+++ /dev/null
-/**
-* 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.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.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.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.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.molecular.l10n.Messages;
-import eu.etaxonomy.taxeditor.store.CdmStore;
-import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;
-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 info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
-import info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea;
-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.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.model.utils.AlignmentModelUtils;
-import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
-import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
-import info.bioinfweb.libralign.pherogram.model.PherogramAlignmentRelation;
-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;
-
-
-
-/**
- * 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"; //$NON-NLS-1$
-
- 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 "; //$NON-NLS-1$
- public static final String CONSENSUS_NAME = "Consensus"; //$NON-NLS-1$
-
-
- 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 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<String, SingleReadAlignment> cdmMap = new TreeMap<String, 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> model = new PackedAlignmentModel<Character>(tokenSet);
- result.setAlignmentModel(model, false);
- model.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);
- readsArea.getSelection().addSelectionListener(ACTION_UPDATER);
- list.add(createIndexArea(alignmentsContainer, readsArea));
- list.add(readsArea); // Make sure READS_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);
- }
- return alignmentsContainer;
- }
-
-
- public AlignmentArea getReadsArea() {
- return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);
- }
-
-
- 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(String sequenceID) {
- return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;
- }
-
-
- public PherogramArea getPherogramArea(String 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); //$NON-NLS-1$
- //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); //$NON-NLS-1$
-
- // Add test consensus sequence:
- AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
- String 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")); //$NON-NLS-1$
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C")); //$NON-NLS-1$
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G")); //$NON-NLS-1$
- tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T")); //$NON-NLS-1$
- 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();
- String id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder),
- getPherogramURI(pherogramInfo),
- 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(Messages.AlignmentEditor_ERROR_SINGLE_READ, null, Messages.AlignmentEditor_ERROR_SINGLE_READ_MESSAGE +
- e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
- }
- }
-
- // Set consensus sequence:
- AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
- String id = consensusModel.addSequence(CONSENSUS_NAME);
- consensusModel.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList(
- sequenceNode.getConsensusSequence().getString(), consensusModel.getTokenSet()));
- //TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
- }
-
-
- @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) {
- 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(String.format(Messages.AlignmentEditor_MUST_HAVE_TYPE,
- AlignmentEditorInput.class.getCanonicalName())); //TODO What should be done here?
- }
- }
-
-
- @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(
- Messages.AlignmentEditor_EDIT_MODE + (getReadsArea().getEditSettings().isInsert() ? Messages.AlignmentEditor_INSERT : Messages.AlignmentEditor_OVERWRITE) + " " + //$NON-NLS-1$
- Messages.AlignmentEditor_INSERTION_PHEROGRAM +
- (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? Messages.AlignmentEditor_LEFT : Messages.AlignmentEditor_RIGHT)); //TODO multi language
- }
-
-
- private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) {
- Iterator<ShiftChange> iterator = model.shiftChangeIterator();
- List<SingleReadAlignment.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 SingleReadAlignment.Shift[shifts.size()]);
- }
-
-
- @Override
- public void doSave(IProgressMonitor monitor) {
- if (getEditorInput() instanceof AlignmentEditorInput) {
- String taskName = Messages.AlignmentEditor_SAVING_ALIGNMENT; //TODO multi language
- monitor.beginTask(taskName, 3);
-
- //re-loading sequence to avoid session conflicts
- Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
- ((AlignmentEditorInput)getEditorInput()).setSequenceNode(sequenceNode);
- 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.setUnderlyingModel(getReadsArea().getAlignmentModel());
- sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values()); // Remove all reads that are not in the alignment anymore.
- Iterator<String> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
- while (iterator.hasNext()) {
- String id = iterator.next();
- SingleReadAlignment singleRead = cdmMap.get(id);
- if (singleRead == null) {
- throw new InternalError(Messages.AlignmentEditor_NEW_READ_FAILURE); //TODO multi language
- //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);
-
- ((AlignmentEditorInput)getEditorInput()).merge();
- // 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.
- }
- }
-
-
- @Override
- public void doSaveAs() {}
-
-
- @Override
- public void init(IEditorSite site, IEditorInput input) throws PartInitException {
- setSite(site);
- setInput(input);
- }
-
-
- @Override
- public boolean isDirty() {
- return dirty;
- }
-
-
- private void setDirty() {
- dirty = true;
- firePropertyChange(IEditorPart.PROP_DIRTY);
- }
-
-
- @Override
- public boolean isSaveAsAllowed() {
- return false; // "Save as" not allowed.
- }
-
-
- @Override
- public void setFocus() {
- if(conversationHolder != null){
- conversationHolder.bind();
- }
- ((AlignmentEditorInput)getEditorInput()).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 Messages.AlignmentEditor_CUTTING_FAILURE; //TODO multi language
- }
- else {
- PherogramArea pherogramArea =
- getPherogramArea(getReadsArea().getSequenceOrder().idByIndex(selection.getCursorRow()));
- if (pherogramArea == null) {
- return Messages.AlignmentEditor_NO_ATTACHED_PHEROGRAM; //TODO multi language
- }
- else {
- if (left) {
- if (pherogramArea.setLeftCutPositionBySelection()) {
- return null;
- }
- else {
- return Messages.AlignmentEditor_LEFT_END_OUTSIDE; //TODO multi language
- }
- }
- else {
- if (pherogramArea.setRightCutPositionBySelection()) {
- return null;
- }
- else {
- return Messages.AlignmentEditor_RIGHT_END_OUTSIDE; //TODO multi language
- }
- }
- }
- }
- }
-
-
- 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++) {
- String sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
- PherogramArea area = getPherogramArea(sequenceID);
- PherogramAreaModel pherogramAlignmentModel = area.getModel();
-
- PherogramAlignmentRelation rightRelation = pherogramAlignmentModel.editableIndexByBaseCallIndex(
- pherogramAlignmentModel.getRightCutPosition());
- int rightBorder;
- if (rightRelation.getCorresponding() == PherogramAlignmentRelation.OUT_OF_RANGE) {
- rightBorder = rightRelation.getBeforeValidIndex() + 1;
- }
- else {
- rightBorder = rightRelation.getAfterValidIndex();
- }
-
- AlignmentModelUtils.reverseComplement(model, sequenceID,
- pherogramAlignmentModel.editableIndexByBaseCallIndex(
- pherogramAlignmentModel.getLeftCutPosition()).getBeforeValidIndex(),
- rightBorder);
- pherogramAlignmentModel.reverseComplement();
- }
- }
-
-
- /**
- * Recreates the whole consensus sequence from all single read sequences. The previous consensus
- * sequence is overwritten.
- */
- @SuppressWarnings("unchecked")
- public <T> void createConsensusSequence() {
- ConsensusSequenceArea area = getConsensusHintDataArea();
- AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
- String 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();
- String 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) != null) {
- 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 String addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
- Integer firstSeqPos, Integer leftCutPos, Integer rightCutPos, SingleReadAlignment.Shift[] shifts)
- throws IOException, UnsupportedChromatogramFormatException {
-
- AlignmentModel model = 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:
- model.addSequence(name);
- String id = model.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, model.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(model.getTokenSet().tokenByRepresentation(
- Character.toString(pherogramProvider.getBaseCall(i))));
- }
- setDirty();
- }
-
- if (tokens != null) { // If either an edited sequence or a pherogram URI was provided.
- model.insertTokensAt(id, 0, tokens);
-
- if (pherogramProvider != null) {
- // Create pherogram area:
- PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(),
- new PherogramAreaModel(pherogramProvider));
-
- // Set position properties and shifts:
- PherogramAreaModel phergramModel = pherogramArea.getModel();
- if ((firstSeqPos != null) && (leftCutPos != null)) {
- phergramModel.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos);
- }
- if (rightCutPos != null) {
- phergramModel.setRightCutPosition(rightCutPos);
- }
- if ((shifts != null) && (shifts.length > 0)) {
- for (int i = 0; i < shifts.length; i++) {
- phergramModel.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;
- }
-
-
- public static URI getPherogramURI(SingleRead pherogramInfo) {
- if (pherogramInfo.getPherogram() != null) {
- return MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
- }
- else {
- return null;
- }
- }
-}
import org.eclipse.ui.actions.ActionFactory;\r
import org.eclipse.ui.commands.ICommandService;\r
\r
+import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;\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
* Listener used to update copy/paste events associated with {@link AlignmentEditor}.\r
- * \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
+ private static final String[] IDS = {ActionFactory.COPY.getCommandId(), ActionFactory.CUT.getCommandId(),\r
ActionFactory.PASTE.getCommandId()};\r
- \r
- \r
+\r
+\r
private void updateEvents() {\r
- ICommandService service = (ICommandService)PlatformUI.getWorkbench().getService(ICommandService.class);\r
+ ICommandService service = 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
+\r
+\r
@Override\r
public void handleEvent(Event event) {\r
- AlignmentEditor editor = AbstractAlignmentEditorHandler.getActiveAlignmentEditor();\r
+ AlignmentEditorE4 editor = AbstractAlignmentEditorHandler.getActiveAlignmentEditor();\r
if (editor != null) {\r
updateEvents();\r
}\r
}\r
\r
- \r
+\r
@Override\r
public void selectionChanged(SelectionChangeEvent e) {\r
- AlignmentEditor editor = AbstractAlignmentEditorHandler.getActiveAlignmentEditor();\r
+ AlignmentEditorE4 editor = AbstractAlignmentEditorHandler.getActiveAlignmentEditor();\r
if (editor != null) {\r
- if ((e.getSource() == editor.getReadsArea().getSelection()) || \r
+ if ((e.getSource() == editor.getReadsArea().getSelection()) ||\r
(e.getSource() == editor.getEditableConsensusArea().getSelection())) {\r
- \r
+\r
updateEvents();\r
}\r
}\r
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;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-
/**
@Override
public boolean mousePressed(TICMouseEvent event) {
- if (event.getClickCount() == 2) { // Double click
- try {
- ShowPherogramHandler.showPherogram(area.getModel());
- }
- catch (PartInitException e) {
- MessagingUtils.errorDialog(Messages.PherogramMouseListener_UNABLE_TO_CREATE_VIEW, null, e.getLocalizedMessage(),
- TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
- }
- return true;
- }
- else {
+// if (event.getClickCount() == 2) { // Double click
+// try {
+ //FIXME E4 implement double click functionality
+// ShowPherogramHandler.showPherogram(area.getModel());
+// }
+// catch (PartInitException e) {
+// MessagingUtils.errorDialog(Messages.PherogramMouseListener_UNABLE_TO_CREATE_VIEW, null, e.getLocalizedMessage(),
+// TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
+// }
+// return true;
+// }
+// else {
return false;
- }
+// }
}
}
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditorActionUpdater;
import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditorInput;
import eu.etaxonomy.taxeditor.molecular.editor.PherogramMouseListener;
-import eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler;
-import eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler;
+import eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleInsertOverwriteHandlerE4;
+import eu.etaxonomy.taxeditor.molecular.editor.e4.handler.ToggleLeftRightInsertionHandlerE4;
import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
import eu.etaxonomy.taxeditor.store.CdmStore;
import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;
@Override
public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
updateStatusBar();
- refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
+ refreshToolbarElement(ToggleLeftRightInsertionHandlerE4.COMMAND_ID);
}
@Override
public void insertChanged(EditSettingsChangeEvent e) {
updateStatusBar();
- refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
+ refreshToolbarElement(ToggleInsertOverwriteHandlerE4.COMMAND_ID);
}
});
}
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;
import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
import info.bioinfweb.libralign.pherogram.view.PherogramView;
/**
* Component that allows to view a pherogram without the distortion due to aligning it to a sequence as in
- * {@link AlignmentEditor}.
+ * {@link AlignmentEditorE4}.
*
* @author Ben Stöver
* @date Nov 20, 2014
import org.eclipse.swt.dnd.TextTransfer;
import org.eclipse.swt.widgets.Shell;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
/**
- * Handler that pastes the current contents of the clipboard into an active instance of {@link AlignmentEditor}.
+ * Handler that pastes the current contents of the clipboard into an active instance of {@link AlignmentEditorE4}.
*
* @author Ben Stöver
* @date 26.08.2015
import org.eclipse.e4.ui.model.application.ui.basic.MPart;
import org.eclipse.e4.ui.services.IServiceConstants;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
/**
* 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.
+ * of {@link AlignmentEditorE4}. A previously present consensus sequence will be overwritten.
*
* @author Ben Stöver
* @date 19.06.2015
* @see UpdateConsensusSequenceHandlerE4
- * @see AlignmentEditor#createConsensusSequence()
+ * @see AlignmentEditorE4#createConsensusSequence()
*/
public class CreateConsensusSequenceHandlerE4 {
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.e4.AlignmentEditorE4;
import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
/**
- * Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditor}.
+ * Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditorE4}.
*
* @author Ben Stöver
* @author pplitzner
import org.eclipse.e4.ui.model.application.ui.basic.MPart;
import org.eclipse.e4.ui.services.IServiceConstants;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
/**
- * Reverse complements the single read sequence in an active {@link AlignmentEditor}, where the alignment cursor
+ * Reverse complements the single read sequence in an active {@link AlignmentEditorE4}, where the alignment cursor
* is currently located.
*
* @author Ben Stöver
import eu.etaxonomy.cdm.model.molecular.SingleRead;
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;
+import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
import eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4;
import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
/**
- * Displays an undistorted pherogram with {@link PherogramViewPart}.
+ * Displays an undistorted pherogram with {@link PherogramPartE4}.
*
* @author Ben Stöver
*/
MPart part = partService.createPart(eu.etaxonomy.taxeditor.molecular.AppModelId.PARTDESCRIPTOR_EU_ETAXONOMY_TAXEDITOR_MOLECULAR_EDITOR_E4_PHEROGRAMPARTE4);
part = partService.showPart(part, PartState.ACTIVATE);
PherogramPartE4 pherogramPart = (PherogramPartE4) part.getObject();
- pherogramPart.init(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));
+ pherogramPart.init(new PherogramComponentModel(AlignmentEditorE4.readPherogram(uri)));
}
}
catch (Exception e) {
import org.eclipse.e4.ui.services.IServiceConstants;
import org.eclipse.jface.resource.ImageDescriptor;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
import eu.etaxonomy.taxeditor.molecular.handler.HandlerTools;
/**
- * Switches an {@link AlignmentEditor} between insertion and overwrite mode.
+ * Switches an {@link AlignmentEditorE4} between insertion and overwrite mode.
*
* @author Ben Stöver
* @date 04.12.2014
import org.eclipse.e4.ui.services.IServiceConstants;
import org.eclipse.jface.resource.ImageDescriptor;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
import eu.etaxonomy.taxeditor.molecular.handler.HandlerTools;
/**
- * Switches an {@link AlignmentEditor} between insertion in the base sequence to
+ * Switches an {@link AlignmentEditorE4} between insertion in the base sequence to
* the left or to the right.
*
* @author Ben Stöver
import org.eclipse.e4.ui.model.application.ui.basic.MPart;
import org.eclipse.e4.ui.services.IServiceConstants;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
+import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
import eu.etaxonomy.taxeditor.molecular.editor.e4.PherogramPartE4;
/**
* Toggles whether probability values (substitution, overcall and undercall) should be displayed
- * in pherogram areas of {@link AlignmentEditor} or {@link PherogramViewPart}.
+ * in pherogram areas of {@link AlignmentEditorE4} or {@link PherogramPartE4}.
*
* @author Ben Stöver
* @date 23.06.2015
import org.eclipse.core.commands.ExecutionException;
import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
+import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;
/**
* Abstract implementation for all handlers triggering actions in an active instance of
- * {@link AlignmentEditor}.
+ * {@link AlignmentEditorE4}.
*
* @author Ben Stöver
* @date 19.06.2015
*/
public abstract class AbstractAlignmentEditorHandler extends AbstractHandler {
- public static AlignmentEditor getActiveAlignmentEditor() {
+ public static AlignmentEditorE4 getActiveAlignmentEditor() {
Object activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- return (AlignmentEditor)activeEditor;
+ if (activeEditor instanceof AlignmentEditorE4) {
+ return (AlignmentEditorE4)activeEditor;
}
else {
return null;
@Override
public Object execute(ExecutionEvent event) throws ExecutionException {
- AlignmentEditor editor = getActiveAlignmentEditor();
+ AlignmentEditorE4 editor = getActiveAlignmentEditor();
if (editor != null) {
doExecute(event, editor);
}
}
- protected abstract void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException;
+ protected abstract void doExecute(ExecutionEvent event, AlignmentEditorE4 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
-/**
-* 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.util.Iterator;
-
-import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.commands.ExecutionEvent;
-import org.eclipse.core.commands.ExecutionException;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
-import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
-import info.bioinfweb.libralign.pherogram.PherogramComponent;
-
-
-
-/**
- * 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 {
- Object activePart = AbstractUtility.getActivePart();
-
- if (activePart instanceof AlignmentEditor) {
- AlignmentEditor editor = (AlignmentEditor)activePart;
- Iterator<String> 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
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
-import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
-import info.bioinfweb.libralign.model.utils.AlignmentModelUtils;
-
-import java.util.Map;
-
-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 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
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;\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.utils.AlignmentModelUtils;\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, String sequenceID, String content) {\r
- area.getActionProvider().deleteSelection(); // Overwrite selected tokens.\r
- area.getActionProvider().elongateSequence(sequenceID, area.getSelection().getCursorColumn());\r
-\r
- @SuppressWarnings("unchecked")\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("")) { //$NON-NLS-1$\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
- String 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
- Messages.AlignmentEditorPasteHandler_PASTING_LINES, null,\r
- String.format(Messages.AlignmentEditorPasteHandler_PASTING_LINES_QUESTION, lines.size()),\r
- MessageDialog.QUESTION,\r
- new String[]{Messages.AlignmentEditorPasteHandler_PASTING_LINES_IGNORE,\r
- Messages.AlignmentEditorPasteHandler_PASTING_LINES_FIRST_LINE, Messages.AlignmentEditorPasteHandler_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
- Messages.AlignmentEditorPasteHandler_PASTE_FAILURE,\r
- String.format(Messages.AlignmentEditorPasteHandler_PASTE_FAILURE_MESSAGE, selection.getCursorHeight(), lines.size(), System.getProperty("line.separator"))); //$NON-NLS-1$\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
+++ /dev/null
-/**
-* 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
-/**
-* 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;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-
-
-
-/**
- * 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(Messages.CutPherogramLeftHandler_CUT_FAILURE, this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);
- }
- }
-}
+++ /dev/null
-/**
-* 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;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-
-
-
-/**
- * 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(Messages.CutPherogramRightHandler_CUT_FAILURE, this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);
- }
- }
-}
+++ /dev/null
-package eu.etaxonomy.taxeditor.molecular.handler;
-
-
-import javax.inject.Named;
-
-import org.eclipse.e4.core.di.annotations.CanExecute;
-import org.eclipse.e4.core.di.annotations.Execute;
-import org.eclipse.e4.core.di.annotations.Optional;
-import org.eclipse.e4.ui.model.application.ui.menu.MHandledMenuItem;
-import org.eclipse.e4.ui.services.IServiceConstants;
-import org.eclipse.jface.viewers.TreeNode;
-
-import eu.etaxonomy.cdm.model.molecular.Sequence;
-
-
-
-/**
- * Opens the alignment editor from the CDM tree.
- *
- * @author Ben Stöver
- * @author pplitzner
- */
-public class EditSequenceHandler {
- private org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(EditSequenceHandler.class);
-
-
- @Execute
- public void execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection) {
- 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(Messages.EditSequenceHandler_COULD_NOT_OPEN, e);
-// }
- }
- }
-
- @CanExecute
- public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {
- boolean canExecute = false;
- if(selectedTreeNode!=null){
- Object value = selectedTreeNode.getValue();
- canExecute = value instanceof Sequence;
- }
- menuItem.setVisible(canExecute);
- return canExecute;
- }
-}
+++ /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2016 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import java.io.File;\r
-import java.io.IOException;\r
-\r
-import javax.inject.Named;\r
-\r
-import org.eclipse.core.runtime.IStatus;\r
-import org.eclipse.e4.core.di.annotations.CanExecute;\r
-import org.eclipse.e4.core.di.annotations.Execute;\r
-import org.eclipse.e4.core.di.annotations.Optional;\r
-import org.eclipse.e4.ui.model.application.ui.menu.MHandledMenuItem;\r
-import org.eclipse.e4.ui.services.IServiceConstants;\r
-import org.eclipse.jface.viewers.TreeNode;\r
-import org.eclipse.jface.wizard.WizardDialog;\r
-import org.eclipse.swt.widgets.Shell;\r
-\r
-import eu.etaxonomy.cdm.model.molecular.Sequence;\r
-import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
-import eu.etaxonomy.taxeditor.molecular.io.CDMPherogramAlignmentObjectTranslator;\r
-import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;\r
-import eu.etaxonomy.taxeditor.molecular.io.SingleReadAlignmentRDFXMLConstants;\r
-import eu.etaxonomy.taxeditor.molecular.io.wizard.ExportSingleReadAlignmentWizard;\r
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;\r
-import eu.etaxonomy.taxeditor.util.ApplicationUtil;\r
-import info.bioinfweb.jphyloio.JPhyloIOEventWriter;\r
-import info.bioinfweb.jphyloio.ReadWriteParameterMap;\r
-import info.bioinfweb.jphyloio.ReadWriteParameterNames;\r
-import info.bioinfweb.jphyloio.dataadapters.implementations.ListBasedDocumentDataAdapter;\r
-import info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory;\r
-import info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory;\r
-\r
-\r
-\r
-/**\r
- * Allows to export a single read alignment to various alignment formats using\r
- * <a href="http://bioinfweb.info/JPhyloIO/"><i>JPhyloIO</i></a>.\r
- *\r
- * @author Ben Stöver\r
- * @date 24.04.2016\r
- */\r
-public class ExportSequenceToFileHandler {\r
- private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();\r
-\r
-\r
- @Execute\r
- public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection,\r
- @Named(IServiceConstants.ACTIVE_SHELL)Shell shell) {\r
- if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence) {\r
- Sequence sequence = (Sequence)treeNodeOfSelection.getValue();\r
-\r
- final ExportSingleReadAlignmentWizard wizard = new ExportSingleReadAlignmentWizard();\r
- final WizardDialog dialog = new WizardDialog(shell, wizard);\r
- if (dialog.open() == IStatus.OK) {\r
- // Prepare writer parameters:\r
- ReadWriteParameterMap parameters = new ReadWriteParameterMap();\r
- parameters.put(ReadWriteParameterNames.KEY_APPLICATION_NAME, ApplicationUtil.getTitle());\r
- //parameters.put(ReadWriteParameterNames.KEY_APPLICATION_VERSION, ApplicationUtil.getVersion()); // Setting the version unnecessary, since its already contained in the title.\r
- parameters.put(ReadWriteParameterNames.KEY_APPLICATION_URL, "http://cybertaxonomy.eu/taxeditor/"); //TODO Specify URL obtained from a central class? //$NON-NLS-1$\r
- parameters.put(ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN, wizard.getModel().getElongationToken());\r
-\r
- // Create and register object translator for writing pherogram alignment shifts:\r
- ObjectTranslatorFactory translatorFactory = new ObjectTranslatorFactory();\r
- translatorFactory.addXSDTranslators(true);\r
- translatorFactory.addTranslator(new CDMPherogramAlignmentObjectTranslator(), true, SingleReadAlignmentRDFXMLConstants.DATA_TYPE_PHERORAGM_ALIGNMENT);\r
- parameters.put(ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY, translatorFactory);\r
-\r
- // Create writer and document adapters:\r
- JPhyloIOEventWriter writer = factory.getWriter(wizard.getModel().getFormatInfo().getFormatID());\r
- ListBasedDocumentDataAdapter document = new ListBasedDocumentDataAdapter();\r
- document.getMatrices().add(new CDMSequenceMatrixAdapter(sequence, wizard.getModel().getConsensusSequenceLabel(),\r
- wizard.getModel().isExportConsensusSequence(), wizard.getModel().isExportSingleReads()));\r
-\r
- // Write document:\r
- File file = new File(wizard.getModel().getFileName());\r
- if (!file.exists() || MessagingUtils.confirmDialog(Messages.exportSequenceToFileHandlerOverwriteTitle, String.format(\r
- Messages.exportSequenceToFileHandlerOverwriteText, file.getAbsolutePath()))) {\r
-\r
- try {\r
- writer.writeDocument(document, file, parameters);\r
- }\r
- catch (IOException e) {\r
- e.printStackTrace();\r
- MessagingUtils.errorDialog(Messages.exportSequenceToFileHandlerIOErrorTitle, this,\r
- String.format(Messages.exportSequenceToFileHandlerIOErrorMessage,\r
- file.getAbsolutePath()), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);\r
- }\r
- }\r
-\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- @CanExecute\r
- public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {\r
- boolean canExecute = false;\r
- if(selectedTreeNode!=null){\r
- Object value = selectedTreeNode.getValue();\r
- canExecute = value instanceof Sequence;\r
- }\r
- menuItem.setVisible(canExecute);\r
- return canExecute;\r
- }\r
-}\r
+++ /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 eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.model.MessagingUtils;
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-
-
-
-/**
- * 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.
-
- @Override
- public Object execute(ExecutionEvent event) throws ExecutionException {
- Object activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- AlignmentEditor alignmentEditor = (AlignmentEditor)activeEditor;
-
- FileDialog fileDialog = new FileDialog(alignmentEditor.getSite().getShell());
- fileDialog.setText(Messages.LoadPherogramHandler_IMPORT_PHEROGRAM);
- fileDialog.setFilterNames(new String[]{Messages.LoadPherogramHandler_ALL_FORMATS, Messages.LoadPherogramHandler_AB1, Messages.LoadPherogramHandler_SCF, Messages.LoadPherogramHandler_ALL});
- fileDialog.setFilterExtensions(new String[]{"*.ab1;*.scf", "*.ab1", "*.scf", "*.*"}); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
-
- String path = fileDialog.open();
- if (path != null) {
- try {
- alignmentEditor.addRead(new File(path).toURI(), false);
- }
- catch (UnsupportedChromatogramFormatException e) {
- MessagingUtils.errorDialog(Messages.LoadPherogramHandler_UNSUPPORTED_FORMAT, this,
- String.format(Messages.LoadPherogramHandler_UNSUPPORTED_FORMAT_MESSAGE, path), TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
- }
- catch (IOException e) {
- MessagingUtils.errorDialog(Messages.LoadPherogramHandler_UNSUPPORTED_FORMAT_FILE, this,
- Messages.LoadPherogramHandler_UNSUPPORTED_FORMAT_FILE_MESSAGE + 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 java.net.URI;
-
-import javax.inject.Named;
-
-import org.eclipse.e4.core.di.annotations.CanExecute;
-import org.eclipse.e4.core.di.annotations.Execute;
-import org.eclipse.e4.core.di.annotations.Optional;
-import org.eclipse.e4.ui.model.application.ui.menu.MHandledMenuItem;
-import org.eclipse.e4.ui.services.IServiceConstants;
-import org.eclipse.jface.viewers.TreeNode;
-import org.eclipse.ui.PartInitException;
-
-import eu.etaxonomy.cdm.model.media.MediaUtils;
-import eu.etaxonomy.cdm.model.molecular.SingleRead;
-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;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
-
-
-
-/**
- * Displays an undistorted pherogram with {@link PherogramViewPart}.
- *
- * @author Ben Stöver
- */
-public class ShowPherogramHandler {
- public static void showPherogram(PherogramComponentModel model) throws PartInitException {
- PherogramViewPart.createView(model);
- }
-
-
- @Execute
- public Object execute(@Optional@Named(IServiceConstants.ACTIVE_SELECTION)TreeNode treeNodeOfSelection) {
- 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(Messages.ShowPherogramHandler_NO_PHEROGRAM, this,
- Messages.ShowPherogramHandler_NO_PHEROGRAM_MESSAGE);
- }
- else {
- showPherogram(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));
- }
- }
- catch (Exception e) {
- MessagingUtils.errorDialog(Messages.ShowPherogramHandler_ERROR, null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,
- e, false);
- }
- }
- return null;
- }
-
- @CanExecute
- public boolean canExecute(@Optional @Named(IServiceConstants.ACTIVE_SELECTION) TreeNode selectedTreeNode, MHandledMenuItem menuItem) {
- boolean canExecute = false;
- if(selectedTreeNode!=null){
- Object value = selectedTreeNode.getValue();
- canExecute = value instanceof SingleRead;
- }
- menuItem.setVisible(canExecute);
- return canExecute;
- }
-}
+++ /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.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;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-
-
-
-/**
- * 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"; //$NON-NLS-1$
-
-
- private final ImageDescriptor INSERT_DESCRIPTOR = HandlerTools.createImageDescriptor("insert-16x16.png"); //$NON-NLS-1$
- private final ImageDescriptor OVERWRITE_DESCRIPTOR = HandlerTools.createImageDescriptor("overwrite-16x16.png"); //$NON-NLS-1$
-
-
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.toggleInsertOverwrite();
- }
-
-
- @Override
- public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
- Object activeEditor = AbstractUtility.getActiveEditor();
- if (activeEditor instanceof AlignmentEditor) {
- if (((AlignmentEditor)activeEditor).isInsertMode()) {
- element.setIcon(INSERT_DESCRIPTOR);
- element.setText("INS"); //$NON-NLS-1$
- element.setTooltip(Messages.ToggleInsertOverwriteHandler_SWITCH_OVERWRITE);
- }
- else {
- element.setIcon(OVERWRITE_DESCRIPTOR);
- element.setText("OVR"); //$NON-NLS-1$
- element.setTooltip(Messages.ToggleInsertOverwriteHandler_SWITCH_INSERTION);
- }
- 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.commands.IElementUpdater;
-import org.eclipse.ui.menus.UIElement;
-
-import eu.etaxonomy.taxeditor.model.AbstractUtility;
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
-import eu.etaxonomy.taxeditor.molecular.l10n.Messages;
-
-
-
-/**
- * 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"; //$NON-NLS-1$
-
-
- private final ImageDescriptor INSERT_LEFT_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-left-16x16.png"); //$NON-NLS-1$
- private final ImageDescriptor INSERT_RIGHT_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-right-16x16.png"); //$NON-NLS-1$
- private final ImageDescriptor INSERT_LEFT_DISABLED_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-left-disabled-16x16.png"); //$NON-NLS-1$
- private final ImageDescriptor INSERT_RIGHT_DISABLED_DESCRIPTOR =
- HandlerTools.createImageDescriptor("pherogram-insert-right-disabled-16x16.png"); //$NON-NLS-1$
-
-
- @Override
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
- editor.toggleLeftRightInsertionInPherogram();
- }
-
-
- @Override
- public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
- Object 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(Messages.ToggleLeftRightInsertionHandler_LEFT);
- element.setTooltip(Messages.ToggleLeftRightInsertionHandler_SWITCH_RIGHT);
- }
- else {
- element.setIcon(INSERT_RIGHT_DESCRIPTOR);
- element.setDisabledIcon(INSERT_RIGHT_DISABLED_DESCRIPTOR);
- element.setText(Messages.ToggleLeftRightInsertionHandler_RIGHT);
- element.setTooltip(Messages.ToggleLeftRightInsertionHandler_SWITCH_LEFT);
- }
- }
- }
-}
+++ /dev/null
-/**
-* 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
-/**
-* 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
-/**
- * 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 AlignmentEditorE4.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;
\r
import eu.etaxonomy.cdm.model.molecular.Sequence;\r
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
+import eu.etaxonomy.taxeditor.molecular.editor.e4.AlignmentEditorE4;\r
import eu.etaxonomy.taxeditor.molecular.l10n.Messages;\r
import info.bioinfweb.commons.bio.CharacterStateSetType;\r
import info.bioinfweb.commons.io.W3CXSConstants;\r
writeMetadataEvents(receiver, sequenceID, PREDICATE_HAS_LEFT_CUT_POSITION, W3CXSConstants.DATA_TYPE_INT, singleRead.getLeftCutPosition());\r
writeMetadataEvents(receiver, sequenceID, PREDICATE_HAS_RIGHT_CUT_POSITION, W3CXSConstants.DATA_TYPE_INT, singleRead.getRightCutPosition());\r
\r
- URI pherogramURI = AlignmentEditor.getPherogramURI(singleRead.getSingleRead());\r
+ URI pherogramURI = AlignmentEditorE4.getPherogramURI(singleRead.getSingleRead());\r
if (pherogramURI != null) {\r
JPhyloIOWritingUtils.writeTerminalResourceMetadata(receiver, createMetadataID(sequenceID, PREDICATE_HAS_PHEROGRAM),\r
null, PREDICATE_HAS_PHEROGRAM, pherogramURI);\r
BGBM BDI Projects / taxeditor.git / commitdiff