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

Package org.moltools.apps.probemaker.ext.acc

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

org.moltools.apps.probemaker.ext.acc.GoodFairAcceptor

Title: GoodFairAcceptor

Description: Accepts good probes immediately and OK probes temporarily. Accepts GOOD quality probes only at the first two levels of testing.

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

    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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  }
    
  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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    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.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"false");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"false");
      
      //First design, expected to result in failure.
      pm.getProbeDesignTask(false, true, false, new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();
      Probe p = proj.getProbes().getSequenceAt(0);
               
      assertEquals("Tag allocation should have failed", 0, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Quality expected to be bad", ProbeMakerConstants.BAD_QUALITY, ProbeMakerPropertyUtils.getRank(p));      
      
      
    //New design, with accept OK pairs. Expected to generate candidates, but fail.      
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"false");
      ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
      task.run();
      long candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
      
      assertEquals("Tag allocation should have failed", 0, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Candidates expected", libraries1_1[0].size() , candCount);
      assertEquals("Quality expected to be bad", ProbeMakerConstants.BAD_QUALITY, ProbeMakerPropertyUtils.getRank(p));      
      
    //New design, with accept OK pairs AND candidates. Expected to generate candidates, and find candidate with warning.      
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"true");
      task = pm.getProbeDesignTask(false, true, true, new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true));
      task.run();
      candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
      System.out.println("Probe");
      for (Iterator<KeyValue> i = p.getPropertySet().getKeyValueIterator();i.hasNext();) {

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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, false,new GoodFairAcceptor(),new BestQualitySelector(),new DefaultProbeDesigner(new GreedyTagAllocator()),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, false,new GoodFairAcceptor(),new BestQualitySelector(),new DefaultProbeDesigner(new GreedyTagAllocator()),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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    });
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"false");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"false");
      
      //First design, expected to result in failure.
      pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
      Probe p = proj.getProbes().getSequenceAt(0);
               
      assertEquals("Tag allocation should have failed", 0, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Quality expected to be bad", ProbeMakerConstants.BAD_QUALITY, ProbeMakerPropertyUtils.getRank(p));      
      
      
    //New design, with accept OK pairs. Expected to generate candidates, but fail.      
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"false");
      ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
      task.run();
      long candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
      
      assertEquals("Tag allocation should have failed", 0, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Candidates expected", libraries1_1[0].size() , candCount);
      assertEquals("Quality expected to be bad", ProbeMakerConstants.BAD_QUALITY, ProbeMakerPropertyUtils.getRank(p));      
      
    //New design, with accept OK pairs AND candidates. Expected to generate candidates, and find candidate with warning.      
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"true");
      task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
      task.run();
      candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
      System.out.println("Probe");
      for (Iterator<KeyValue> i = p.getPropertySet().getKeyValueIterator();i.hasNext();) {

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Related Classes of org.moltools.apps.probemaker.ext.acc.GoodFairAcceptor

org.moltools.apps.probemaker.test.ProjectIOTest

org.moltools.apps.probemaker.test.TagAllocationTest

org.moltools.apps.probemaker.test.TagOccurrenceModuleTest

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