Package org.moltools.apps.probemaker.ext.target

Examples of org.moltools.apps.probemaker.ext.target.AlleleSpecificPadlockTarget

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  ProbeMakerPlugIn pm = new ProbeMakerPlugIn();
 
  @Override
  protected void setUp() throws Exception {
   
    t1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
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    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultProbeDesigner.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultTSSConstructor.defaultParameters);
   
    ProbeMakerTarget pt1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    proj.getTargets().addSequence(pt1);
   
    pm.setProject(proj);
  }
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  }
 
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    ProbeMakerTarget t1 = new AlleleSpecificPadlockTarget("T1","ACTACGAGCGACGAGC|ACACGCTACATCGAGC","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    VariantTarget t2 = new MinisequencingTarget("T2","ACTACGAGCGACGAGCSACACGCTACATCGAGC","Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t2.setVariant(t2.getVariants()[0]);
    ProbeMakerTarget t3 = new UnchangedTarget("T3","ACGTCAGCGAGCGACGACTACTACGAC","Target 3"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    project = new Project("IOTest"); //$NON-NLS-1$
    pm.setProject(project);
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    Project proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
       
    pm.setProject(proj);
   
    AlleleSpecificPadlockTarget t1 = new AlleleSpecificPadlockTarget("T1", "GGGGGGGGGGGGGGGGGGGGGG|GGGGGGGGGGGGGGGGGGGGGGGG", "Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    AlleleSpecificPadlockTarget t2 = new AlleleSpecificPadlockTarget("T2", "GGGGGGGGGGGGGGGGGGGGGG|GGGGGGGGGGGGGGGGGGGGGGGG", "Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
     
 
    //Add one target
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t1);
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    plc.checkTemplatingByTarget(p);
   
    assertEquals(0,ProbeMakerPropertyUtils.getAllMessages(p).size());
   
    //Get a variant of an allele specific padlock
    AlleleSpecificPadlockTarget target2 = new AlleleSpecificPadlockTarget("T2","ATACAGTCGTCCGGGTCGAAWAGAGCATCGACGCGGATCAA","Target 2");
    target = target2.expand().get(0);
   
    pair = tpd.designTSSPair(target);
   
    p = new DefaultProbe(pair,0,0,NucleotideSequence.DNA);
    plc.checkTemplatingByTarget(p);
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  ProbeMakerPlugIn pm = new ProbeMakerPlugIn();
 
  @Override
  protected void setUp() throws Exception {
   
    t1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
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    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultProbeDesigner.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultTSSConstructor.defaultParameters);
   
    ProbeMakerTarget pt1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    proj.getTargets().addSequence(pt1);
   
    pm.setProject(proj);
  }
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  //Add more tags (10 total)
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();

    t1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCCCCCCCA/TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t2 = new AlleleSpecificPadlockTarget("T2","CCCCCCCCCCCCCCCCCCCCCCCCCDAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t1.setVariant(t1.getVariants()[0]);
    t2.setVariant(t2.getVariants()[0]);


    //Make tag library with ten tags
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  }
 
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    ProbeMakerTarget t1 = new AlleleSpecificPadlockTarget("T1","ACTACGAGCGACGAGC|ACACGCTACATCGAGC","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    VariantTarget t2 = new MinisequencingTarget("T2","ACTACGAGCGACGAGCSACACGCTACATCGAGC","Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t2.setVariant(t2.getVariants()[0]);
    ProbeMakerTarget t3 = new UnchangedTarget("T3","ACGTCAGCGAGCGACGACTACTACGAC","Target 3"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    project = new Project("IOTest"); //$NON-NLS-1$
    pm.setProject(project);
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    Project proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
       
    pm.setProject(proj);
   
    AlleleSpecificPadlockTarget t1 = new AlleleSpecificPadlockTarget("T1", "GGGGGGGGGGGGGGGGGGGGGG|GGGGGGGGGGGGGGGGGGGGGGGG", "Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    AlleleSpecificPadlockTarget t2 = new AlleleSpecificPadlockTarget("T2", "GGGGGGGGGGGGGGGGGGGGGG|GGGGGGGGGGGGGGGGGGGGGGGG", "Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
     
 
    //Add one target
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t1);
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Related Classes of org.moltools.apps.probemaker.ext.target.AlleleSpecificPadlockTarget

  • org.moltools.apps.probemaker.seq.Polymorphism
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
  • org.moltools.apps.probemaker.test.PadlockTSSLigationTest
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
  • org.moltools.apps.probemaker.test.TSSConstructionTest
  • org.moltools.design.data.impl.SimpleSubSequenceTemplate
  • org.moltools.design.data.TargettedSequence
  • org.moltools.lib.seq.alphabet.Nucleotide
  • org.moltools.lib.seq.SequenceElement
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