Package org.moltools.apps.probemaker

Examples of org.moltools.apps.probemaker.ProbeMakerPlugIn

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    super(arg0);
  }
 
  @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"); //$NON-NLS-1$
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  }
 
  public void testOne() throws Exception {
   
    pm = new ProbeMakerPlugIn();
    Project proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
       
    pm.setProject(proj);
   
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    super(arg0);
  }
 
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultProbeDesigner.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultTSSConstructor.defaultParameters);
   
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    //Logger.getRootLogger().setLevel(Level.DEBUG);
  }
 
  @Override
  protected void setUp() throws DuplicateIDException, FileNotFoundException, IOException, SequenceFormatException {
    pm = new ProbeMakerPlugIn();
    project = new Project("Mfold_test"); //$NON-NLS-1$
    pm.setProject(project);
    m = new DINAMeltSecStructModule();   
    project.getSettings().addCandidateModuleStage1(m);   
    Collection<Probe> seqs = SequenceIO.readSequences(new InputStreamReader(getClass().getResourceAsStream("mfold_test.lib")),new IDAndNameFastaFormatter<Probe>(),DefaultProbe.getSequenceBuilder()); //$NON-NLS-1$
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    super(arg0);
  }
 
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultProbeDesigner.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultTSSConstructor.defaultParameters);
   
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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]);
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    super(arg0);
  }
 
  @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"); //$NON-NLS-1$
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  }
 
  public void testOne() throws Exception {
   
    pm = new ProbeMakerPlugIn();
    Project proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
       
    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]);
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    //Logger.getRootLogger().setLevel(Level.DEBUG);
  }
 
  @Override
  protected void setUp() throws DuplicateIDException, FileNotFoundException, IOException, SequenceFormatException {
    pm = new ProbeMakerPlugIn();
    project = new Project("Mfold_test"); //$NON-NLS-1$
    pm.setProject(project);
    m = new DINAMeltSecStructModule();   
    project.getSettings().addCandidateModuleStage1(m);   
    Collection<Probe> seqs = SequenceIO.readSequences(new InputStreamReader(getClass().getResourceAsStream("mfold_test.lib")),new IDAndNameFastaFormatter<Probe>(),DefaultProbe.getSequenceBuilder()); //$NON-NLS-1$
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Related Classes of org.moltools.apps.probemaker.ProbeMakerPlugIn

  • net.sf.apptools.actions.ActionSet
  • net.sf.apptools.data.BooleanDescriptor
  • net.sf.apptools.data.DataDescriptor
  • net.sf.apptools.data.DataHolder
  • net.sf.apptools.data.DefaultDataHolder
  • net.sf.apptools.data.OptionDescriptor
  • net.sf.apptools.data.PlugInClassListSelectionDescriptor
  • net.sf.apptools.data.StringDataDescriptor
  • net.sf.apptools.log.ErrorHandler
  • net.sf.apptools.task.Task
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