eu.etaxonomy.taxeditor.help/toc.xml -text
eu.etaxonomy.taxeditor.help/tocgettingstarted.xml -text
eu.etaxonomy.taxeditor.help/tocnameparser.xml -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorActionUpdater.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractFocusedAlignmentAreaHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AlignmentEditorCutHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AlignmentEditorPasteHandler.java -text
eu.etaxonomy.taxeditor.navigation/.classpath -text
eu.etaxonomy.taxeditor.navigation/.project -text
eu.etaxonomy.taxeditor.navigation/META-INF/MANIFEST.MF -text
eu.etaxonomy.taxeditor.cdmlib/.classpath merge=ours
eu.etaxonomy.taxeditor.cdmlib/build.properties merge=ours
eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product merge=ours
-eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.with.jre merge=ours
\ No newline at end of file
+eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.with.jre merge=ours
class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
</handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCopyHandler"
+ commandId="org.eclipse.ui.edit.copy">
+ <activeWhen>
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </activeWhen>
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorCutHandler"
+ commandId="org.eclipse.ui.edit.cut">
+ <activeWhen>
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </activeWhen>
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.AlignmentEditorPasteHandler"
+ commandId="org.eclipse.ui.edit.paste">
+ <activeWhen>
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </activeWhen>
+ </handler>
</extension>
<extension
point="org.eclipse.ui.bindings">
package eu.etaxonomy.taxeditor.molecular.editor;
+import info.bioinfweb.commons.swt.SWTUtils;
import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter;
import org.biojava.bio.chromatogram.ChromatogramFactory;
import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.jface.action.Action;
import org.eclipse.swt.SWT;
+import org.eclipse.swt.dnd.Clipboard;
import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Display;
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.actions.ActionFactory;
import org.eclipse.ui.commands.ICommandService;
import org.eclipse.ui.part.EditorPart;
setDirty();
}
};
+ private final AlignmentEditorActionUpdater ACTION_UPDATER = new AlignmentEditorActionUpdater();
+ public final Clipboard CLIPBOARD = new Clipboard(Display.getCurrent()); //TODO Move to global EDITor class.
+
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() {
+ public AlignmentEditor()
+ {
super();
conversationHolder = CdmStore.createConversation();
//conversationHolder = null;
private void registerEditSettingListener(MultipleAlignmentsContainer container) {
- container.getEditSettings().addListener(new EditSettingsListener() {
- @Override
- public void workingModeChanged(EditSettingsChangeEvent e) {} // Currently nothing to do
+ 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 insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
+ updateStatusBar();
+ refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
+ }
- @Override
- public void insertChanged(EditSettingsChangeEvent e) {
- updateStatusBar();
- refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
- }
- });
+ @Override
+ public void insertChanged(EditSettingsChangeEvent e) {
+ updateStatusBar();
+ refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
+ }
+ });
}
- private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {
+ 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) {
+ private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
AlignmentArea result = new AlignmentArea(container);
result.setAllowVerticalScrolling(allowVerticalScrolling);
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;
- }
+ AlignmentArea result = new AlignmentArea(container);
+ result.setAllowVerticalScrolling(false);
+ result.getDataAreas().getBottomAreas().add(
+ new ConsensusSequenceArea(result.getContentArea(), labeledArea));
+ return result;
+ }
private MultipleAlignmentsContainer getAlignmentsContainer() {
AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
+ readsArea.getSelection().addSelectionListener(ACTION_UPDATER);
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.
+ AlignmentArea editableConsensusArea = createEditableAlignmentArea(alignmentsContainer, false);
+ editableConsensusArea.getSelection().addSelectionListener(ACTION_UPDATER);
+ list.add(editableConsensusArea); // Make sure COMSENSUS_AREA_INDEX is correct.
list.add(createConsensusHintArea(alignmentsContainer, readsArea));
registerEditSettingListener(alignmentsContainer);
}
- private AlignmentArea getEditableConsensusArea() {
+ public AlignmentArea getEditableConsensusArea() {
return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX);
}
+ /**
+ * Checks whether {@link #getReadsArea()} or {@link #getEditableConsensusArea()} currently
+ * have the user focus and returns the according component.
+ *
+ * @return either the reads or the consensus alignment area or {@code null} if none of these
+ * components is currently focused
+ */
+ public AlignmentArea getFocusedArea() {
+ AlignmentArea result = getReadsArea();
+ if (hasFocus(result)) {
+ return result;
+ }
+ else {
+ result = getEditableConsensusArea();
+ if (hasFocus(result)) {
+ return result;
+ }
+ else {
+ return null;
+ }
+ }
+ }
+
+
+ /**
+ * Checks whether the specified alignment area or one of its subcomponents currently has the
+ * focus.
+ *
+ * @param area the alignment area to be checked (Can only be {@link #getReadsArea()} or
+ * {@link #getEditableConsensusArea()}.)
+ * @return {@code true} if the specified component is focused and is either equal to
+ * {@link #getReadsArea()} or {@link #getEditableConsensusArea()}or {@code false} otherwise
+ */
+ private boolean hasFocus(AlignmentArea area) {
+ return SWTUtils.childHasFocus((Composite)area.getToolkitComponent());
+ }
+
+
public boolean hasPherogram(int sequenceID) {
return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;
}
}
- /* (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);
+ Display.getCurrent().addFilter(SWT.FocusIn, ACTION_UPDATER);
+ Display.getCurrent().addFilter(SWT.FocusOut, ACTION_UPDATER);
updateStatusBar();
if (getEditorInput() instanceof AlignmentEditorInput) {
}
- private void updateStatusBar() {
+ @Override
+ public void dispose() {
+ Display.getCurrent().removeFilter(SWT.FocusIn, ACTION_UPDATER);
+ Display.getCurrent().removeFilter(SWT.FocusOut, ACTION_UPDATER);
+ CLIPBOARD.dispose();
+ ((AlignmentEditorInput)getEditorInput()).dispose();
+ super.dispose();
+ }
+
+
+ private void updateStatusBar() {
IActionBars bars = getEditorSite().getActionBars();
bars.getStatusLineManager().setMessage("Edit mode: " +
(getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + " " +
}
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
- */
@Override
public void doSave(IProgressMonitor monitor) {
if (getEditorInput() instanceof AlignmentEditorInput) {
}
- /* (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);
- System.out.println("AlignmentEditor.init(): " + ActionFactory.COPY.getId());
- site.getActionBars().setGlobalActionHandler(ActionFactory.COPY.getId(), new Action(ActionFactory.COPY.getId()) {
- @Override
- public boolean isEnabled() {
- System.out.println("isEnabled()");
- return true;
- }
-
- @Override
- public void run() {
- System.out.println("run");
- super.run();
- }
- });
}
- /* (non-Javadoc)
- * @see org.eclipse.ui.part.EditorPart#isDirty()
- */
@Override
public boolean isDirty() {
return 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){
+ if(conversationHolder != null){
conversationHolder.bind();
}
((AlignmentEditorInput)getEditorInput()).bind();
}
- @Override
- public void dispose() {
- ((AlignmentEditorInput)getEditorInput()).dispose();
- }
-
public boolean isInsertMode() {
return getAlignmentsContainer().getEditSettings().isInsert();
}
--- /dev/null
+package eu.etaxonomy.taxeditor.molecular.editor;\r
+\r
+\r
+import org.eclipse.swt.widgets.Event;\r
+import org.eclipse.swt.widgets.Listener;\r
+import org.eclipse.ui.PlatformUI;\r
+import org.eclipse.ui.actions.ActionFactory;\r
+import org.eclipse.ui.commands.ICommandService;\r
+\r
+import eu.etaxonomy.taxeditor.molecular.handler.AbstractAlignmentEditorHandler;\r
+import info.bioinfweb.libralign.alignmentarea.selection.SelectionChangeEvent;\r
+import info.bioinfweb.libralign.alignmentarea.selection.SelectionListener;\r
+\r
+\r
+\r
+/**\r
+ * Listener used to update copy/paste events associated with {@link AlignmentEditor}.\r
+ * \r
+ * @author Ben Stöver\r
+ * @date 25.08.2015\r
+ */\r
+public class AlignmentEditorActionUpdater implements SelectionListener, Listener {\r
+ private static final String[] IDS = {ActionFactory.COPY.getCommandId(), ActionFactory.CUT.getCommandId(), \r
+ ActionFactory.PASTE.getCommandId()};\r
+ \r
+ \r
+ private void updateEvents() {\r
+ ICommandService service = (ICommandService)PlatformUI.getWorkbench().getService(ICommandService.class);\r
+ for (int i = 0; i < IDS.length; i++) {\r
+ service.refreshElements(IDS[i], null);\r
+ }\r
+ }\r
+ \r
+ \r
+ @Override\r
+ public void handleEvent(Event event) {\r
+ AlignmentEditor editor = AbstractAlignmentEditorHandler.getActiveAlignmentEditor();\r
+ if (editor != null) {\r
+ updateEvents();\r
+ }\r
+ }\r
+\r
+ \r
+ @Override\r
+ public void selectionChanged(SelectionChangeEvent e) {\r
+ AlignmentEditor editor = AbstractAlignmentEditorHandler.getActiveAlignmentEditor();\r
+ if (editor != null) {\r
+ if ((e.getSource() == editor.getReadsArea().getSelection()) || \r
+ (e.getSource() == editor.getEditableConsensusArea().getSelection())) {\r
+ \r
+ updateEvents();\r
+ }\r
+ }\r
+ }\r
+}\r
* @date 19.06.2015
*/
public abstract class AbstractAlignmentEditorHandler extends AbstractHandler {
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
+ public static AlignmentEditor getActiveAlignmentEditor() {
IEditorPart activeEditor = AbstractUtility.getActiveEditor();
if (activeEditor instanceof AlignmentEditor) {
- doExecute(event, (AlignmentEditor)activeEditor);
+ return (AlignmentEditor)activeEditor;
+ }
+ else {
+ return null;
+ }
+ }
+
+
+ @Override
+ public Object execute(ExecutionEvent event) throws ExecutionException {
+ AlignmentEditor editor = getActiveAlignmentEditor();
+ if (editor != null) {
+ doExecute(event, editor);
}
return null;
}
- public abstract void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException;
+ protected abstract void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException;
}
--- /dev/null
+package eu.etaxonomy.taxeditor.molecular.handler;\r
+\r
+\r
+import info.bioinfweb.libralign.alignmentarea.AlignmentArea;\r
+\r
+import org.eclipse.core.commands.ExecutionEvent;\r
+import org.eclipse.core.commands.ExecutionException;\r
+\r
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
+\r
+\r
+\r
+public abstract class AbstractFocusedAlignmentAreaHandler extends AbstractAlignmentEditorHandler {\r
+ @Override\r
+ protected void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
+ AlignmentArea focusedArea = editor.getFocusedArea();\r
+ if (focusedArea != null) {\r
+ doExecute2(event, editor, focusedArea);\r
+ }\r
+ }\r
+ \r
+ \r
+ protected abstract void doExecute2(ExecutionEvent event, AlignmentEditor editor, AlignmentArea focusedArea);\r
+}\r
--- /dev/null
+package eu.etaxonomy.taxeditor.molecular.handler;
+
+
+import java.util.Map;
+
+import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
+import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
+import info.bioinfweb.libralign.model.AlignmentModelUtils;
+
+import org.eclipse.core.commands.ExecutionEvent;
+import org.eclipse.swt.dnd.TextTransfer;
+import org.eclipse.swt.dnd.Transfer;
+import org.eclipse.ui.commands.IElementUpdater;
+import org.eclipse.ui.menus.UIElement;
+
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
+
+
+
+/**
+ * Handler that copies the currently selected nucleotides from an alignment editor to the clipboard.
+ * <p>
+ * The copied contents either come from the single reads or the consensus sequence alignment area,
+ * depending on which component currently has the focus. If none of these components has the focus,
+ * nothing will be copied, even if nucleotides are currently selected.
+ * <p>
+ * If the selection contains parts of multiple sequence, these are separated by the line separator
+ * of the current operating system.
+ *
+ * @author Ben Stöver
+ * @date 25.08.2015
+ */
+public class AlignmentEditorCopyHandler extends AbstractFocusedAlignmentAreaHandler implements IElementUpdater {
+ @Override
+ @SuppressWarnings("unchecked")
+ protected void doExecute2(ExecutionEvent event, AlignmentEditor editor, AlignmentArea focusedArea) {
+ SelectionModel selection = focusedArea.getSelection();
+ if (!selection.isEmpty()) {
+ editor.CLIPBOARD.setContents(new Object[]{AlignmentModelUtils.selectionAsString(focusedArea, false)},
+ new Transfer[]{TextTransfer.getInstance()});
+ }
+ }
+
+
+ @Override
+ public boolean isEnabled() {
+ AlignmentEditor editor = getActiveAlignmentEditor();
+ if (editor != null) {
+ AlignmentArea focusedArea = editor.getFocusedArea();
+ if (focusedArea != null) {
+ return !focusedArea.getSelection().isEmpty();
+ }
+ }
+ return false;
+ }
+
+
+ @Override
+ public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
+ setBaseEnabled(isEnabled());
+ }
+}
--- /dev/null
+package eu.etaxonomy.taxeditor.molecular.handler;\r
+\r
+\r
+import info.bioinfweb.libralign.alignmentarea.AlignmentArea;\r
+\r
+import org.eclipse.core.commands.ExecutionEvent;\r
+\r
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
+\r
+\r
+\r
+/**\r
+ * Handler that cuts the currently selected nucleotides from an alignment editor to the clipboard.\r
+ * <p>\r
+ * The cut contents either come from the single reads or the consensus sequence alignment area,\r
+ * depending on which component currently has the focus. If none of these components has the focus,\r
+ * nothing will be cut, even if nucleotides are currently selected.\r
+ * <p>\r
+ * If the selection contains parts of multiple sequence, these are separated by the line separator\r
+ * of the current operating system. \r
+ * \r
+ * @author Ben Stöver\r
+ * @date 25.08.2015\r
+ */\r
+public class AlignmentEditorCutHandler extends AlignmentEditorCopyHandler {\r
+ @Override\r
+ protected void doExecute2(ExecutionEvent event, AlignmentEditor editor, AlignmentArea focusedArea) {\r
+ super.doExecute2(event, editor, focusedArea); // Copy selected contents.\r
+ focusedArea.getActionProvider().deleteSelection();\r
+ }\r
+}\r
--- /dev/null
+package eu.etaxonomy.taxeditor.molecular.handler;\r
+\r
+\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Scanner;\r
+\r
+import info.bioinfweb.libralign.alignmentarea.AlignmentArea;\r
+import info.bioinfweb.libralign.alignmentarea.order.SequenceOrder;\r
+import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;\r
+import info.bioinfweb.libralign.model.AlignmentModel;\r
+import info.bioinfweb.libralign.model.AlignmentModelUtils;\r
+\r
+import org.eclipse.core.commands.ExecutionEvent;\r
+import org.eclipse.jface.dialogs.MessageDialog;\r
+import org.eclipse.swt.dnd.TextTransfer;\r
+import org.eclipse.ui.commands.IElementUpdater;\r
+import org.eclipse.ui.handlers.HandlerUtil;\r
+import org.eclipse.ui.menus.UIElement;\r
+\r
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
+\r
+\r
+\r
+/**\r
+ * Handler that pastes the current contents of the clipboard into an active instance of {@link AlignmentEditor}.\r
+ * \r
+ * @author Ben Stöver\r
+ * @date 26.08.2015\r
+ */\r
+public class AlignmentEditorPasteHandler extends AbstractFocusedAlignmentAreaHandler implements IElementUpdater {\r
+ private void pasteString(AlignmentArea area, int sequenceID, String content) {\r
+ area.getActionProvider().deleteSelection(); // Overwrite selected tokens.\r
+ area.getActionProvider().elongateSequence(sequenceID, area.getSelection().getCursorColumn());\r
+\r
+ AlignmentModel<Object> alignmentModel = (AlignmentModel<Object>)area.getAlignmentModel();\r
+ alignmentModel.insertTokensAt(sequenceID, area.getSelection().getCursorColumn(), \r
+ AlignmentModelUtils.charSequenceToTokenList(content, alignmentModel.getTokenSet(),\r
+ true, alignmentModel.getTokenSet().getGapToken()));\r
+ }\r
+ \r
+ \r
+ @Override\r
+ protected void doExecute2(ExecutionEvent event, AlignmentEditor editor, AlignmentArea focusedArea) {\r
+ SelectionModel selection = focusedArea.getSelection();\r
+ String clipboardText = (String)editor.CLIPBOARD.getContents(TextTransfer.getInstance());\r
+ if (clipboardText != null) {\r
+ List<String> lines = new ArrayList<String>();\r
+ Scanner scanner = new Scanner(clipboardText);\r
+ try {\r
+ while (scanner.hasNext()) {\r
+ lines.add(scanner.nextLine());\r
+ }\r
+ if (lines.get(lines.size() - 1).equals("")) {\r
+ lines.remove(lines.size() - 1);\r
+ }\r
+ }\r
+ finally {\r
+ scanner.close();\r
+ }\r
+ \r
+ if (!lines.isEmpty()) { //TODO Can lines be empty? (Can an empty string "" be copied to the clipboard?)\r
+ if (selection.getCursorHeight() == 1) { // If the consensus sequence is focused, this is the only possible case.\r
+ int sequenceID = focusedArea.getSequenceOrder().idByIndex(selection.getCursorRow());\r
+ if (lines.size() == 1) {\r
+ pasteString(focusedArea, sequenceID, lines.get(0));\r
+ }\r
+ else {\r
+ MessageDialog dialog = new MessageDialog(HandlerUtil.getActiveWorkbenchWindow(event).getShell(), //TODO Can the window be null? \r
+ "Pasting multiple lines", null,\r
+ "The text to be pasted contains mutlitple lines (" + lines.size() + \r
+ ") although the current cursor height is one. What do you want to do?", \r
+ MessageDialog.QUESTION, \r
+ new String[]{"Ingnore line breaks and paste as one sequence", \r
+ "Only paste the first line from the clipboard", "Cancel"}, \r
+ 0);\r
+ //TODO Does the dialog have to be disposed in some way?\r
+ \r
+ switch (dialog.open()) {\r
+ case 0: // Paste all lines in one sequence.\r
+ pasteString(focusedArea, sequenceID, clipboardText);\r
+ break;\r
+ case 1: // Paste only first line.\r
+ pasteString(focusedArea, sequenceID, lines.get(0));\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ else {\r
+ if (selection.getCursorHeight() == lines.size()) {\r
+ SequenceOrder order = focusedArea.getSequenceOrder();\r
+ for (int i = 0; i < selection.getCursorHeight(); i++) {\r
+ pasteString(focusedArea, order.idByIndex(selection.getCursorRow() + i), lines.get(i)); // Multiple calls of deleteSelection() in here are unnecessary, but should have no effect.\r
+ }\r
+ }\r
+ else {\r
+ MessageDialog.openError(HandlerUtil.getActiveWorkbenchWindow(event).getShell(), //TODO Can the window be null?\r
+ "Unable to paste multiple lines", \r
+ "The current cursor height (" + selection.getCursorHeight() + \r
+ ") does not match the number of lines to be pasted (" + lines.size() + ")." + \r
+ System.getProperty("line.separator") + System.getProperty("line.separator") + \r
+ "You can either change the cursor height accordingly or set the cursor height to one "\r
+ + "allowing you to paste all lines from the clipboad into one sequence.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ @Override\r
+ public boolean isEnabled() {\r
+ AlignmentEditor editor = getActiveAlignmentEditor();\r
+ if (editor != null) {\r
+ AlignmentArea focusedArea = editor.getFocusedArea();\r
+ return (focusedArea != null);\r
+ }\r
+ else {\r
+ return false;\r
+ }\r
+ }\r
+\r
+\r
+ @Override\r
+ public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {\r
+ setBaseEnabled(isEnabled());\r
+ }\r
+}\r
* @author pplitzner
*/
public class EditSequenceHandler extends AbstractHandler {
+ private org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(EditSequenceHandler.class);
- 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);
BGBM BDI Projects / taxeditor.git / commitdiff