Examples of StreamErrorHandler

Examples of net.sf.apptools.log.StreamErrorHandler

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    proj.getTargets().addSequence(t1);   
    proj.getTargets().addSequence(t2);   
    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);
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Examples of net.sf.apptools.log.StreamErrorHandler

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    proj.getSettings().addCandidateModuleStage1(dummy);
    pm.setProject(proj);
    TargetHandler.expandTargets(pm.getProject().getTargets());

    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);
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Examples of net.sf.apptools.log.StreamErrorHandler

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  }

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

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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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Examples of net.sf.apptools.log.StreamErrorHandler

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  }
  
 
  protected void doTest(TSSConstructor tsc, String expect5, String expect3) throws ClusterException {
    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(tsc), new StreamErrorHandler(System.out,true));
    task.run();
   
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
   
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Examples of net.sf.apptools.log.StreamErrorHandler

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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();
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Examples of net.sf.apptools.log.StreamErrorHandler

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    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl}));
   
    //Design
    ProbeDesigner pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, true, new AllAcceptor(),new NoSelector(), pd, 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, true, new AllAcceptor(), new NoSelector(), pd, new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();
   
        
//  Store to project file
    f = new File("temp2.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
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Examples of net.sf.apptools.log.StreamErrorHandler

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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, 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 net.sf.apptools.log.StreamErrorHandler

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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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Examples of net.sf.apptools.log.StreamErrorHandler

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    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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