Package org.moltools.apps.probemaker

Examples of org.moltools.apps.probemaker.ProbeDesignTask.run()


  
 
  protected void doTest(TSSConstructor tsc, String expect5, String expect3) throws ClusterException {
    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), pd, tsc, new StreamErrorHandler(System.out,true));
    task.run();
   
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
   
    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
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    //New design, with accept OK pairs. Expected to generate candidates, but fail.     
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"false");
      ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
      task.run();
      long candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
     
      assertEquals("Tag allocation should have failed", 0, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Candidates expected", libraries1_1[0].size() , candCount);
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    //New design, with accept OK pairs AND candidates. Expected to generate candidates, and find candidate with warning.     
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"true");
      task = pm.getProbeDesignTask(false, true, true, new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
      task.run();
      candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
      System.out.println("Probe");
      for (Iterator<KeyValue> i = p.getPropertySet().getKeyValueIterator();i.hasNext();) {
        System.out.println(i.next());
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    dummy.setData(DummyModule.KEY_WARNING_CHANCE, new Integer(100));
    proj.getSettings().addCandidateModuleStage1(dummy);

    ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();

    //Check the number of candidates tested
    long candCount = task.getCandidatesGenerated();  
    assertTrue("Tag selection, 10 candidates expected, " + candCount + " generated.",candCount==10); //$NON-NLS-1$ //$NON-NLS-2$
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    pm.setProject(proj);

    GreedyTagAllocator ta = new GreedyTagAllocator();          
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();

    long candCount = task.getCandidatesGenerated();

    //Check the number of candidates tested
    assertEquals("Constant spacer, 10 candidates expected, " + candCount + " generated.", candCount, 10); //$NON-NLS-1$ //$NON-NLS-2$
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    ta = new GreedyTagAllocator();
    //ta.setDebug(3,System.out);

    task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSConstructor() ,new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();

    //Check the number of candidates tested
    candCount = task.getCandidatesGenerated();

    assertTrue("Variable spacer, 40 candidates expected, " + candCount + " generated.", candCount==40); //$NON-NLS-1$ //$NON-NLS-2$
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    //Run test to fail all    
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));

    task.run();
    long candCount = task.getCandidatesGenerated();

    assertTrue("Pairwise allocation (Stage 1 module), 10 candidates expected, " + candCount + " generated.",candCount == 10); //$NON-NLS-1$ //$NON-NLS-2$

    //Move dummy to arm stage, check that there are no candidates generated
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    proj.getSettings().getCandidateModulesStage1().clear();
    proj.getSettings().getArmModules().add(dummy);

    task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();   
    candCount = task.getCandidatesGenerated();

    assertTrue("Pairwise allocation (TSS module), 0 candidates expected, " + candCount + " generated.",candCount==0); //$NON-NLS-1$ //$NON-NLS-2$

//  Expand target and test use unique mode, 2 candidates expected
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    TargetHandler.expandTargets(pm.getProject().getTargets());
    proj.getSettings().getArmModules().clear();   

    task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();
    candCount = task.getCandidatesGenerated();
    Probe p1 = pm.getProject().getProbes().getSequenceAt(0);
    Probe p2 = pm.getProject().getProbes().getSequenceAt(1);

    assertTrue("2 candidates expected, " + candCount + " generated.",candCount == 2); //$NON-NLS-1$ //$NON-NLS-2$
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//  Expand target and test use per group, no modules, 2 candidates expected       
    libraries1_10[0].setMode(TagLibrary.USE_PER_GROUP);          

    task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();
    candCount = task.getCandidatesGenerated();
    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);

    assertTrue("2 candidates expected, " + candCount + " generated.",candCount == 2); //$NON-NLS-1$ //$NON-NLS-2$
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