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.commons.bio.biojava3.alignment.SimpleAlignment;

import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;

import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;

import info.bioinfweb.libralign.AlignmentArea;

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.pherogram.BioJavaPherogramProvider;

import info.bioinfweb.libralign.pherogram.PherogramProvider;

import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider;

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

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

import java.io.File;

import org.biojava.bio.chromatogram.ChromatogramFactory;

import org.biojava3.core.sequence.DNASequence;

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.IEditorInput;

import org.eclipse.ui.IEditorSite;

import org.eclipse.ui.PartInitException;

import org.eclipse.ui.part.EditorPart;

/**

 * 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 pplitzner

 * @author Ben Stöver

 * @date 04.08.2014

 */

public class AlignmentEditor extends EditorPart {

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

    private AlignmentArea alignmentArea;

	private AlignmentArea createAlignmentArea() {

		try {

			//ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf");

			//System.out.println(AlignmentEditor.class.getResource("/"));

			//System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf"));

//			BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(

//					new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));

		    //TODO Replace this absolute path with a path working with every workspace location.

			Alignment<DNASequence, NucleotideCompound> alignment =

					new SimpleAlignment<DNASequence, NucleotideCompound>();

			alignment.add("Read 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCA-CCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));

			alignment.add("Read 2", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));

			//alignment.add("Consensus edit 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));

//			StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());

//			for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {

//				seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());

//			}

//			alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) +

//					seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49)));  // One A is deleted for shift change specified below.

			BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =

					new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(

							new BioJavaTokenSet<NucleotideCompound>(

									AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),

							alignment);

			AlignmentArea result = new AlignmentArea();

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

			SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result.getContentArea());

			//sequenceIndexArea.setFirstIndex(5);

			//sequenceIndexArea.setHeight(25);

			result.getContentArea().getDataAreas().getTopAreas().add(sequenceIndexArea);

//			PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);

//			pherogramArea.setFirstSeqPos(34 + 5);

//			pherogramArea.setLeftCutPosition(34);

//			pherogramArea.setRightCutPosition(820);

//			pherogramArea.getAlignmentModel().setShiftChange(38, -1);

//			pherogramArea.getAlignmentModel().setShiftChange(49, 2);

//			result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea);

			PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(

				    new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1")));

			PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);

			pherogramArea.setFirstSeqPos(1);

			pherogramArea.setLeftCutPosition(13);

			pherogramArea.setRightCutPosition(697);

			pherogramArea.getAlignmentModel().setShiftChange(14, 1);

			pherogramArea.getAlignmentModel().setShiftChange(35, 1);

			result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);

	  		pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(

  				new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1"))));

			pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);

			pherogramArea.setFirstSeqPos(1);

			pherogramArea.setLeftCutPosition(267);

			pherogramArea.getAlignmentModel().setShiftChange(273, -1);

			pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale());

			result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);

	  	    result.getContentArea().getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result.getContentArea()));

			return result;

		}

		catch (Exception e) {

			throw new RuntimeException(e);

		}

//		Alignment<DNASequence, NucleotideCompound> alignment =

//				new SimpleAlignment<DNASequence, NucleotideCompound>();

//		alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));

//		alignment.add("Sequence 2", new DNASequence("AT-GTTG"));

//		alignment.add("Sequence 3", new DNASequence("AT-GTAG"));

//

//		BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =

//				new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(

//						new BioJavaTokenSet<NucleotideCompound>(

//								AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),

//						alignment);

//

//		AlignmentArea result = new AlignmentArea();

//		result.setSequenceProvider(sequenceProvider, false);

//		SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);

//		//sequenceIndexArea.setFirstIndex(5);

//		//sequenceIndexArea.setHeight(25);

//		result.getDataAreas().getTopAreas().add(sequenceIndexArea);

//		result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));

//		return result;

	}

    /* (non-Javadoc)

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

     */

    @Override

    public void createPartControl(Composite parent) {

    	alignmentArea = createAlignmentArea();

		Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);

		//getSite().setSelectionProvider(provider)

    }

    /* (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;

    }

    /* (non-Javadoc)

     * @see org.eclipse.ui.part.WorkbenchPart#setFocus()

     */

    @Override

    public void setFocus() {

    	//alignmentArea.getToolkitComponent().redistributeHeight();

    }

}