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Revision 6829d79d

Added by Ben Stöver over 9 years ago

AlignmentEditor adjusted to recent changes in LibrAlign.

View differences:

eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
28 28 
import org.biojava.bio.chromatogram.ChromatogramFactory;
29 29 
import org.biojava3.core.sequence.DNASequence;
30 30 
import org.biojava3.core.sequence.compound.NucleotideCompound;
31 
import org.eclipse.core.resources.ResourcesPlugin;
32 
import org.eclipse.core.runtime.IConfigurationElement;
33 31 
import org.eclipse.core.runtime.IProgressMonitor;
34 32 
import org.eclipse.swt.SWT;
35 33 
import org.eclipse.swt.widgets.Composite;
......
85 83 
							alignment);
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87 85 
			AlignmentArea result = new AlignmentArea();
88 
			result.setSequenceProvider(sequenceProvider, false);
89 
			SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
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			result.getContentArea().setSequenceProvider(sequenceProvider, false);
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			SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result.getContentArea());
90 88 
			//sequenceIndexArea.setFirstIndex(5);
91 89 
			//sequenceIndexArea.setHeight(25);
92 
			result.getDataAreas().getTopAreas().add(sequenceIndexArea);
90 
			result.getContentArea().getDataAreas().getTopAreas().add(sequenceIndexArea);
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//			PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);
95 93 
//			pherogramArea.setFirstSeqPos(34 + 5);
......
101 99 

  		




  102
  100
  
    
			PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(


  		




  103
  101
  
    
				    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")));


  		




  104
  
  
    
			PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);


  		




  
  102
  
    
			PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);


  		




  105
  103
  
    
			pherogramArea.setFirstSeqPos(1);


  		




  106
  104
  
    
			pherogramArea.setLeftCutPosition(13);


  		




  107
  105
  
    
			pherogramArea.setRightCutPosition(697);


  		




  108
  106
  
    
			pherogramArea.getAlignmentModel().setShiftChange(14, 1);


  		




  109
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			pherogramArea.getAlignmentModel().setShiftChange(35, 1);


  		




  110
  
  
    
			result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);


  		




  
  108
  
    
			result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);


  		




  111
  109
  
    

  		




  112
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	  		pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(


  		




  113
  111
  
    
  				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"))));


  		




  114
  
  
    
			pherogramArea = new PherogramArea(result, pherogramProvider);


  		




  
  112
  
    
			pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);


  		




  115
  113
  
    
			pherogramArea.setFirstSeqPos(1);


  		




  116
  114
  
    
			pherogramArea.setLeftCutPosition(267);


  		




  117
  115
  
    
			pherogramArea.getAlignmentModel().setShiftChange(273, -1);


  		




  118
  116
  
    
			pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale());


  		




  119
  
  
    
			result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);


  		




  
  117
  
    
			result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);


  		




  120
  118
  
    

  		




  121
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  122
  
  
    
	  	    result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));


  		




  
  120
  
    
	  	    result.getContentArea().getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result.getContentArea()));


  		




  123
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			return result;


  		




  124
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		}


  		




  125
  123
  
    
		catch (Exception e) {


  		




  ......




  156
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    public void createPartControl(Composite parent) {


  		




  157
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    	alignmentArea = createAlignmentArea();


  		




  158
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		Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);


  		




  
  157
  
    
		//getSite().setSelectionProvider(provider)


  		




  159
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    }


  		




  160
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  161
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  ......




  214
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     */


  		




  215
  214
  
    
    @Override


  		




  216
  215
  
    
    public void setFocus() {


  		




  217
  
  
    
    	alignmentArea.getToolkitComponent().redistributeHeight();


  		




  
  216
  
    
    	//alignmentArea.getToolkitComponent().redistributeHeight();


  		




  218
  217
  
    
    }


  		




  219
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}


  		












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