Examples of BestQualitySelector

org.moltools.apps.probemaker.ext.sel.BestQualitySelector
A ProbeSelector Plugin that selects the probe candidate with the highest quality and if more than one with the same quality, the one with the lowest secondary structure Tm. If there are multiple probes with same quality and Tm, the first of them will be returned.

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

Examples of org.moltools.apps.probemaker.ext.sel.BestQualitySelector

  }
    
  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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Examples of org.moltools.apps.probemaker.ext.sel.BestQualitySelector

    });
      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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Examples of org.moltools.apps.probemaker.ext.sel.BestQualitySelector

  }
    
  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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Examples of org.moltools.apps.probemaker.ext.sel.BestQualitySelector

    });
      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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