Package org.moltools.apps.probemaker

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

72
73
74
75
76
77
78
79
80
81
82
  
 
  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();
   
    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
View Full Code Here
370
371
372
373
374
375
376
377
378
379
380
    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);      //$NON-NLS-1$ //$NON-NLS-2$
  }
View Full Code Here
402
403
404
405
406
407
408
409
410
411
412
    //Two probes single tag unique, with dummy. Expect first ok, second bad
    proj.getSettings().getCandidateModulesStage2().add(dummy);
      
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();
   
    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getAllMessages(p1).size(),1);
View Full Code Here
440
441
442
443
444
445
446
447
448
449
450
    TargetHandler.expandTargets(proj.getTargets());
    proj.getTargets().addSequence(t2);
   
    task = pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();

    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);
    Probe p3 = proj.getProbes().getSequenceAt(2);
View Full Code Here
467
468
469
470
471
472
473
474
475
476
477
    TargetHandler.expandTargets(proj.getTargets());
    proj.getTargets().addSequence(t2);
   
    task = pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();

    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);
    p3 = proj.getProbes().getSequenceAt(2);
View Full Code Here
503
504
505
506
507
508
509
510
511
512
513
    TargetHandler.expandTargets(pm.getProject().getTargets());

    ProbeDesignTask task = pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));

    task.run();

    Probe p = proj.getProbes().getSequenceAt(0);
    Probe p2 = proj.getProbes().getSequenceAt(1);

    //Move dummy to arm stage
View Full Code Here
513
514
515
516
517
518
519
520
521
522
523
    //Move dummy to arm stage
    proj.getSettings().getCandidateModulesStage1().clear();
    proj.getSettings().addCandidateModuleStage2(dummy);
    task = pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
    task.run();

    Probe p3 = proj.getProbes().getSequenceAt(0);
    Probe p4 = proj.getProbes().getSequenceAt(1);

//  Check that both probes of fair rank  
View Full Code Here
404
405
406
407
408
409
410
411
412
413
414
    //Two probes single tag unique, with dummy. Expect first ok, second bad
    proj.getSettings().getCandidateModulesStage2().add(dummy);
      
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
   
    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getAllMessages(p1).size(),1);
View Full Code Here
442
443
444
445
446
447
448
449
450
451
452
    TargetHandler.expandTargets(proj.getTargets());
    proj.getTargets().addSequence(t2);
   
    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();

    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);
    Probe p3 = proj.getProbes().getSequenceAt(2);
View Full Code Here
469
470
471
472
473
474
475
476
477
478
479
    TargetHandler.expandTargets(proj.getTargets());
    proj.getTargets().addSequence(t2);
   
    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();

    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);
    p3 = proj.getProbes().getSequenceAt(2);
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.