Revision 61650dda
Added by Patrick Plitzner over 6 years ago
| eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SpecimenPropertyTester.java | ||
|---|---|---|
| 6 | 6 |
import org.eclipse.jface.viewers.TreeNode; |
| 7 | 7 |
|
| 8 | 8 |
import eu.etaxonomy.cdm.model.molecular.Sequence; |
| 9 |
import eu.etaxonomy.cdm.model.molecular.SingleRead; |
|
| 9 | 10 |
import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen; |
| 10 | 11 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
| 11 | 12 |
import eu.etaxonomy.taxeditor.editor.EditorUtil; |
| ... | ... | |
| 20 | 21 |
*/ |
| 21 | 22 |
public class SpecimenPropertyTester extends PropertyTester {
|
| 22 | 23 |
private static final String SEQUENCE = "isSequence"; //$NON-NLS-1$ |
| 24 |
private static final String SINGLE_READ = "isSingleRead"; //$NON-NLS-1$ |
|
| 23 | 25 |
private static final String IS_SPECIMEN_OR_OBSERVATION_BASE = "isSpecimenOrObservationBase"; //$NON-NLS-1$ |
| 24 | 26 |
private static final String IS_ADD_DERIVATE_ALLOWED = "isAddDerivateAllowed"; //$NON-NLS-1$ |
| 25 | 27 |
private static final String IS_ADD_MEDIA_ALLOWED = "isAddMediaAllowed"; //$NON-NLS-1$ |
| ... | ... | |
| 37 | 39 |
if (SEQUENCE.equals(property)) {
|
| 38 | 40 |
return isSequence(treeNodeOfSelection.getValue()); |
| 39 | 41 |
} |
| 42 |
else if (SINGLE_READ.equals(property)) {
|
|
| 43 |
return isSingleRead(treeNodeOfSelection.getValue()); |
|
| 44 |
} |
|
| 40 | 45 |
else if (IS_SPECIMEN_OR_OBSERVATION_BASE.equals(property)) {
|
| 41 | 46 |
return isSpecimenOrObservationBase(treeNodeOfSelection.getValue()); |
| 42 | 47 |
} |
| ... | ... | |
| 66 | 71 |
&& !(object instanceof MediaSpecimen); |
| 67 | 72 |
} |
| 68 | 73 |
|
| 74 |
private boolean isSingleRead(Object object) {
|
|
| 75 |
return (object instanceof SingleRead); |
|
| 76 |
} |
|
| 77 |
|
|
| 69 | 78 |
private boolean isSequence(Object object) {
|
| 70 | 79 |
return (object instanceof Sequence); |
| 71 | 80 |
} |
| eu.etaxonomy.taxeditor.molecular/fragment.e4xmi | ||
|---|---|---|
| 2 | 2 |
<fragment:ModelFragments xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:commands="http://www.eclipse.org/ui/2010/UIModel/application/commands" xmlns:fragment="http://www.eclipse.org/ui/2010/UIModel/fragment" xmlns:menu="http://www.eclipse.org/ui/2010/UIModel/application/ui/menu" xmlns:ui="http://www.eclipse.org/ui/2010/UIModel/application/ui" xmi:id="_OhwnQCTfEeeiN5lBIuqN3g"> |
| 3 | 3 |
<fragments xsi:type="fragment:StringModelFragment" xmi:id="__mwtMDVpEee_b7RlBzTDRw" featurename="commands" parentElementId="xpath:/"> |
| 4 | 4 |
<elements xsi:type="commands:Command" xmi:id="_JZdQ0H2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.editSequence" commandName="%command.EDIT_SEQUENCE"/> |
| 5 |
<elements xsi:type="commands:Command" xmi:id="_IXQocH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile" commandName="%command.label.EXPORT_SEQUENCE_TO_FILE"/> |
|
| 6 |
<elements xsi:type="commands:Command" xmi:id="_m9gZAH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.showPherogram" commandName="%command.name.SHOW_PHEROGRAM"/> |
|
| 5 | 7 |
</fragments> |
| 6 | 8 |
<fragments xsi:type="fragment:StringModelFragment" xmi:id="_RCmzgH2sEeeVL5aZ55YsWA" featurename="handlers" parentElementId="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView"> |
| 7 | 9 |
<elements xsi:type="commands:Handler" xmi:id="_XuBioH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" command="_JZdQ0H2sEeeVL5aZ55YsWA"/> |
| 10 |
<elements xsi:type="commands:Handler" xmi:id="_QwuNwH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" command="_IXQocH22EeeVL5aZ55YsWA"/> |
|
| 11 |
<elements xsi:type="commands:Handler" xmi:id="_reIrkH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" contributionURI="bundleclass://eu.etaxonomy.taxeditor.molecular/eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" command="_m9gZAH22EeeVL5aZ55YsWA"/> |
|
| 8 | 12 |
</fragments> |
| 9 | 13 |
<fragments xsi:type="fragment:StringModelFragment" xmi:id="_o08AQH2sEeeVL5aZ55YsWA" featurename="children" parentElementId="eu.etaxonomy.taxeditor.editor.popupmenu.specimeneditor" positionInList="before:eu.etaxonomy.taxeditor.editor.menuseparator.beforeDelete"> |
| 10 | 14 |
<elements xsi:type="menu:HandledMenuItem" xmi:id="_txARoH2sEeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandlabeledit_sequence" label="%command.label.EDIT_SEQUENCE" command="_JZdQ0H2sEeeVL5aZ55YsWA"> |
| 11 | 15 |
<visibleWhen xsi:type="ui:CoreExpression" xmi:id="_wpbQQH2sEeeVL5aZ55YsWA" coreExpressionId="isSequence"/> |
| 12 | 16 |
</elements> |
| 17 |
<elements xsi:type="menu:HandledMenuItem" xmi:id="_VRC-UH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandlabelexport_sequence_to_file" label="%command.label.EXPORT_SEQUENCE_TO_FILE" command="_IXQocH22EeeVL5aZ55YsWA"> |
|
| 18 |
<visibleWhen xsi:type="ui:CoreExpression" xmi:id="_ZLzjsH22EeeVL5aZ55YsWA" coreExpressionId="isSequence"/> |
|
| 19 |
</elements> |
|
| 20 |
<elements xsi:type="menu:HandledMenuItem" xmi:id="_xftzgH22EeeVL5aZ55YsWA" elementId="eu.etaxonomy.taxeditor.molecular.handledmenuitem.commandnameshow_pherogram" label="%command.name.SHOW_PHEROGRAM" command="_m9gZAH22EeeVL5aZ55YsWA"> |
|
| 21 |
<visibleWhen xsi:type="ui:CoreExpression" xmi:id="_0tfXEH22EeeVL5aZ55YsWA" coreExpressionId="isSingleRead"/> |
|
| 22 |
</elements> |
|
| 13 | 23 |
</fragments> |
| 14 | 24 |
</fragment:ModelFragments> |
| eu.etaxonomy.taxeditor.molecular/plugin.xml | ||
|---|---|---|
| 22 | 22 |
</extension> |
| 23 | 23 |
<extension |
| 24 | 24 |
point="org.eclipse.ui.commands"> |
| 25 |
<command |
|
| 26 |
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" |
|
| 27 |
id="eu.etaxonomy.taxeditor.molecular.showPherogram" |
|
| 28 |
name="%command.name.SHOW_PHEROGRAM"> |
|
| 29 |
</command> |
|
| 30 | 25 |
<command |
| 31 | 26 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" |
| 32 | 27 |
name="%command.name.CUT_PHEROGRAM_LEFT"> |
| ... | ... | |
| 71 | 66 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion" |
| 72 | 67 |
name="%command.name.TOGGLE_LEFT_RIGHT_INSERTION"> |
| 73 | 68 |
</command> |
| 74 |
<command |
|
| 75 |
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler" |
|
| 76 |
id="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile" |
|
| 77 |
name="%command.name.EXPORT_SEQUENCE_TO_FILE"> |
|
| 78 |
</command> |
|
| 79 | 69 |
</extension> |
| 80 | 70 |
<extension |
| 81 | 71 |
point="org.eclipse.ui.menus"> |
| ... | ... | |
| 180 | 170 |
</visibleWhen> |
| 181 | 171 |
</menu> |
| 182 | 172 |
</menuContribution> |
| 183 |
<menuContribution |
|
| 184 |
locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.derivative.reuseSingleReadMenuItem"> |
|
| 185 |
<separator |
|
| 186 |
name="eu.etaxonomy.taxeditor.molecular.separator5" |
|
| 187 |
visible="true"> |
|
| 188 |
</separator> |
|
| 189 |
<command |
|
| 190 |
commandId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile" |
|
| 191 |
label="%command.label.EXPORT_SEQUENCE_TO_FILE" |
|
| 192 |
style="push"> |
|
| 193 |
<visibleWhen |
|
| 194 |
checkEnabled="true"> |
|
| 195 |
<reference |
|
| 196 |
definitionId="isSequence"> |
|
| 197 |
</reference> |
|
| 198 |
</visibleWhen> |
|
| 199 |
</command> |
|
| 200 |
<command |
|
| 201 |
commandId="eu.etaxonomy.taxeditor.molecular.showPherogram" |
|
| 202 |
label="%command.label.SHOW_PHEROGRAM" |
|
| 203 |
style="push"> |
|
| 204 |
<visibleWhen |
|
| 205 |
checkEnabled="true"> |
|
| 206 |
<reference |
|
| 207 |
definitionId="isSingleRead"> |
|
| 208 |
</reference> |
|
| 209 |
</visibleWhen> |
|
| 210 |
</command> |
|
| 211 |
</menuContribution> |
|
| 212 | 173 |
</extension> |
| 213 | 174 |
<extension |
| 214 | 175 |
point="org.eclipse.ui.handlers"> |
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java | ||
|---|---|---|
| 10 | 10 |
package eu.etaxonomy.taxeditor.molecular.handler; |
| 11 | 11 |
|
| 12 | 12 |
|
| 13 |
import info.bioinfweb.jphyloio.JPhyloIOEventWriter; |
|
| 14 |
import info.bioinfweb.jphyloio.ReadWriteParameterMap; |
|
| 15 |
import info.bioinfweb.jphyloio.ReadWriteParameterNames; |
|
| 16 |
import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter; |
|
| 17 |
import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory; |
|
| 18 |
import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory; |
|
| 19 |
|
|
| 20 | 13 |
import java.io.File; |
| 21 | 14 |
import java.io.IOException; |
| 22 | 15 |
|
| 23 |
import org.eclipse.core.commands.AbstractHandler; |
|
| 24 |
import org.eclipse.core.commands.ExecutionEvent; |
|
| 25 |
import org.eclipse.core.commands.ExecutionException; |
|
| 16 |
import javax.inject.Named; |
|
| 17 |
|
|
| 26 | 18 |
import org.eclipse.core.runtime.IStatus; |
| 27 |
import org.eclipse.jface.viewers.ISelection; |
|
| 19 |
import org.eclipse.e4.core.di.annotations.Execute; |
|
| 20 |
import org.eclipse.e4.core.di.annotations.Optional; |
|
| 21 |
import org.eclipse.e4.ui.services.IServiceConstants; |
|
| 28 | 22 |
import org.eclipse.jface.viewers.TreeNode; |
| 29 | 23 |
import org.eclipse.jface.wizard.WizardDialog; |
| 30 |
import org.eclipse.ui.handlers.HandlerUtil;
|
|
| 24 |
import org.eclipse.swt.widgets.Shell;
|
|
| 31 | 25 |
|
| 32 | 26 |
import eu.etaxonomy.cdm.model.molecular.Sequence; |
| 33 |
import eu.etaxonomy.taxeditor.editor.EditorUtil; |
|
| 34 | 27 |
import eu.etaxonomy.taxeditor.model.MessagingUtils; |
| 35 | 28 |
import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin; |
| 36 | 29 |
import eu.etaxonomy.taxeditor.molecular.io.CDMPherogramAlignmentObjectTranslator; |
| ... | ... | |
| 39 | 32 |
import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard; |
| 40 | 33 |
import eu.etaxonomy.taxeditor.molecular.l10n.Messages; |
| 41 | 34 |
import eu.etaxonomy.taxeditor.util.ApplicationUtil; |
| 35 |
import info.bioinfweb.jphyloio.JPhyloIOEventWriter; |
|
| 36 |
import info.bioinfweb.jphyloio.ReadWriteParameterMap; |
|
| 37 |
import info.bioinfweb.jphyloio.ReadWriteParameterNames; |
|
| 38 |
import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter; |
|
| 39 |
import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory; |
|
| 40 |
import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory; |
|
| 42 | 41 |
|
| 43 | 42 |
|
| 44 | 43 |
|
| ... | ... | |
| 49 | 48 |
* @author Ben Stöver |
| 50 | 49 |
* @date 24.04.2016 |
| 51 | 50 |
*/ |
| 52 |
public class ExportSequenceToFileHandler extends AbstractHandler {
|
|
| 51 |
public class ExportSequenceToFileHandler {
|
|
| 53 | 52 |
private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory(); |
| 54 | 53 |
|
| 55 | 54 |
|
| 56 |
@Override |
|
| 57 |
public Object execute(ExecutionEvent event) throws ExecutionException {
|
|
| 58 |
ISelection currentSelection = HandlerUtil.getCurrentSelection(event); |
|
| 59 |
TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection); |
|
| 55 |
@Execute |
|
| 56 |
public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection, |
|
| 57 |
@Named(IServiceConstants.ACTIVE_SHELL)Shell shell) {
|
|
| 60 | 58 |
if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {
|
| 61 | 59 |
Sequence sequence = (Sequence)treeNodeOfSelection.getValue(); |
| 62 | 60 |
|
| 63 | 61 |
final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard(); |
| 64 |
final WizardDialog dialog = new WizardDialog(HandlerUtil.getActiveShell(event), wizard);
|
|
| 62 |
final WizardDialog dialog = new WizardDialog(shell, wizard);
|
|
| 65 | 63 |
if (dialog.open() == IStatus.OK) {
|
| 66 | 64 |
// Prepare writer parameters: |
| 67 | 65 |
ReadWriteParameterMap parameters = new ReadWriteParameterMap(); |
| eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java | ||
|---|---|---|
| 1 | 1 |
package eu.etaxonomy.taxeditor.molecular.handler; |
| 2 | 2 |
|
| 3 | 3 |
|
| 4 |
import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel; |
|
| 5 |
|
|
| 6 | 4 |
import java.net.URI; |
| 7 | 5 |
|
| 8 |
import org.eclipse.core.commands.AbstractHandler; |
|
| 9 |
import org.eclipse.core.commands.ExecutionEvent; |
|
| 10 |
import org.eclipse.core.commands.ExecutionException; |
|
| 11 |
import org.eclipse.jface.viewers.ISelection; |
|
| 6 |
import javax.inject.Named; |
|
| 7 |
|
|
| 8 |
import org.eclipse.e4.core.di.annotations.Execute; |
|
| 9 |
import org.eclipse.e4.core.di.annotations.Optional; |
|
| 10 |
import org.eclipse.e4.ui.services.IServiceConstants; |
|
| 12 | 11 |
import org.eclipse.jface.viewers.TreeNode; |
| 13 | 12 |
import org.eclipse.ui.PartInitException; |
| 14 |
import org.eclipse.ui.handlers.HandlerUtil; |
|
| 15 | 13 |
|
| 16 | 14 |
import eu.etaxonomy.cdm.model.media.MediaUtils; |
| 17 | 15 |
import eu.etaxonomy.cdm.model.molecular.SingleRead; |
| 18 |
import eu.etaxonomy.taxeditor.editor.EditorUtil; |
|
| 19 | 16 |
import eu.etaxonomy.taxeditor.model.MessagingUtils; |
| 20 | 17 |
import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin; |
| 21 | 18 |
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor; |
| 22 | 19 |
import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart; |
| 23 | 20 |
import eu.etaxonomy.taxeditor.molecular.l10n.Messages; |
| 21 |
import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel; |
|
| 24 | 22 |
|
| 25 | 23 |
|
| 26 | 24 |
|
| ... | ... | |
| 29 | 27 |
* |
| 30 | 28 |
* @author Ben Stöver |
| 31 | 29 |
*/ |
| 32 |
public class ShowPherogramHandler extends AbstractHandler {
|
|
| 30 |
public class ShowPherogramHandler {
|
|
| 33 | 31 |
public static void showPherogram(PherogramComponentModel model) throws PartInitException {
|
| 34 | 32 |
PherogramViewPart.createView(model); |
| 35 | 33 |
} |
| 36 | 34 |
|
| 37 | 35 |
|
| 38 |
@Override |
|
| 39 |
public Object execute(ExecutionEvent event) throws ExecutionException {
|
|
| 40 |
ISelection currentSelection = HandlerUtil.getCurrentSelection(event); |
|
| 41 |
TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection); |
|
| 36 |
@Execute |
|
| 37 |
public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection) {
|
|
| 42 | 38 |
if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {
|
| 43 | 39 |
//TODO Can the parent node (containing the cut positions) be extracted from SingleRead? |
| 44 | 40 |
try {
|
Also available in: Unified diff
ref #6902 migrate remaining context menu items for molecular module