EDIT

// $Id$

/**

* Copyright (C) 2014 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.taxeditor.molecular.editor;

import info.bioinfweb.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.PherogramAreaModel;

import info.bioinfweb.libralign.pherogram.model.ShiftChange;

import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider;

import info.bioinfweb.libralign.pherogram.provider.PherogramProvider;

import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider;

import info.bioinfweb.tic.SWTComponentFactory;

import java.io.File;

import java.io.IOException;

import java.io.InputStream;

import java.net.URI;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.TreeMap;

import org.biojava.bio.chromatogram.ChromatogramFactory;

import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;

import org.eclipse.core.runtime.IProgressMonitor;

import org.eclipse.swt.SWT;

import org.eclipse.swt.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.store.CdmStore;

import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;

/**

 * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to

 * a consensus sequence.

 * <p>

 * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.

 *

 * @author Ben Stöver

 * @author pplitzner

 * @date 04.08.2014

 */

public class AlignmentEditor extends EditorPart {

    public static final String ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor";

	public static final int READS_AREA_INDEX = 1;

    public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;

    public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1;

	public static final int PHEROGRAM_AREA_INDEX = 0;

	public static final int CONSENSUS_DATA_AREA_INDEX = 0;

	public static final String DEFAULT_READ_NAME_PREFIX = "Read ";

	public static final String CONSENSUS_NAME = "Consensus";

    private final ConversationHolder conversationHolder;

	private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() {

				@Override

				public <T> void afterTokenChange(TokenChangeEvent<T> e) {

					setDirty();

				}

				@Override

				public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) {

					setDirty();

				}

				@Override

				public <T> void afterSequenceChange(SequenceChangeEvent<T> e) {

					setDirty();

				}

				@Override

				public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider,

						AlignmentModel<U> newProvider) {  // Not expected.

					setDirty();

				}

			};

	private 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);

            //addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false);

            addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/Test_qualityScore.scf").toURI(), false);

			// Add test consensus sequence:

			AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();

			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"));

			tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));

			tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G"));

			tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T"));

			consensusModel.insertTokensAt(id, 0, tokens);

		}

		catch (Exception e) {

			throw new RuntimeException(e);

		}

    }

    private void readCDMData(Sequence sequenceNode) {

    	//TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).

		// Add reads:

		for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) {

			try {

				SingleRead pherogramInfo = singleReadAlignment.getSingleRead();

				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("Error", null, "A single read was skipped because of the following error:\n\n" +

                        e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);

			}

		}

		// Set consensus sequence:

		AlignmentModel 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("The editor input must have the 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("Edit mode: " +

        		(getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + "  " +

        		"Insertion in pherogram: " +

	       		(getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));

    }

    private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) {

    	Iterator<ShiftChange> iterator = model.shiftChangeIterator();

    	List<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 = "Saving alignment";

            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("Creating new reads from AlignmentEditor not implemented.");

    				//TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved?

    				//singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence);

    			}

    			singleRead.setEditedSequence(stringProvider.getSequence(id));

    			PherogramArea pherogramArea = getPherogramArea(id);

    			if (pherogramArea != null) {

        			PherogramAreaModel model = pherogramArea.getModel();

        			singleRead.setReverseComplement(model.getPherogramProvider() instanceof ReverseComplementPherogramProvider);  // Works only if ReverseComplementPherogramProvider instances are not nested.

        			singleRead.setShifts(convertToCDMShifts(getPherogramArea(id).getModel()));

        			singleRead.setFirstSeqPosition(model.getFirstSeqPos());

        			singleRead.setLeftCutPosition(model.getLeftCutPosition());

        			singleRead.setRightCutPosition(model.getRightCutPosition());

    			}

    		}

    		if (!conversationHolder.isBound()) {

                conversationHolder.bind();

            }

            monitor.worked(1);

            ((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 "Cutting pherograms is only possible if exactly one row is selected.";

        }

        else {

            PherogramArea pherogramArea =

                    getPherogramArea(getReadsArea().getSequenceOrder().idByIndex(selection.getCursorRow()));

            if (pherogramArea == null) {

                return "There is no pherogram attached to the current sequence.";

            }

            else {

                if (left) {

                    if (pherogramArea.setLeftCutPositionBySelection()) {

                        return null;

                    }

                    else {

                        return "The left end of the selection lies outside the pherogram attached to this sequence.";

                    }

                }

                else {

                    if (pherogramArea.setRightCutPositionBySelection()) {

                        return null;

                    }

                    else {

                        return "The right end of the selection lies outside the pherogram attached to this sequence.";

                    }

                }

            }

        }

    }

    public String cutPherogramLeft() {

        return cutPherogram(true);

    }

    public String cutPherogramRight() {

        return cutPherogram(false);

    }

    public void reverseComplementSelectedSequences() {

    	SelectionModel selection = getReadsArea().getSelection();

    	AlignmentModel<?> model = getReadsArea().getAlignmentModel();

    	for (int row = selection.getFirstRow(); row < selection.getFirstRow() + selection.getCursorHeight(); row++) {

    		String sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);

			PherogramArea area = getPherogramArea(sequenceID);

			PherogramAreaModel pherogramAlignmentModel = area.getModel();

			AlignmentModelUtils.reverseComplement(model, sequenceID,

			        pherogramAlignmentModel.editableIndexByBaseCallIndex(

			                pherogramAlignmentModel.getLeftCutPosition()).getBeforeValidIndex(),

			        pherogramAlignmentModel.editableIndexByBaseCallIndex(

			                pherogramAlignmentModel.getRightCutPosition()).getAfterValidIndex());

			pherogramAlignmentModel.reverseComplement();

		}

    }

    /**

     * Recreates the whole consensus sequence from all single read sequences. The previous consensus

     * sequence is overwritte.

     */

    @SuppressWarnings("unchecked")

    public <T> void createConsensusSequence() {

        ConsensusSequenceArea area = getConsensusHintDataArea();

        AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();

        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;

        }

    }

}