Package net.sf.apptools.task

Examples of net.sf.apptools.task.Task.run()

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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();   
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    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();   
   
    StringReader sr = new StringReader(">PROBE_1 Probe 1\nATCGACGAGCGAC|ACTAGCGAGCGAC|ATCGACGACGGAC|ACTACGAGCGAC\n" + //$NON-NLS-1$
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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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  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();   
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    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();   
   
    StringReader sr = new StringReader(">PROBE_1 Probe 1\nATCGACGAGCGAC|ACTAGCGAGCGAC|ATCGACGACGGAC|ACTACGAGCGAC\n" + //$NON-NLS-1$
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    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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