final String SEQUENCE = "isSequence";
- private static final String SINGLE_READ = "isSingleRead";
-
-
- public SpecimenPropertyTester() {}
-
-
- /* (non-Javadoc)
- * @see org.eclipse.core.expressions.IPropertyTester#test(java.lang.Object, java.lang.String, java.lang.Object[], java.lang.Object)
- */
- /** {@inheritDoc} */
- @Override
- public boolean test(Object receiver, String property, Object[] args, Object expectedValue) {
- if (receiver instanceof IStructuredSelection) {
- IStructuredSelection selection = (IStructuredSelection) receiver;
- TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(selection);
- if (treeNodeOfSelection!=null) {
- if (SEQUENCE.equals(property)) {
- return isSequence(treeNodeOfSelection.getValue());
- }
- else if (SINGLE_READ.equals(property)) {
- return isSingleReadAlignment(treeNodeOfSelection.getValue());
- }
- }
- }
- return false;
- }
-
-
- private boolean isSequence(Object object) {
- return (object instanceof Sequence);
- }
-
-
- private boolean isSingleReadAlignment(Object object) {
- return (object instanceof SingleRead);
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import java.util.Map;
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.jface.resource.ImageDescriptor;
-import org.eclipse.ui.IEditorPart;
-import org.eclipse.ui.PlatformUI;
-import org.eclipse.ui.commands.ICommandService;
-import org.eclipse.ui.commands.IElementUpdater;
-import org.eclipse.ui.menus.UIElement;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-/**
- * Switches an {@link AlignmentEditor} between insertion and overwrite mode.
- *
- * @author Ben Stöver
- * @date 04.12.2014
- */
-public class ToggleInsertOverwriteHandler extends AbstractAlignmentEditorHandler implements IElementUpdater {
- public static final String COMMAND_ID =
- "eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite";
-
-
- private final ImageDescriptor INSERT_DESCRIPTOR = HandlerTools.createImageDescriptor("insert-16x16.png");
- private final ImageDescriptor OVERWRITE_DESCRIPTOR = HandlerTools.createImageDescriptor("overwrite-16x16.png");
-
-
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.toggleInsertOverwrite();
- }
-
-
- @Override
- public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- if (((AlignmentEditor)activeEditor).isInsertMode()) {
- element.setIcon(INSERT_DESCRIPTOR);
- element.setText("INS");
- element.setTooltip("Click to switch to overwrite mode");
- }
- else {
- element.setIcon(OVERWRITE_DESCRIPTOR);
- element.setText("OVR");
- element.setTooltip("Click to switch to insertion mode");
- }
- ((ICommandService)PlatformUI.getWorkbench().getService(ICommandService.class)).refreshElements(
- ToggleLeftRightInsertionHandler.COMMAND_ID, null);
- }
- }
-}
+++ /dev/null
-/**
- * Copyright (C) 2007 EDIT
- * European Distributed Institute of Taxonomy
- * http://www.e-taxonomy.eu
- *
- * The contents of this file are subject to the Mozilla Public License Version 1.1
- * See LICENSE.TXT at the top of this package for the full license terms.
- */
-
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-import java.util.Map;
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-import org.eclipse.jface.resource.ImageDescriptor;
-import org.eclipse.ui.IEditorPart;
-import org.eclipse.ui.commands.IElementUpdater;
-import org.eclipse.ui.menus.UIElement;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-/**
- * Switches an {@link AlignmentEditor} between insertion in the base sequence to
- * the left or to the right.
- *
- * @author Ben Stöver
- * @date 04.12.2014
- */
-public class ToggleLeftRightInsertionHandler extends AbstractAlignmentEditorHandler implements IElementUpdater {
- public static final String COMMAND_ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion";
-
-
- private final ImageDescriptor INSERT_LEFT_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-left-16x16.png");
- private final ImageDescriptor INSERT_RIGHT_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-right-16x16.png");
- private final ImageDescriptor INSERT_LEFT_DISABLED_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-left-disabled-16x16.png");
- private final ImageDescriptor INSERT_RIGHT_DISABLED_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-right-disabled-16x16.png");
-
-
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.toggleLeftRightInsertionInPherogram();
- }
-
-
- @Override
- public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- setBaseEnabled(((AlignmentEditor)activeEditor).isInsertMode());
- if (((AlignmentEditor)activeEditor).isInsertLeftInPherogram()) {
- element.setIcon(INSERT_LEFT_DESCRIPTOR);
- element.setDisabledIcon(INSERT_LEFT_DISABLED_DESCRIPTOR);
- element.setText("Left");
- element.setTooltip("Switch to insert pherogram distorsions right of future edits.");
- }
- else {
- element.setIcon(INSERT_RIGHT_DESCRIPTOR);
- element.setDisabledIcon(INSERT_RIGHT_DISABLED_DESCRIPTOR);
- element.setText("Right");
- element.setTooltip("Switch to insert pherogram distorsions left of future edits.");
- }
- }
- }
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import info.bioinfweb.libralign.pherogram.PherogramComponent;
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-
-
-/**
- * @author BenStoever
- * @date 23.06.2015
- *
- */
-public class ToggleShowPherogramBaseCallLinesHandler extends AbstractPherogramComponentHandler {
- @Override
- public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {
- component.getFormats().toggleShowBaseCallLines();
- }
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import info.bioinfweb.libralign.pherogram.PherogramComponent;
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
-
-
-
-
-/**
- * Toggles whether probability values (substitution, overcall and undercall) should be displayed
- * in pherogram areas of {@link AlignmentEditor} or {@link PherogramViewPart}.
- *
- * @author Ben Stöver
- * @date 23.06.2015
- */
-public class ToggleShowPherogramProbabilitiesHandler extends AbstractPherogramComponentHandler {
- @Override
- public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {
- component.getFormats().toggleShowProbabilityValues();
- }
-}
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-
-
-
-
-public class UpdateConsensusSequenceHandler extends AbstractAlignmentEditorHandler {
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.updateConsensusSequence();
- }
-}
+++ /dev/null
-// $Id$
-/**
- * Copyright (C) 2015 EDIT
- * European Distributed Institute of Taxonomy
- * http://www.e-taxonomy.eu
- *
- * The contents of this file are subject to the Mozilla Public License Version 1.1
- * See LICENSE.TXT at the top of this package for the full license terms.
- */
-/**
- * Contains handlers that trigger actions in an active instance of
- * {@link main.java.eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor}. Handlers opening
- * an alignment editor or pherogram view are not contained in here.
- *
- * @author Ben Stöver
- */
-package eu.etaxonomy.taxeditor.molecular.handler;
\ No newline at end of file
<dynamic
class="eu.etaxonomy.taxeditor.navigation.RecentNamesContributionItem"
id="eu.etaxonomy.taxeditor.navigation.recentnames">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</dynamic>
</menuContribution>
<menuContribution
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.navigation.navigator">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="org.eclipse.ui.views.showView"
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.navigation.key.polytomous.polytomousKeyViewPart">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
</menuContribution>
<menuContribution
id="eu.etaxonomy.taxeditor.navigation.search.toolbar">
<control
class="eu.etaxonomy.taxeditor.navigation.search.SearchBar">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</control>
</toolbar>
</menuContribution>
commandId="eu.etaxonomy.taxeditor.navigation.command.create.taxonNode"
label="%command.label.13"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<separator
name="eu.etaxonomy.navigation.menu.new.separator1"
id="eu.etaxonomy.taxeditor.navigation.create.classificationHandler"
label="%command.label.14"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
</menuContribution>
<menuContribution
</with>
</definition>
</extension>
+ <extension
+ point="eu.etaxonomy.taxeditor.store.cdmViewer">
+ <cdmViewer
+ class="eu.etaxonomy.taxeditor.navigation.NavigationCdmViewer">
+ </cdmViewer>
+ </extension>
</plugin>
import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;
import eu.etaxonomy.cdm.api.service.IClassificationService;
import eu.etaxonomy.cdm.model.common.CdmBase;
+
import eu.etaxonomy.cdm.model.taxon.TaxonNaturalComparator;
-import eu.etaxonomy.cdm.model.taxon.TaxonNode;
-import eu.etaxonomy.cdm.model.taxon.TaxonNodeByRankAndNameComparator;
+import eu.etaxonomy.cdm.model.taxon.TaxonNodeComparator;
import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap;
import eu.etaxonomy.taxeditor.model.DataChangeBridge;
import eu.etaxonomy.taxeditor.model.IDataChangeBehavior;
/** {@inheritDoc} */
@Override
protected IAdaptable getInitialInput() {
- Comparator<TaxonNode> comparator;
+ Comparator comparator;
if (PreferencesUtil.getSortNodesNaturally()){
comparator = new TaxonNaturalComparator();
} else{
- comparator = new TaxonNodeByRankAndNameComparator();
+ comparator = new TaxonNodeComparator();
}
TaxonNodeNavigatorComparator viewerComparator = new TaxonNodeNavigatorComparator(comparator);
this.getCommonViewer().setComparator(viewerComparator);
package eu.etaxonomy.taxeditor.navigation.navigator;
+import java.util.Arrays;
import java.util.Comparator;
+
import org.eclipse.jface.viewers.Viewer;
import org.eclipse.jface.viewers.ViewerComparator;
+
+import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+
import eu.etaxonomy.cdm.model.taxon.TaxonNaturalComparator;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.taxeditor.ui.section.supplemental.IdentifiableSourceElement;
public class TaxonNodeNavigatorComparator extends ViewerComparator{
- public TaxonNodeNavigatorComparator(Comparator<TaxonNode> comparator){
+ public TaxonNodeNavigatorComparator(Comparator<TaxonBase> comparator){
super(comparator);
}
ITaxonTreeNode treeNode = treeNodes.iterator().next();
ITaxonTreeNode taxonNode =treeNode;
TaxonNodeDeletionConfigurator configNodes = new TaxonNodeDeletionConfigurator();
+ //configNodes.setDeleteTaxon(false);
if (taxonNode instanceof Classification && taxonNode.hasChildNodes()){
if(!DeleteConfiguratorDialog.openConfirmWithConfigurator(config, HandlerUtil.getActiveShell(event), "Confirm Deletion", "Do you really want to delete the classification? The tree has children, they will be deleted, too.")){
return null;
}
}else{
- if(!DeleteConfiguratorDialog.openConfirmWithConfigurator(config, HandlerUtil.getActiveShell(event), "Confirm Deletion", "Do you really want to delete the selected node?")){
+ if(!DeleteConfiguratorDialog.openConfirmWithConfigurator(configNodes, HandlerUtil.getActiveShell(event), "Confirm Deletion", "Do you really want to delete the selected node?")){
return null;
- }
+ }
+ config.setTaxonNodeConfig(configNodes);
}
}
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.view.derivateSearch.DerivateSearchView">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<separator
name="eu.etaxonomy.taxeditor.store.showViewMenu.details"
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.view.detail">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<command
commandId="org.eclipse.ui.views.showView"
name="org.eclipse.ui.views.showView.viewId"
value="eu.etaxonomy.taxeditor.view.supplementalData">
</parameter>
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<!-- Originally used by validation framework, currently not in use -->
<!-- <command
</parameter>
<visibleWhen
checkEnabled="true">
- <and>
- <reference
- definitionId="isShowExperimentalFeatures">
- </reference>
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </and>
+ <reference
+ definitionId="isShowExperimentalFeatures">
+ </reference>
</visibleWhen>
</command>
</menu>
</menuContribution>
+ <menuContribution
+ class="eu.etaxonomy.taxeditor.editor.definedterm.DefinedTermMenuFactory"
+ locationURI="menu:org.eclipse.ui.main.menu.window?before=eu.etaxonomy.taxeditor.application.windowMenu.last">
+ </menuContribution>
<menuContribution
locationURI="menu:org.eclipse.ui.main.menu.file?after=eu.etaxonomy.taxeditor.application.filemenu.io">
<command
commandId="eu.etaxonomy.taxeditor.store.operations.showLoginWindow"
label="%command.label.5"
style="push">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
</command>
<separator
name="eu.etaxonomy.taxeditor.application.filemenu.login"
</visibleWhen>
</command>
</menuContribution>
- <menuContribution
- allPopups="false"
- locationURI="menu:org.eclipse.ui.main.menu.window?before=eu.etaxonomy.taxeditor.application.windowMenu.last">
- <dynamic
- class="eu.etaxonomy.taxeditor.editor.definedterm.DefinedTermMenu"
- id="eu.etaxonomy.taxeditor.editor.definedterm.DefinedTermMenu">
- <visibleWhen
- checkEnabled="true">
- <reference
- definitionId="isCdmStoreConnected">
- </reference>
- </visibleWhen>
- </dynamic>
- </menuContribution>
</extension>
<extension
point="org.eclipse.ui.handlers">
</annotation>
<complexType>
<sequence>
- <element ref="cdmViewer" minOccurs="0" maxOccurs="unbounded"/>
- <element ref="viewCommandMapping" minOccurs="0" maxOccurs="unbounded"/>
+ <element ref="cdmViewer" minOccurs="1" maxOccurs="unbounded"/>
</sequence>
<attribute name="point" type="string" use="required">
<annotation>
</complexType>
</element>
- <element name="viewCommandMapping">
- <annotation>
- <documentation>
- Maps a viewing class, like editors or views, to a command which opens it.
- </documentation>
- </annotation>
- <complexType>
- <attribute name="commandId" type="string" use="required">
- <annotation>
- <documentation>
- The command which opens the viewer to show the selected object
- </documentation>
- <appInfo>
- <meta.attribute kind="identifier" basedOn="org.eclipse.ui.commands/command/@id"/>
- </appInfo>
- </annotation>
- </attribute>
- <attribute name="viewerName" type="string">
- <annotation>
- <documentation>
- The name of the viewer which shows the selected element
- </documentation>
- </annotation>
- </attribute>
- <attribute name="selection" type="string" use="required">
- <annotation>
- <documentation>
- The class of the selected element
- </documentation>
- <appInfo>
- <meta.attribute kind="java"/>
- </appInfo>
- </annotation>
- </attribute>
- </complexType>
- </element>
-
<annotation>
<appInfo>
<meta.section type="since"/>
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2009 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-
-package eu.etaxonomy.taxeditor.editor.definedterm;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.EnumSet;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.eclipse.jface.action.IContributionItem;
-import org.eclipse.jface.action.MenuManager;
-import org.eclipse.jface.action.Separator;
-import org.eclipse.swt.SWT;
-import org.eclipse.ui.PlatformUI;
-import org.eclipse.ui.actions.CompoundContributionItem;
-import org.eclipse.ui.menus.CommandContributionItem;
-import org.eclipse.ui.menus.CommandContributionItemParameter;
-
-import eu.etaxonomy.cdm.model.common.TermType;
-
-/**
- * Menu used in the store plugin xml to dynamically generate menu (sub-menu) contribution items
- * for term types which when clicked open the defined term editor for the chosen term type
- *
- * @author pplitzner
- * @date 21 Jul 2015
- *
- */
-
-public class DefinedTermMenu extends CompoundContributionItem {
-
-
- @Override
- protected IContributionItem[] getContributionItems() {
- Collection<IContributionItem> items = new ArrayList<IContributionItem>();
- MenuManager dtMenuManager =
- new MenuManager("Term Editor","eu.etaxonomy.taxeditor.store.definedTermEditorMenu");
-
- dtMenuManager.setVisible(true);
-
- items.add(dtMenuManager);
- List<TermType> ttList = new ArrayList<TermType>(EnumSet.allOf(TermType.class));
- Collections.sort(ttList,new SortByTermTypeMessage());
- for (TermType tt : ttList)
- {
- // if term type has a parent, do not add it
- // it will be added in the recursive call
- if(tt.getKindOf() == null) {
- IContributionItem ici = addChildTermsToMenuManager(tt);
- if(ici != null) {
- dtMenuManager.add(ici);
- }
- }
- }
- return items.toArray(new IContributionItem[]{});
- }
-
- private IContributionItem addChildTermsToMenuManager(TermType termType) {
-
- //FIXME : need a better way to find out if a term type can be editable (ticket 3853)
- if(termType.getEmptyDefinedTermBase() != null) {
- Set<TermType> children = termType.getGeneralizationOf();
- // term type has no children, so create menu item
- if(children.isEmpty()) {
- return createMenuItem(termType);
- }
- // term type has children, so create sub menu
- MenuManager dtMenuManager =
- new MenuManager(termType.getMessage(),"eu.etaxonomy.taxeditor.store." + termType.getKey() + "Menu");
- dtMenuManager.setVisible(true);
- dtMenuManager.add(createDefaultMenuItem(termType));
-
- Separator sep = new Separator();
- dtMenuManager.add(sep);
- // add child items to the sub menu
- for(TermType tt : children) {
- IContributionItem item = addChildTermsToMenuManager(tt);
- if(item != null) {
- dtMenuManager.add(item);
- }
- }
- return dtMenuManager;
- } else {
- return null;
- }
-
- }
-
- private CommandContributionItem createMenuItem(TermType termType) {
-
- Map<String, String> params = new HashMap<String, String>();
- params.put("eu.etaxonomy.taxeditor.store.openDefinedTermEditor.termTypeUuid",
- termType.getUuid().toString());
-
- CommandContributionItemParameter p = new CommandContributionItemParameter(
- PlatformUI.getWorkbench(),
- "",
- "eu.etaxonomy.taxeditor.store.openDefinedTermEditor",
- params,
- null,
- null,
- null,
- termType.getMessage(),
- "",
- "",
- SWT.PUSH,
- "",
- true);
-
- CommandContributionItem item = new CommandContributionItem(p);
- return item;
-
- }
-
- private CommandContributionItem createDefaultMenuItem(TermType termType) {
-
- Map<String, String> params = new HashMap<String, String>();
- params.put("eu.etaxonomy.taxeditor.store.openDefinedTermEditor.termTypeUuid",
- termType.getUuid().toString());
-
- CommandContributionItemParameter p = new CommandContributionItemParameter(
- PlatformUI.getWorkbench(),
- "",
- "eu.etaxonomy.taxeditor.store.openDefinedTermEditor",
- params,
- null,
- null,
- null,
- "Other " + termType.getMessage() + "s",
- "",
- "",
- SWT.PUSH,
- "",
- true);
-
-
-
- CommandContributionItem item = new CommandContributionItem(p);
- return item;
-
- }
-
- private class SortByTermTypeMessage implements Comparator<TermType> {
- @Override
- public int compare(TermType t1, TermType t2) {
- return t1.getMessage().compareTo(t2.getMessage());
- }
- }
-
-
-}
// $Id$
/**
* Copyright (C) 2009 EDIT
-* European Distributed Institute of Taxonomy
+* European Distributed Institute of Taxonomy
* http://www.e-taxonomy.eu
-*
+*
* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
/**
* Menu factory used in the store plugin xml to dynamically generate menu (sub-menu) contribution items
* for term types which when clicked open the defined term editor for the chosen term type
- *
+ *
* @author c.mathew
* @date 18 Jul 2013
*
*/
-public class DefinedTermMenuFactory extends ExtensionContributionFactory {
-
+public class DefinedTermMenuFactory extends ExtensionContributionFactory {
+
@Override
public void createContributionItems(IServiceLocator serviceLocator,
- IContributionRoot additions) {
- MenuManager dtMenuManager =
- new MenuManager("Term Editor","eu.etaxonomy.taxeditor.store.definedTermEditorMenu");
-
- dtMenuManager.setVisible(true);
-
- additions.addContributionItem(dtMenuManager, null);
- List<TermType> ttList = new ArrayList<TermType>(EnumSet.allOf(TermType.class));
- Collections.sort(ttList,new SortByTermTypeMessage());
- for (TermType tt : ttList)
- {
- // if term type has a parent, do not add it
- // it will be added in the recursive call
- if(tt.getKindOf() == null) {
- IContributionItem ici = addChildTermsToMenuManager(tt, serviceLocator);
- if(ici != null) {
- dtMenuManager.add(ici);
- }
- }
- }
+ IContributionRoot additions) {
+
+ MenuManager dtMenuManager =
+ new MenuManager("Term Editor","eu.etaxonomy.taxeditor.store.definedTermEditorMenu");
+
+ dtMenuManager.setVisible(true);
+
+ additions.addContributionItem(dtMenuManager, null);
+ List<TermType> ttList = new ArrayList<TermType>(EnumSet.allOf(TermType.class));
+ Collections.sort(ttList,new SortByTermTypeMessage());
+ for (TermType tt : ttList)
+ {
+ // if term type has a parent, do not add it
+ // it will be added in the recursive call
+ if(tt.getKindOf() == null) {
+ IContributionItem ici = addChildTermsToMenuManager(tt, serviceLocator);
+ if(ici != null) {
+ dtMenuManager.add(ici);
+ }
+ }
+ }
}
-
+
private IContributionItem addChildTermsToMenuManager(TermType termType, IServiceLocator serviceLocator) {
-
+
//FIXME : need a better way to find out if a term type can be editable (ticket 3853)
if(termType.getEmptyDefinedTermBase() != null) {
Set<TermType> children = termType.getGeneralizationOf();
// term type has no children, so create menu item
- if(children.isEmpty()) {
+ if(children.isEmpty()) {
return createMenuItem(termType, serviceLocator);
}
- // term type has children, so create sub menu
- MenuManager dtMenuManager =
- new MenuManager(termType.getMessage(),"eu.etaxonomy.taxeditor.store." + termType.getKey() + "Menu");
+ // term type has children, so create sub menu
+ MenuManager dtMenuManager =
+ new MenuManager(termType.getMessage(),"eu.etaxonomy.taxeditor.store." + termType.getKey() + "Menu");
dtMenuManager.setVisible(true);
dtMenuManager.add(createDefaultMenuItem(termType, serviceLocator));
Separator sep = new Separator();
dtMenuManager.add(sep);
// add child items to the sub menu
- for(TermType tt : children) {
+ for(TermType tt : children) {
IContributionItem item = addChildTermsToMenuManager(tt,serviceLocator);
- if(item != null) {
+ if(item != null) {
dtMenuManager.add(item);
- }
- }
+ }
+ }
return dtMenuManager;
} else {
return null;
}
-
+
}
-
+
private CommandContributionItem createMenuItem(TermType termType, IServiceLocator serviceLocator) {
-
+
Map<String, String> params = new HashMap<String, String>();
params.put("eu.etaxonomy.taxeditor.store.openDefinedTermEditor.termTypeUuid",
- termType.getUuid().toString());
-
+ termType.getUuid().toString());
+
CommandContributionItemParameter p = new CommandContributionItemParameter(
- serviceLocator,
+ serviceLocator,
"",
"eu.etaxonomy.taxeditor.store.openDefinedTermEditor",
params,
null,
termType.getMessage(),
"",
- "",
+ "",
SWT.PUSH,
"",
true);
-
- CommandContributionItem item = new CommandContributionItem(p);
+
+ CommandContributionItem item = new CommandContributionItem(p);
return item;
-
+
}
-
+
private CommandContributionItem createDefaultMenuItem(TermType termType, IServiceLocator serviceLocator) {
-
+
Map<String, String> params = new HashMap<String, String>();
params.put("eu.etaxonomy.taxeditor.store.openDefinedTermEditor.termTypeUuid",
- termType.getUuid().toString());
-
+ termType.getUuid().toString());
+
CommandContributionItemParameter p = new CommandContributionItemParameter(
- serviceLocator,
+ serviceLocator,
"",
"eu.etaxonomy.taxeditor.store.openDefinedTermEditor",
params,
null,
"Other " + termType.getMessage() + "s",
"",
- "",
+ "",
SWT.PUSH,
"",
true);
-
-
-
- CommandContributionItem item = new CommandContributionItem(p);
+
+
+
+ CommandContributionItem item = new CommandContributionItem(p);
return item;
-
+
}
-
+
private class SortByTermTypeMessage implements Comparator<TermType> {
- @Override
- public int compare(TermType t1, TermType t2) {
+ public int compare(TermType t1, TermType t2) {
return t1.getMessage().compareTo(t2.getMessage());
}
}
-
+
}
import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
import eu.etaxonomy.cdm.api.service.config.TaxonBaseDeletionConfigurator;
+import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator;
/**
* Abstract subclass of MessageDialog providing the functionality to configure
}
else if(configurator instanceof SpecimenDeleteConfigurator){
composite.addConfiguratorComposite(new DeleteSpecimenConfiguratorComposite((SpecimenDeleteConfigurator) configurator, composite.getSectionConfigure(), SWT.NONE));
+ } else if(configurator instanceof TaxonNodeDeletionConfigurator){
+ composite.addConfiguratorComposite(new DeleteNodeConfiguratorComposite((TaxonNodeDeletionConfigurator) configurator, composite.getSectionConfigure(), SWT.NONE));
}
+
return composite;
}
--- /dev/null
+package eu.etaxonomy.taxeditor.ui.dialog.deleteConfigurator;
+/**
+* Copyright (C) 2015 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+import org.eclipse.core.databinding.DataBindingContext;
+import org.eclipse.core.databinding.beans.PojoProperties;
+import org.eclipse.core.databinding.observable.value.IObservableValue;
+import org.eclipse.jface.databinding.swt.WidgetProperties;
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.widgets.Button;
+import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Display;
+import org.eclipse.ui.forms.widgets.FormToolkit;
+import org.eclipse.swt.events.DisposeEvent;
+import org.eclipse.swt.events.DisposeListener;
+import org.eclipse.swt.layout.RowLayout;
+
+import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
+import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator;
+/**
+ * @author kluther
+ * @date Jul 13, 2015
+ *
+ */
+public class DeleteNodeConfiguratorComposite extends Composite {
+ // $Id$
+
+ private final DataBindingContext m_bindingContext;
+
+ private final FormToolkit toolkit = new FormToolkit(Display.getCurrent());
+ private final TaxonNodeDeletionConfigurator configurator;
+ private final Button btnDeleteTaxon;
+
+
+ /**
+ * Create the composite.
+ * @param parent
+ * @param style
+ */
+ public DeleteNodeConfiguratorComposite(TaxonNodeDeletionConfigurator configurator, Composite parent, int style) {
+ super(parent, style);
+ this.configurator = configurator;
+ addDisposeListener(new DisposeListener() {
+ @Override
+ public void widgetDisposed(DisposeEvent e) {
+ toolkit.dispose();
+ }
+ });
+ toolkit.paintBordersFor(this);
+ setLayout(new RowLayout(SWT.VERTICAL));
+ setBackground(getBackground());
+
+ btnDeleteTaxon = new Button(this, SWT.CHECK);
+ btnDeleteTaxon.setText("Delete taxon if possible");
+
+ m_bindingContext = initDataBindings();
+
+ }
+
+ protected DataBindingContext initDataBindings() {
+ DataBindingContext bindingContext = new DataBindingContext();
+ //
+ IObservableValue observeSelectionBtnDeleteTaxonObserveWidget = WidgetProperties.selection().observe(btnDeleteTaxon);
+ IObservableValue deleteTaxonIfPossibleConfiguratorObserveValue = PojoProperties.value("deleteTaxon").observe(configurator);
+ bindingContext.bindValue(observeSelectionBtnDeleteTaxonObserveWidget, deleteTaxonIfPossibleConfiguratorObserveValue, null, null);
+ //
+ return bindingContext;
+ }
+ }
+
+
import java.net.URI;
import org.eclipse.swt.SWT;
-import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Label;
/**
public URI getUri(){
try {
- labelException.setBackground(getPersistentBackground());
labelException.setText("");
return new URI(super.getText());
} catch (Exception e) {
- labelException.setBackground(Display.getCurrent().getSystemColor(SWT.COLOR_RED));
labelException.setText(e.getMessage());
return null;
}
false,
false,
null,
+ null,
presenceAbsenceTermColors,
languages);
try {
URI uri = text_uri.getUri();
getEntity().setUri(uri);
- if(uri==null){
- //buffer URI if parsing error occurred
- MediaDetailElement parentMediaDetailElement = getParentMediaDetailElement();
- if(parentMediaDetailElement!=null){
- parentMediaDetailElement.setUriBuffer(text_uri.getText());
- }
- }
+
loadImage(getEntity().getUri(), true);
*/
package eu.etaxonomy.taxeditor.ui.section.media;
-import java.net.URI;
import java.util.List;
import java.util.Set;
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
import eu.etaxonomy.cdm.model.media.MediaUtils;
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
import eu.etaxonomy.taxeditor.preference.IPreferenceKeys;
import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
private ICdmFormElement parentFormElement;
private int style;
- /**
- * Used to store the URI even if it is invalid and thus cannot be stored in CDM
- */
- private String uriBuffer;
-
public MediaDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {
super(formFactory, formElement);
}
public void handleEvent(Object eventSource){
if(eventSource==textUri){
textUri.setBackground(getPersistentBackground());
- URI uri = textUri.getUri();
- singleMediaRepresentationPart.setUri(uri);
- if(uri==null){
- uriBuffer=textUri.getText();
- }
+ singleMediaRepresentationPart.setUri(textUri.getUri());
}
}
- public void toggleAdvancedMediaView() {
- if (getEntity().getRepresentations() != null
- && (getEntity().getRepresentations().size() > 1 ||
- (getEntity().getRepresentations().size() == 1
- && getEntity().getRepresentations().iterator().next().getParts().size() > 1))) {
- MessagingUtils.informationDialog("Toggling not possible",
- "Media has consists of multiple representations or representatio parts");
- // toggling is only possible if there are no more than one
- // MediaRepresentation resp. MediaRepresentationParts
- return;
- }
+ public void toggleAdvancedMediaView(){
isAdvancedMediaView = !isAdvancedMediaView;
showAdvancedView();
reflowParentScrolledForm(true);
section_mediaRepresentation = formFactory.createMediaRepresentationSection(getConversationHolder(), parentFormElement, style);
section_mediaRepresentation.setLayoutData(LayoutConstants.FILL_HORIZONTALLY(2, 1));
section_mediaRepresentation.setEntity(getEntity());
- //set buffered uri as text if uri had parsing problems in simple view
- if(uriBuffer!=null){
- section_mediaRepresentation.getLayoutComposite().getChildren();
- }
}
else{
if(section_mediaRepresentation!=null){
removeElementsAndControls(section_mediaRepresentation);
}
textUri = formFactory.createUriWithLabelElement(parentFormElement, "Media URI", null, style);
- URI uri = singleMediaRepresentationPart.getUri();
- textUri.setUri(uri);
- //set buffered uri as text if uri had parsing problems in advanced view
- if(uri==null && uriBuffer!=null){
- textUri.setText(uriBuffer);
- textUri.getUri();
- }
+ textUri.setUri(singleMediaRepresentationPart.getUri());
textUri.getLayoutComposite().layout();
}
}
return isAdvancedMediaView;
}
- public void setUriBuffer(String uriBuffer) {
- this.uriBuffer = uriBuffer;
- }
-
- public String getUriBuffer() {
- return uriBuffer;
- }
-
}
text_size.setText(FileUtils.byteCountToDisplaySize(entity.getSize()));
}
if(entity.getUri() != null){
- text_uri.setUri(entity.getUri());
- } else {
- String uriBuffer = getParentMediaDetailElement().getUriBuffer();
- if(uriBuffer!=null){
- text_uri.setText(uriBuffer);
- text_uri.getUri();//just to update the error label
- }
- }
+ text_uri.setText(entity.getUri().toString());
+ }
}
@Override
if(eventSource == text_uri){
URI uri = text_uri.getUri();
getEntity().setUri(uri);
- if(uri==null){
- //buffer URI if parsing error occurred
- MediaDetailElement parentMediaDetailElement = getParentMediaDetailElement();
- if(parentMediaDetailElement!=null){
- parentMediaDetailElement.setUriBuffer(text_uri.getText());
- }
- }
-
firePropertyChangeEvent(this);
}
}
- protected MediaDetailElement getParentMediaDetailElement() {
- ICdmFormElement parentElement = getParentElement();
- while(parentElement!=null){
- parentElement = parentElement.getParentElement();
- if(parentElement instanceof MediaDetailElement){
- return (MediaDetailElement) parentElement;
- }
- }
- return null;
- }
-
}
import java.util.Map;
import java.util.Map.Entry;
-import org.eclipse.core.commands.Command;
-import org.eclipse.core.commands.common.NotDefinedException;
import org.eclipse.jface.action.ContributionItem;
import org.eclipse.jface.action.IContributionItem;
import org.eclipse.jface.viewers.ISelection;
import org.eclipse.ui.IWorkbenchWindow;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.actions.CompoundContributionItem;
-import org.eclipse.ui.commands.ICommandService;
-import org.eclipse.ui.handlers.IHandlerService;
-
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
/**
* Generic context menu for opening elements in the taxeditor.
new ContributionItem() {
@Override
public void fill(Menu menu, int index) {
- final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
- final ISelection selection = window.getActivePage().getSelection();
-
MenuItem addItem = new MenuItem(menu, SWT.CASCADE);
addItem.setText("Open in...");
Menu addMenu = new Menu(menu);
addItem.setMenu(addMenu);
+ final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
+ final ISelection selection = window.getActivePage().getSelection();
if(selection instanceof IStructuredSelection){
Object firstElement = ((IStructuredSelection) selection).getFirstElement();
- Map<String, String> availableViewers = CdmViewerUtil.getAvailableViewers(firstElement);
- for(Entry<String, String> entry:availableViewers.entrySet()){
- final String commandId = entry.getKey();
- String viewerName = entry.getValue();
+ Map<Entry<Class<?>, String>, ICdmViewer> nameViewerMap = CdmViewerUtil.getNameViewerMap(firstElement);
+ for(Entry<Entry<Class<?>, String>, ICdmViewer> entry:nameViewerMap.entrySet()){
+ Entry<Class<?>, String> viewerClass = entry.getKey();
MenuItem menuItem = new MenuItem(addMenu, SWT.NONE);
- menuItem.setText(viewerName);
- menuItem.addSelectionListener(new SelectionAdapter() {
-
- @Override
- public void widgetSelected(SelectionEvent e) {
- ICommandService commandService = (ICommandService)PlatformUI.getWorkbench().getService(ICommandService.class);
-
- Command command = commandService.getCommand(commandId);
- if(command.isEnabled()) {
- IHandlerService handlerService = (IHandlerService)PlatformUI.getWorkbench().getService(IHandlerService.class);
- try {
- handlerService.executeCommand(commandId, null);
- } catch (NotDefinedException nde) {
- throw new RuntimeException("Could not find open command: " + commandId);
- } catch (Exception exception) {
- MessagingUtils.error(getClass(), "An exception occured while trying execute "+commandId, exception);
- }
- }
- }
- }) ;
+ menuItem.setText(viewerClass.getValue());
+ menuItem.addSelectionListener(new OpenInViewerListener(entry.getValue(), firstElement, viewerClass.getKey()));
}
}
}
public static Map<Entry<Class<?>, String>, ICdmViewer> getNameViewerMap(Object input){
Map<Entry<Class<?>, String>, ICdmViewer> nameViewerMap = new HashMap<Entry<Class<?>, String>, ICdmViewer>();
-
+
IExtensionRegistry reg = Platform.getExtensionRegistry();
IConfigurationElement[] extensions = reg
.getConfigurationElementsFor("eu.etaxonomy.taxeditor.store.cdmViewer");
return nameViewerMap;
}
- public static Map<String, String> getAvailableViewers(Object input){
- Map<String, String> commandViewerNameMap = new HashMap<String, String>();
-
- if(input!=null){
- IExtensionRegistry reg = Platform.getExtensionRegistry();
- IConfigurationElement[] extensions = reg
- .getConfigurationElementsFor("eu.etaxonomy.taxeditor.store.cdmViewer");
- for (IConfigurationElement configElement : extensions) {
- if(configElement.getName().equals("viewCommandMapping")){
- String commandId = configElement.getAttribute("commandId");
- String viewerName = configElement.getAttribute("viewerName");
- try {
- Object selectionObject = configElement.createExecutableExtension("selection");
- Class<? extends Object> selectionClass = selectionObject.getClass();
- if(input.getClass().isAssignableFrom(selectionClass)){
- commandViewerNameMap.put(commandId, viewerName);
- }
- } catch (CoreException e) {
- MessagingUtils.error(CdmViewerChooser.class, "Could not initalize selection class element of cdmViewer extension", e);
- }
- }
- }
- }
- return commandViewerNameMap;
- }
-
}
<java.codelevel>1.6</java.codelevel>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<cdmlib.version>3.8.0-SNAPSHOT</cdmlib.version>
+ <!-- TODO can we use project.version ????? -->
<tycho.version>0.22.0</tycho.version>
<taxeditor.version>3.8.0-SNAPSHOT</taxeditor.version>
<update.dir>snapshot</update.dir>
<module>eu.etaxonomy.taxeditor.application</module>
<module>eu.etaxonomy.taxeditor.feature.platform</module>
<module>eu.etaxonomy.taxeditor.feature</module>
- <module>eu.etaxonomy.taxeditor.molecular</module>
- <module>eu.etaxonomy.taxeditor.molecular.lib</module>
<module>eu.etaxonomy.taxeditor</module>
</modules>
<scm>