Package org.moltools.apps.probemaker.ext.tc

Examples of org.moltools.apps.probemaker.ext.tc.DefaultTSSConstructor

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    lib1.addSequence(new SimpleNucleotideSequence("TAG_A","AAAAAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    lib1.addSequence(new SimpleNucleotideSequence("TAG_T","TTTTTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    lib1.setMode(TagLibrary.USE_UNIQUE_TAG);
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {lib1}));

    pm.getProbeDesignTask(false,true, false,new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSConstructor(),null).run();

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

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

    //Test with forbidden tags
    tom.setData(DefaultTagOccurrenceModule.KEY_SEQUENCE_POSITIONS,"1"); //$NON-NLS-1$
    tom.setData(DefaultTagOccurrenceModule.KEY_COMPLEMENT_POSITIONS,"1"); //$NON-NLS-1$

    pm.getProbeDesignTask(false,true, false,new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSConstructor(),null).run();

    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);

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

    //Test with forbidden complement only tags
    tom.setData(DefaultTagOccurrenceModule.KEY_SEQUENCE_POSITIONS,""); //$NON-NLS-1$

    pm.getProbeDesignTask(false,true, false,new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSConstructor(),null).run();

    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.GOOD_QUALITY);
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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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  public void testSwitchedPolarityTSSConstruction() throws ClusterException {
    doTest(new TemplateTSSConstructor(),"CCCCCCCCCCCCCCCCCCCC","AAAAAAAAAAAAAAAAAAAAAAAAA"); //$NON-NLS-1$ //$NON-NLS-2$
  }
 
  public void testDefaultTSSConstruction() throws ClusterException {
    doTest(new DefaultTSSConstructor(),"GGGGGGGGGGGGGGG","TTTTTTTTTTTTTTTTTTTTTTTTT"); //$NON-NLS-1$ //$NON-NLS-2$
  }
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  }
   
  public void testProjectIO() throws IOException, SequenceFormatException, DuplicateIDException {
    File f1 = new File("IOTest.prx"); //$NON-NLS-1$
    File f2 = new File("IOTest2.prx"); //$NON-NLS-1$
    Task t = pm.getProbeDesignTask(false,true, null, new DefaultNamingScheme(), new GoodFairAcceptor(),new BestQualitySelector(),new DefaultProbeDesigner(new GreedyTagAllocator()),new DefaultTSSPairDesigner(new DefaultTSSConstructor()),new StreamErrorHandler(System.err,true));
    t.run();   
   
    TagAllocationTable tat1 = pm.getProject().getTagAllocationTable();
   
    new ProjectXMLIOTask(pm,null,new FileWriter(f1)).run();
    new ProjectXMLIOTask(pm,null,new FileReader(f1)).run();   
    new ProjectXMLIOTask(pm,null,new FileWriter(f2)).run();
    new ProjectXMLIOTask(pm,null,new FileReader(f2)).run();   
    assertEquals(f1.length(),f2.length());
    TagAllocationTable tat2 = pm.getProject().getTagAllocationTable();
   
    assertTrue(tat1.equals(tat2));
   
    t = pm.getProbeDesignTask(false,true, null, new DefaultNamingScheme(), new GoodFairAcceptor(),new BestQualitySelector(),new DefaultProbeDesigner(new GreedyTagAllocator()),new DefaultTSSPairDesigner(new DefaultTSSConstructor()),null);
    t.run();   

    new ProjectXMLIOTask(pm,null,new FileWriter(f2)).run();
    new ProjectXMLIOTask(pm,null,new FileReader(f2)).run();   
   
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    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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  }
 
 
  public void testTemplatingByTarget() {
   
    TSSConstructor con = new DefaultTSSConstructor();
    DefaultTSSPairDesigner tpd = new DefaultTSSPairDesigner(con);
 
    ProbeMakerTarget target = new PadlockTarget("T1","ATACAGTCGTCCGGGTCGAA|AAGAGCATCGACGCGGATCAAGCCTATCGTCACGCGA","Target 1");
    TSSPair pair = tpd.designTSSPair(target);
   
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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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  public void testSwitchedPolarityTSSConstruction() throws ClusterException {
    doTest(new TemplateTSSConstructor(),"CCCCCCCCCCCCCCCCCCCC","AAAAAAAAAAAAAAAAAAAAAAAAA"); //$NON-NLS-1$ //$NON-NLS-2$
  }
 
  public void testDefaultTSSConstruction() throws ClusterException {
    doTest(new DefaultTSSConstructor(),"GGGGGGGGGGGGGGG","TTTTTTTTTTTTTTTTTTTTTTTTT"); //$NON-NLS-1$ //$NON-NLS-2$
  }
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    lib1.addSequence(new SimpleNucleotideSequence("TAG_A","AAAAAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    lib1.addSequence(new SimpleNucleotideSequence("TAG_T","TTTTTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    lib1.setMode(TagLibrary.USE_UNIQUE_TAG);
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {lib1}));

    pm.getProbeDesignTask(false,true, null, new DefaultNamingScheme(), new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSPairDesigner(new DefaultTSSConstructor()),null).run();

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

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

    //Test with forbidden tags
    tom.setData(DefaultTagOccurrenceModule.KEY_SEQUENCE_POSITIONS,"1"); //$NON-NLS-1$
    tom.setData(DefaultTagOccurrenceModule.KEY_COMPLEMENT_POSITIONS,"1"); //$NON-NLS-1$

    pm.getProbeDesignTask(false,true, null, new DefaultNamingScheme(), new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSPairDesigner(new DefaultTSSConstructor()),null).run();

    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);

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

    //Test with forbidden complement only tags
    tom.setData(DefaultTagOccurrenceModule.KEY_SEQUENCE_POSITIONS,""); //$NON-NLS-1$

    pm.getProbeDesignTask(false,true, null, new DefaultNamingScheme(), new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSPairDesigner(new DefaultTSSConstructor()),null).run();

    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);

    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.GOOD_QUALITY);
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    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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Related Classes of org.moltools.apps.probemaker.ext.tc.DefaultTSSConstructor

  • org.moltools.apps.probemaker.messages.Message
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
  • org.moltools.apps.probemaker.test.PadlockTSSLigationTest
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
  • org.moltools.apps.probemaker.test.TagOccurrenceModuleTest
  • org.moltools.apps.probemaker.test.TSSConstructionTest
  • org.moltools.design.calc.ApproximateMeltingPointCalculator
  • org.moltools.design.calc.NNMeltingPointCalculator
  • org.moltools.design.data.PropertyAcceptorNucleotideSequence
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