Examples of PairwiseTagAllocator

Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    proj.getTargets().addSequence(t1);
    proj.setTagSettings(new DefaultTagSettings(new TagLibrary[] { tags }));
   
//  Design without test
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(),new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();   
    Probe p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 0 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 0); //$NON-NLS-1$ //$NON-NLS-2$
   
   
//  Design again with test
    proj.getSettings().addCandidateModuleStage1(new DefaultHybInterferenceModule());   
   
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(),new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();   
    p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 2 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 2);     //$NON-NLS-1$ //$NON-NLS-2$
   
  }
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    tl.setMode(TagLibrary.USE_UNIQUE_TAG);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl}));
   
    //Design
    ProbeDesigner pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, null, new DefaultNamingScheme(), new AllAcceptor(),new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
       
//  Store to project file
    File f = new File("temp.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,null,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,null,new FileReader(f)).run();
   
    //Add new target
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t2);
   
//  Design with append       
    pm.getProbeDesignTask(true, false, null, new DefaultNamingScheme(), new AllAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
   
        
//  Store to project file
    f = new File("temp2.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
      
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t1);
    pm.getProject().getTargets().addSequence(t2);
   
    db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(new SimpleNucleotideSequence("Tag 1","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 2","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 3","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 4","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    tl = new DefaultTagLibrary(db,"Unique"); //$NON-NLS-1$
    tl.setMode(TagLibrary.USE_PER_GROUP);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl, tl}));
   
//  Design
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), eh).run();   

    TagAllocationTable tat1 = pm.getProject().getTagAllocationTable();
   
//  Store to project file
    f = new File("temp3.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
   
    TagAllocationTable tat2 = pm.getProject().getTagAllocationTable();
   
    assertEquals(tat1, tat2);
   
//  Design
    pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, null, new DefaultNamingScheme(), new AllAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), eh).run();           
   
    new ProbeAnalysisTask(pm.getProject(),null).run();
  }
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    proj.getTargets().addSequence(t1);
    proj.setTagSettings(new DefaultTagSettings(new TagLibrary[] { tags }));
   
//  Design without test
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();   
    Probe p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 0 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 0); //$NON-NLS-1$ //$NON-NLS-2$
   
   
//  Design again with test
    proj.getSettings().addCandidateModuleStage1(new DefaultHybInterferenceModule());   
   
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();   
    p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 2 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 2);     //$NON-NLS-1$ //$NON-NLS-2$
   
  }
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    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); //$NON-NLS-1$ //$NON-NLS-2$
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    proj.getTargets().addSequence(t1);   
    proj.getTargets().addSequence(t2);   
    pm.setProject(proj);
   
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();

    Probe p1 = proj.getProbes().getSequenceAt(0);
    Probe p2 = proj.getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.GOOD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);

    proj.getTagAllocationTable().clearUsed();
   
    //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);
    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.OK_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);
    assertEquals(task.getCandidatesGenerated(),1);
   
    proj.getTagAllocationTable().clearUsed();
   
    //Test single-tag use same
    libraries1_1[0].setMode(TagLibrary.USE_SAME_TAG);
    proj.setTagSettings(new DefaultTagSettings(libraries1_1));
    proj.getSettings().getCandidateModulesStage2().clear();
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();

    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.GOOD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.GOOD_QUALITY);

//  Test single-tag use unique in group with one expanded
    //expect first probe to succeed but be set to bad when second one failed
    //Third probe then set to good
    proj.getTagAllocationTable().clearUsed();
    libraries1_1[0].setMode(TagLibrary.USE_UNIQUE_IN_GROUP);
    proj.setTagSettings(new DefaultTagSettings(libraries1_1));
    proj.getTargets().clear();
    proj.getTargets().addSequence(t1);
    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);

   
    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.BAD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);
   
    assertEquals(ProbeMakerPropertyUtils.getRank(p3),ProbeMakerConstants.GOOD_QUALITY);
    assertEquals(task.getCandidatesGenerated(),2);
   
    libraries1_1[0].setMode(TagLibrary.USE_UNIQUE_TAG);
   
//  Test single-tag use same with one expanded
    libraries2_1_1[0].setMode(TagLibrary.USE_UNIQUE_TAG);
    libraries2_1_1[1].setMode(TagLibrary.USE_UNIQUE_IN_GROUP);
    proj.setTagSettings(new DefaultTagSettings(libraries2_1_1));

    proj.getTargets().clear();
    proj.getTargets().addSequence(t1);
    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);
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    proj.getSettings().addCandidateModuleStage1(dummy);
    pm.setProject(proj);
    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
    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);
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    tl.setMode(TagLibrary.USE_UNIQUE_TAG);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl}));
   
    //Design
    ProbeDesigner pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, true, new AllAcceptor(),new NoSelector(), pd, new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();
       
//  Store to project file
    File f = new File("temp.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,null,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,null,new FileReader(f)).run();
   
    //Add new target
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t2);
   
//  Design with append       
    pm.getProbeDesignTask(true, false, true, new AllAcceptor(), new NoSelector(), pd, new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();
   
        
//  Store to project file
    f = new File("temp2.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
      
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t1);
    pm.getProject().getTargets().addSequence(t2);
   
    db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(new SimpleNucleotideSequence("Tag 1","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 2","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 3","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 4","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    tl = new DefaultTagLibrary(db,"Unique"); //$NON-NLS-1$
    tl.setMode(TagLibrary.USE_PER_GROUP);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl, tl}));
   
//  Design
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(), new NoSelector(), pd, new DefaultTSSConstructor(), eh).run();   

    TagAllocationTable tat1 = pm.getProject().getTagAllocationTable();
   
//  Store to project file
    f = new File("temp3.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
   
    TagAllocationTable tat2 = pm.getProject().getTagAllocationTable();
   
    assertEquals(tat1, tat2);
   
//  Design
    pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false,  true, new AllAcceptor(), new NoSelector(), pd, new DefaultTSSConstructor(), eh).run();           
   
    new ProbeAnalysisTask(pm.getProject(),null).run();
  }
View Full Code Here

Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    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); //$NON-NLS-1$ //$NON-NLS-2$
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    proj.getTargets().addSequence(t1);   
    proj.getTargets().addSequence(t2);   
    pm.setProject(proj);
   
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();

    Probe p1 = proj.getProbes().getSequenceAt(0);
    Probe p2 = proj.getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.GOOD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);

    proj.getTagAllocationTable().clearUsed();
   
    //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);
    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.OK_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);
    assertEquals(task.getCandidatesGenerated(),1);
   
    proj.getTagAllocationTable().clearUsed();
   
    //Test single-tag use same
    libraries1_1[0].setMode(TagLibrary.USE_SAME_TAG);
    proj.setTagSettings(new DefaultTagSettings(libraries1_1));
    proj.getSettings().getCandidateModulesStage2().clear();
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();

    p1 = proj.getProbes().getSequenceAt(0);
    p2 = proj.getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.GOOD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.GOOD_QUALITY);

//  Test single-tag use unique in group with one expanded
    //expect first probe to succeed but be set to bad when second one failed
    //Third probe then set to good
    proj.getTagAllocationTable().clearUsed();
    libraries1_1[0].setMode(TagLibrary.USE_UNIQUE_IN_GROUP);
    proj.setTagSettings(new DefaultTagSettings(libraries1_1));
    proj.getTargets().clear();
    proj.getTargets().addSequence(t1);
    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);

   
    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.BAD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);
   
    assertEquals(ProbeMakerPropertyUtils.getRank(p3),ProbeMakerConstants.GOOD_QUALITY);
    assertEquals(task.getCandidatesGenerated(),2);
   
    libraries1_1[0].setMode(TagLibrary.USE_UNIQUE_TAG);
   
//  Test single-tag use same with one expanded
    libraries2_1_1[0].setMode(TagLibrary.USE_UNIQUE_TAG);
    libraries2_1_1[1].setMode(TagLibrary.USE_UNIQUE_IN_GROUP);
    proj.setTagSettings(new DefaultTagSettings(libraries2_1_1));

    proj.getTargets().clear();
    proj.getTargets().addSequence(t1);
    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);
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Examples of org.moltools.apps.probemaker.ext.ta.PairwiseTagAllocator

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    proj.getSettings().addCandidateModuleStage1(dummy);
    pm.setProject(proj);
    TargetHandler.expandTargets(pm.getProject().getTargets());

    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();

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

    //Move dummy to arm stage
    proj.getSettings().getCandidateModulesStage1().clear();
    proj.getSettings().addCandidateModuleStage2(dummy);
    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();

    Probe p3 = proj.getProbes().getSequenceAt(0);
    Probe p4 = proj.getProbes().getSequenceAt(1);
View Full Code Here
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