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.editor.molecular;

import info.bioinfweb.libralign.alignmentarea.AlignmentArea;

import info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea;

import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;

import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;

import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;

import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent;

import info.bioinfweb.libralign.editsettings.EditSettingsListener;

import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;

import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;

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

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

import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider;

import info.bioinfweb.libralign.sequenceprovider.implementations.PackedSequenceDataProvider;

import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;

import info.bioinfweb.libralign.sequenceprovider.tokenset.TokenSet;

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.Map;

import java.util.TreeMap;

import org.biojava.bio.chromatogram.ChromatogramFactory;

import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;

import org.biojava3.core.sequence.compound.DNACompoundSet;

import org.biojava3.core.sequence.compound.NucleotideCompound;

import org.eclipse.core.runtime.IProgressMonitor;

import org.eclipse.swt.SWT;

import org.eclipse.swt.widgets.Composite;

import org.eclipse.ui.IActionBars;

import org.eclipse.ui.IEditorInput;

import org.eclipse.ui.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.taxeditor.editor.handler.ToggleInsertOverwriteHandler;

import eu.etaxonomy.taxeditor.editor.handler.ToggleLeftRightInsertionHandler;

/**

 * 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.editor.molecular.AlignmentEditor";

	public static final int READS_AREA_INDEX = 1;

	public static final int CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;

	public static final String DEFAULT_READ_NAME_PREFIX = "Read ";

    private MultipleAlignmentsContainer alignmentsContainer = null;

    private Map<Integer, URI> uriMap = new TreeMap<Integer, URI>();  //TODO Move this to ContigSequenceDataProvider

    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 result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(false);

		result.getContentArea().getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea()));

		return result;

    }

    private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {

		AlignmentArea result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(allowVerticalScrolling);

		TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(new DNACompoundSet(), true);

		SequenceDataProvider<NucleotideCompound> provider = new PackedSequenceDataProvider<NucleotideCompound>(tokenSet);

		result.getContentArea().setSequenceProvider(provider, false);

		return result;

	}

    private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container, 

    		SequenceDataProvider<?> sequenceProvider) {

		AlignmentArea result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(false);

		result.getContentArea().getDataAreas().getBottomAreas().add(

				new ConsensusSequenceArea(result.getContentArea(), sequenceProvider));

		return result;

    }

    private MultipleAlignmentsContainer getAlignmentsContainer() {

    	if (alignmentsContainer == null) {

    		alignmentsContainer = new MultipleAlignmentsContainer();

    		AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();

    		list.add(createIndexArea(alignmentsContainer));

    		AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);

    		list.add(readsArea);  // Make sure READS_AREA_INDEX is correct.

    		list.add(createEditableAlignmentArea(alignmentsContainer, false));  // Make sure COMSENSUS_AREA_INDEX is correct.

    		list.add(createConsensusHintArea(alignmentsContainer, 

    				readsArea.getContentArea().getSequenceProvider()));

    		registerEditSettingListener(alignmentsContainer);

       	}

		return alignmentsContainer;

	}

    private AlignmentArea getReadsArea() {

    	return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);

    }

    private AlignmentArea getConsensusArea() {

    	return getAlignmentsContainer().getAlignmentAreas().get(CONSENSUS_AREA_INDEX);

    }

	/* (non-Javadoc)

     * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)

     */

    @Override

    public void createPartControl(Composite parent) {

		getAlignmentsContainer().createSWTWidget(parent, SWT.NONE);

		updateStatusBar();

		// Just for testing:

		try {

			addRead(new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI());

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

			// Add test consensus sequence:

			SequenceDataProvider consensusProvider = getConsensusArea().getContentArea().getSequenceProvider();

			int id = consensusProvider.addSequence("Consensus");

			Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.

			tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('A'));

			tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('C'));

			tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('G'));

			tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('T'));

			consensusProvider.insertTokensAt(id, 0, tokens);

		}

		catch (Exception e) {

			throw new RuntimeException(e);

		}

    }

    private void updateStatusBar() {

        IActionBars bars = getEditorSite().getActionBars();

        bars.getStatusLineManager().setMessage("Edit mode: " + 

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

        		"Insertion in pherogram: " +

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

    }

    /* (non-Javadoc)

     * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)

     */

    @Override

    public void doSave(IProgressMonitor monitor) {

        // TODO Auto-generated method stub

    }

    /* (non-Javadoc)

     * @see org.eclipse.ui.part.EditorPart#doSaveAs()

     */

    @Override

    public void doSaveAs() {

        // TODO Auto-generated method stub

    }

    /* (non-Javadoc)

     * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)

     */

    @Override

    public void init(IEditorSite site, IEditorInput input) throws PartInitException {

        setSite(site);

        setInput(input);

    }

    /* (non-Javadoc)

     * @see org.eclipse.ui.part.EditorPart#isDirty()

     */

    @Override

    public boolean isDirty() {

        // TODO Auto-generated method stub

        return false;

    }

    /* (non-Javadoc)

     * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()

     */

    @Override

    public boolean isSaveAsAllowed() {

        // TODO Auto-generated method stub

        return false;

    }

    @Override

    public void setFocus() {}

    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();

    }

	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().getContentArea().getSequenceProvider().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) 

				!= SequenceDataProvider.NO_SEQUENCE_FOUND) {

			index++;

		}

		return DEFAULT_READ_NAME_PREFIX + index;

	}

    public void addRead(URI pherogramURI) throws IOException, UnsupportedChromatogramFormatException {

    	addRead(newReadName(), pherogramURI);

    }

    public void addRead(String name, URI pherogramURI) throws IOException, UnsupportedChromatogramFormatException {

		AlignmentContentArea contentArea = getReadsArea().getContentArea();

		SequenceDataProvider provider = contentArea.getSequenceProvider();

		PherogramProvider pherogramProvider = readPherogram(pherogramURI);  // Must happen before a sequence is added, because it might throw an exception.

        // Create sequence:

		provider.addSequence(name);

		int id = provider.sequenceIDByName(name);

		// Copy base call sequence into alignment:

		Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.

		for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {

			tokens.add(provider.getTokenSet().tokenByKeyChar(

				pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));

		}

		provider.insertTokensAt(id, 0, tokens);

		// Add data area:

		PherogramArea pherogramArea = new PherogramArea(contentArea, pherogramProvider);

		pherogramArea.addMouseListener(new PherogramMouseListener(pherogramURI));

		contentArea.getDataAreas().getSequenceAreas(id).add(pherogramArea);

		// Save source URI:

		uriMap.put(id, pherogramURI);

	}

}