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// $Id$
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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.editor.molecular;
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import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
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import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
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import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
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import info.bioinfweb.libralign.AlignmentArea;
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import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
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import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
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import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
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import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
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import org.biojava3.core.sequence.DNASequence;
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import org.biojava3.core.sequence.compound.NucleotideCompound;
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import org.eclipse.core.runtime.IProgressMonitor;
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import org.eclipse.swt.SWT;
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import org.eclipse.swt.widgets.Composite;
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import org.eclipse.ui.IEditorInput;
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import org.eclipse.ui.IEditorSite;
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import org.eclipse.ui.PartInitException;
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import org.eclipse.ui.part.EditorPart;
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/**
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* Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
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* a consensus sequence.
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* <p>
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* The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
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*
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* @author pplitzner
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* @author Ben St?ver
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* @date 04.08.2014
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*/
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public class AlignmentEditor extends EditorPart {
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public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
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private AlignmentArea alignmentArea;
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private AlignmentArea createAlignmentArea() {
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Alignment<DNASequence, NucleotideCompound> alignment =
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new SimpleAlignment<DNASequence, NucleotideCompound>();
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alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
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alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
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alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
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BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
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new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
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new BioJavaTokenSet<NucleotideCompound>(
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AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
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alignment);
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AlignmentArea result = new AlignmentArea();
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result.setSequenceProvider(sequenceProvider, false);
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SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
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//sequenceIndexArea.setFirstIndex(5);
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//sequenceIndexArea.setHeight(25);
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result.getDataAreas().getTopAreas().add(sequenceIndexArea);
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result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
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return result;
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
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*/
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@Override
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public void createPartControl(Composite parent) {
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alignmentArea = createAlignmentArea();
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Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
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*/
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@Override
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public void doSave(IProgressMonitor monitor) {
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// TODO Auto-generated method stub
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.EditorPart#doSaveAs()
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*/
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@Override
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public void doSaveAs() {
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// TODO Auto-generated method stub
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
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*/
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@Override
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public void init(IEditorSite site, IEditorInput input) throws PartInitException {
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setSite(site);
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setInput(input);
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.EditorPart#isDirty()
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*/
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@Override
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public boolean isDirty() {
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// TODO Auto-generated method stub
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return false;
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
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*/
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@Override
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public boolean isSaveAsAllowed() {
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// TODO Auto-generated method stub
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return false;
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}
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/* (non-Javadoc)
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* @see org.eclipse.ui.part.WorkbenchPart#setFocus()
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*/
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@Override
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public void setFocus() {
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// TODO Auto-generated method stub
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}
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}
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