EDIT

import java.io.File;

import java.io.IOException;

import java.io.InputStream;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

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.

    private MultipleAlignmentsContainer alignmentsContainer = null;

    @Inject

    private MDirtyable dirty;

    public AlignmentEditorE4() {

    }

    private void refreshToolbarElement(String id) {

		ICommandService commandService =

				PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);

		}

    }

    private void registerEditSettingListener(MultipleAlignmentsContainer container) {

        container.getEditSettings().addListener(new EditSettingsListener() {

            @Override

        });

    }

    private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {

		AlignmentArea result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(false);

		return result;

    }

    private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {

		AlignmentArea result = new AlignmentArea(container);

		result.setAllowVerticalScrolling(allowVerticalScrolling);

		return result;

	}

    private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,

    		AlignmentArea labeledArea) {

		return result;

    }

    private MultipleAlignmentsContainer getAlignmentsContainer() {

    	if (alignmentsContainer == null) {

    		alignmentsContainer = new MultipleAlignmentsContainer();

    	}

    }

    /**

     * Checks whether the specified alignment area or one of its subcomponents currently has the

     * focus.

    	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);

        }

    }

    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:

		}

    }

    	//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:

		//TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?

    }

    @PostConstruct

    public void createPartControl(Composite parent) {

        if (CdmStore.isActive()){

            if(sequenceNode!=null && sequenceNode.getId()!=0){

                sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid());

            }

        }

        else {

            createTestContents();  // This case will removed after the test phase and an exception should probably be thrown.