Examples of 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, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSPairDesigner(new DefaultTSSConstructor()) ,new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();


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

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


    //Run test to fail all     
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    
    candCount = task.getCandidatesGenerated();    
    assertTrue("20 candidates expected, " + candCount + " generated.",candCount == 20);      //$NON-NLS-1$ //$NON-NLS-2$

Examples of GoodAcceptor

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

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