Examples of GreedyTagAllocator

org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator
This is the central class for Probe design. Probes created by a ProbeFactory are sent to this class to undergo tag allocation by subsequent calls to the allocateTagsToGroup method. This is performed by an instance of the TagSelector class. This class needs to know what constant or variable elements to add to the probe. This is set with the setTagUsage method, which sets a number of TagLibrary objects to be used and the modes in which these libraries will be used. When the tag usage is set the parameters for spacer use are also interpreted.
Copyright: Copyright (c) 2002,2005
@author Johan Stenberg @version 1.0

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

  }
    
  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.ta.GreedyTagAllocator

    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, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(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, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(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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Examples of org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator

    });
      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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Examples of org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator

    proj.getSettings().addCandidateModuleStage1(dummy);


    pm.setProject(proj);


    //Make a new design after clearing tag usage    
    Task task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    Probe p = proj.getProbes().getSequenceAt(0);
    assertTrue("Tag allocated despite warning message",p.getTags().size() == 0); //$NON-NLS-1$


    proj.getSettings().getCandidateModulesStage1().clear();

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

    pm.setProject(proj);
    
    dummy.setData(DummyModule.KEY_WARNING_CHANCE, new Integer(100));
    proj.getSettings().addCandidateModuleStage1(dummy);


    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();


    //Check the number of candidates tested
    long candCount = task.getCandidatesGenerated();   
    assertTrue("Tag selection, 10 candidates expected, " + candCount + " generated.",candCount==10); //$NON-NLS-1$ //$NON-NLS-2$

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

    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_USE_SPACER,"TRUE"); //$NON-NLS-1$
    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_PREFERRED_LENGTH,String.valueOf(61));
    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_SPACER_SEQUENCE,"CT");     //$NON-NLS-1$
    pm.setProject(proj);


    GreedyTagAllocator ta = new GreedyTagAllocator();           
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();


    long candCount = task.getCandidatesGenerated();


    //Check the number of candidates tested
    assertEquals("Constant spacer, 10 candidates expected, " + candCount + " generated.", candCount, 10); //$NON-NLS-1$ //$NON-NLS-2$


    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_SPACER_SEQUENCE,""); //$NON-NLS-1$


    ta = new GreedyTagAllocator();
    //ta.setDebug(3,System.out);


    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSPairDesigner(new DefaultTSSConstructor()) ,new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();

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

//  Expand target and test use unique mode, 2 candidates expected
    TargetHandler.expandTargets(pm.getProject().getTargets());
    proj.getSettings().getArmModules().clear();    


    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    candCount = task.getCandidatesGenerated();
    Probe p1 = pm.getProject().getProbes().getSequenceAt(0);
    Probe p2 = pm.getProject().getProbes().getSequenceAt(1);


    assertTrue("2 candidates expected, " + candCount + " generated.",candCount == 2); //$NON-NLS-1$ //$NON-NLS-2$
    assertTrue("Same tags allocated in unique mode!",p1.getTagAt(0)!=p2.getTagAt(0)); //$NON-NLS-1$


//  Expand target and test use per group, no modules, 2 candidates expected        
    libraries1_10[0].setMode(TagLibrary.USE_PER_GROUP);           


    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    candCount = task.getCandidatesGenerated();
    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);


    assertTrue("2 candidates expected, " + candCount + " generated.",candCount == 2); //$NON-NLS-1$ //$NON-NLS-2$
    assertTrue("Different tags allocated in group mode!",p1.getTagAt(0)==p2.getTagAt(0)); //$NON-NLS-1$


//  Still expanded targets, per group mode, greedy allocator, dummy module in stage 1.
    //Expect 20 candidates generated
    libraries1_10[0].setMode(TagLibrary.USE_PER_GROUP);           
    proj.getSettings().getCandidateModulesStage1().add(dummy);    
       
    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    
    candCount = task.getCandidatesGenerated();    
    assertTrue("20 candidates expected, " + candCount + " generated.",candCount == 20);      //$NON-NLS-1$ //$NON-NLS-2$
  }

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

  }


  protected Probe[] performModeTest(byte mode) {
    pm.getProject().getTagSettings().getTagLibraries()[0].setMode(mode);
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
    
    Probe[] probes = pm.getProject().getProbes().getSequenceList().toArray(new Probe[5]);
    return probes;
  }

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