EDIT

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditor.java -text

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditor.java -text

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text

org.eclipse.ui/SHOW_PROGRESS_ON_STARTUP = true

org.eclipse.ui/SHOW_TRADITIONAL_STYLE_TABS=false

org.eclipse.ui/DOCK_PERSPECTIVE_BAR=top-right

            class="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"

            commandId="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler">

      </handler>

   </extension>

   <extension

         name="%extension.name"

            id="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"

            name="Open Alignment Editor">

      </command>

   </extension>

   <extension

            id="eu.etaxonomy.taxeditor.bindings.scheme.default"

            name="%scheme.name">

      </scheme>

   </extension>

    <extension

         point="org.eclipse.ui.importWizards">

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.sequenceprovider.implementations.BioJavaSequenceDataProvider;

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

import org.biojava.bio.chromatogram.ChromatogramFactory;

import org.biojava3.core.sequence.DNASequence;

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

 * 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;

//			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.

					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());

//			}

					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);

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

			PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(

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

			pherogramArea.setFirstSeqPos(1);

			pherogramArea.setLeftCutPosition(13);

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

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

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

			pherogramArea.setFirstSeqPos(1);

			pherogramArea.setLeftCutPosition(267);

			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);

		}

//				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"));

//				new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(

//						new BioJavaTokenSet<NucleotideCompound>(

//								AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),

//						alignment);

//		AlignmentArea result = new AlignmentArea();

//		result.setSequenceProvider(sequenceProvider, false);

//		SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);

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

//		return result;

	}

    /* (non-Javadoc)

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

     */

		//getSite().setSelectionProvider(provider)

    }

    /* (non-Javadoc)

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

     */

    }

    /* (non-Javadoc)

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

     */

        // TODO Auto-generated method stub

    }

    /* (non-Javadoc)

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

        setSite(site);

        setInput(input);

    }

    /* (non-Javadoc)

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

        return false;

    }

    /* (non-Javadoc)

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

     */

        // TODO Auto-generated method stub

        return false;

    }

    /* (non-Javadoc)

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