Examples of org.moltools.apps.probemaker.seq.Probe

Package org.moltools.apps.probemaker.seq

Examples of org.moltools.apps.probemaker.seq.Probe

org.moltools.apps.probemaker.seq.Probe
This interface contains common methods for different kinds of oligonucleotide probes. @author Johan Stenberg

      super.abort();
      designer.abort();      


      //Recalculate the probe qualities and finish up the work
      for (Iterator<Probe> i = probes.iterator(); i.hasNext(); ) {
        Probe p = i.next();
        Analyzer.calculateAndSetQuality(p);
      }
    }
    log.end();

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    String[] options = new String[tempprobes.size()];
    ChangeableIndexedSequenceDB<Probe> tempshow = new ListSequenceDB<Probe>();
    Iterator<Probe> tpi = tempprobes.iterator();
    for (int i = 1; i <= options.length; i++) {
      options[i - 1] = String.valueOf(i);
      Probe tempshowprobe = (tpi.next()).getCopy();
      tempshowprobe.setName(Messages.getString("GUISelector.NAME_CANDIDATE") + String.valueOf(i)); //$NON-NLS-1$
      try {
        tempshow.addSequence(tempshowprobe);
      } 
      catch (DuplicateIDException e) {
        //Should not happen here

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    for (Iterator<Probe> pi = probes.iterator(); pi.hasNext(); ) {
      if (isAborted()) {
        return;
      }
      try {
        Probe p = pi.next();
        setStatus(CoreMessages.getString("ProbeAnalysisTask.MESSAGE_ANALYZING") + p.getName(),0); //$NON-NLS-1$
        reAnalyzeProbe(p);
        increaseProgress();
      }
      catch (Exception ex) {
        //Print the error
        handleError(ex);
      }
    }
    //Recalculate the probe qualities and finish up the work
    for (Iterator<Probe> i = probes.iterator(); i.hasNext(); ) {
      Probe p = i.next();
      Analyzer.calculateAndSetQuality(p);
    }
    
    elapsedTime = new Date().getTime() - startTime;
    setCompleted();

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    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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      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();) {
        System.out.println(i.next());
      }
      System.out.println("TSS Pair");
      for (Iterator<KeyValue> i = p.getTSSPair().getPropertySet().getKeyValueIterator();i.hasNext();) {
        System.out.println(i.next());
      }
      System.out.println("5'");
      for (Iterator<KeyValue> i = p.getTSSPair().getFivePrime().getPropertySet().getKeyValueIterator();i.hasNext();) {
        System.out.println(i.next());
      }
      System.out.println("3'");
      for (Iterator<KeyValue> i = p.getTSSPair().getThreePrime().getPropertySet().getKeyValueIterator();i.hasNext();) {
        System.out.println(i.next());
      }
      
      assertEquals("Tag allocation should have succeeded", 1, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Candidates expected", libraries1_1[0].size(), candCount);
      assertEquals("Quality expected to be OK", ProbeMakerConstants.OK_QUALITY, ProbeMakerPropertyUtils.getRank(p));      
      
      
    }

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    pm.setProject(proj);


    //Make a new design after clearing tag usage    
    Task task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), 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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    task = pm.getProbeDesignTask(false, true, true, new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), 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, true, new GoodAcceptor(), 
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), 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);

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    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);


    NucleotideSequence tag1 = libraries2_1_1[0].getSequenceAt(0);
    
    assertEquals(proj.getTagAllocationTable().getUserIDs(tag1).contains(p1.getID()),false);
    assertEquals(proj.getTagAllocationTable().getUserIDs(tag1).contains(p3.getID()),true);
    
    assertEquals(2, task.getCandidatesGenerated());
    assertEquals(ProbeMakerPropertyUtils.getRank(p1),ProbeMakerConstants.BAD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p2),ProbeMakerConstants.BAD_QUALITY);
    assertEquals(ProbeMakerPropertyUtils.getRank(p3),ProbeMakerConstants.GOOD_QUALITY);

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    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);


//  Check that both probes of fair rank   
    assertTrue("Probe 1 (stage 1) expected to be of fair quality",ProbeMakerPropertyUtils.getRank(p)==ProbeMakerConstants.OK_QUALITY); //$NON-NLS-1$
    assertTrue("Probe 2 (stage 1) expected to be of fair quality",ProbeMakerPropertyUtils.getRank(p2)==ProbeMakerConstants.OK_QUALITY); //$NON-NLS-1$

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    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

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