Examples of GoodAcceptor

org.moltools.apps.probemaker.ext.acc.GoodAcceptor

GoodAcceptor

A probe acceptor plug-in that accepts GOOD quality candidates and TSS pairs only, at all the three levels of testing. This acceptor enables the pair-wise acceptance mode.

Copyright: Copyright (c) 2002, 2005
@author Johan Stenberg @version 1.0

Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

  }
   
  
  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();

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

  }
   
  
  protected void doTest(TSSConstructor tsc, String expect5, String expect3) throws ClusterException {
    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(tsc), new StreamErrorHandler(System.out,true));
    task.run();
    
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    proj.getTargets().addSequence(t1);
    pm.setProject(proj);


    //First design, expected to result in a tag being allocated,
    //and the tag allocation table marking the tag as used
    pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();
    Probe p = proj.getProbes().getSequenceAt(0);
    
    assertTrue("Tag allocation failed", p.getTags().size()==1);    //$NON-NLS-1$


    //New design, without tag reset, expected to fail because tag is already used
    pm.getProbeDesignTask(false, false, false, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();   
    p = proj.getProbes().getSequenceAt(0);
    
    assertTrue("Tag allocation should have failed due to no tags left, but seems to have succeeded",p.getTags().size() == 0); //$NON-NLS-1$
    
    //New design, with reset. Expected to succeed because no tags should be used now
    pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();           
    p = proj.getProbes().getSequenceAt(0);    
    
    assertTrue("Tag allocation failed after reset",p.getTags().size() == 1);     //$NON-NLS-1$


  }

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    proj.getSettings().addCandidateModuleStage1(dummy);


    pm.setProject(proj);


    //Make a new design after clearing tag usage    
    Task task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();
    Probe p = proj.getProbes().getSequenceAt(0);
    assertTrue("Tag allocated despite warning message",p.getTags().size() == 0); //$NON-NLS-1$


    proj.getSettings().getCandidateModulesStage1().clear();

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    pm.setProject(proj);
    
    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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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_PREFERRED_LENGTH,String.valueOf(61));
    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_SPACER_SEQUENCE,"CT");     //$NON-NLS-1$
    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); //$NON-NLS-1$ //$NON-NLS-2$


    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_SPACER_SEQUENCE,""); //$NON-NLS-1$


    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();

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    proj.getTargets().addSequence(t1);    
    proj.getSettings().addCandidateModuleStage1(dummy);
    pm.setProject(proj);


    //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
    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
    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); //$NON-NLS-1$ //$NON-NLS-2$
    assertTrue("Same tags allocated in unique mode!",p1.getTagAt(0)!=p2.getTagAt(0)); //$NON-NLS-1$


//  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); //$NON-NLS-1$ //$NON-NLS-2$
    assertTrue("Different tags allocated in group mode!",p1.getTagAt(0)==p2.getTagAt(0)); //$NON-NLS-1$


//  Still expanded targets, per group mode, greedy allocator, dummy module in stage 1.
    //Expect 20 candidates generated
    libraries1_10[0].setMode(TagLibrary.USE_PER_GROUP);           
    proj.getSettings().getCandidateModulesStage1().add(dummy);    
       
    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();    
    assertTrue("20 candidates expected, " + candCount + " generated.",candCount == 20);      //$NON-NLS-1$ //$NON-NLS-2$

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    proj.getTargets().addSequence(t1);
    pm.setProject(proj);


    //First design, expected to result in a tag being allocated,
    //and the tag allocation table marking the tag as used
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
    Probe p = proj.getProbes().getSequenceAt(0);
    
    assertTrue("Tag allocation failed", p.getTags().size()==1);    //$NON-NLS-1$


    //New design, without tag reset, expected to fail because tag is already used
    pm.getProbeDesignTask(false, false, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();   
    p = proj.getProbes().getSequenceAt(0);
    
    assertTrue("Tag allocation should have failed due to no tags left, but seems to have succeeded",p.getTags().size() == 0); //$NON-NLS-1$
    
    //New design, with reset. Expected to succeed because no tags should be used now
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();           
    p = proj.getProbes().getSequenceAt(0);    
    
    assertTrue("Tag allocation failed after reset",p.getTags().size() == 1);     //$NON-NLS-1$


  }

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    proj.getSettings().addCandidateModuleStage1(dummy);


    pm.setProject(proj);


    //Make a new design after clearing tag usage    
    Task task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    Probe p = proj.getProbes().getSequenceAt(0);
    assertTrue("Tag allocated despite warning message",p.getTags().size() == 0); //$NON-NLS-1$


    proj.getSettings().getCandidateModulesStage1().clear();

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Examples of org.moltools.apps.probemaker.ext.acc.GoodAcceptor

    pm.setProject(proj);
    
    dummy.setData(DummyModule.KEY_WARNING_CHANCE, new Integer(100));
    proj.getSettings().addCandidateModuleStage1(dummy);


    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(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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