Examples of TagAllocationTable

org.moltools.apps.probemaker.design.TagAllocationTable
This class is responsible for keeping track of how tags are used in a project. The designer objects register and unregister tag usage with this table, and query tag usage for tag allocation. Eventually, this table will also manage the tag allocation rules and take over that task from the tag libraries. @author Johan Stenberg

Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    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();

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Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl, tl}));
    
//  Design
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), eh).run();    


    TagAllocationTable tat1 = pm.getProject().getTagAllocationTable();
    
//  Store to project file
    f = new File("temp3.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
    
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
    
    TagAllocationTable tat2 = pm.getProject().getTagAllocationTable();
    
    assertEquals(tat1, tat2);
    
//  Design
    pd = new DefaultProbeDesigner(new PairwiseTagAllocator());

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Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    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();

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Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl, tl}));
    
//  Design
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(), new NoSelector(), pd, new DefaultTSSConstructor(), eh).run();    


    TagAllocationTable tat1 = pm.getProject().getTagAllocationTable();
    
//  Store to project file
    f = new File("temp3.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
    
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
    
    TagAllocationTable tat2 = pm.getProject().getTagAllocationTable();
    
    assertEquals(tat1, tat2);
    
//  Design
    pd = new DefaultProbeDesigner(new PairwiseTagAllocator());

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Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    settings = s;
    targets = new ListSequenceDB<ProbeMakerTarget>();
    probes = new ListSequenceDB<Probe>();
    tagSettings = new DefaultTagSettings(new TagLibrary[0], new int[0]);
    name = _name;
    tagAllocationTable = new TagAllocationTable();
  }

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Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    g2 = new ProbeGroup(null,"G2"); //$NON-NLS-1$
    g1.addMember(c1);
    g2.addMember(c2);
    g2.addMember(c3);


    tat = new TagAllocationTable();
    tat.setTagLibraries(libs);


  }

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Examples of org.moltools.apps.probemaker.design.TagAllocationTable

    db1.addSequence(new SimpleNucleotideSequence("T11","")); //$NON-NLS-1$ //$NON-NLS-2$
    db1.addSequence(new SimpleNucleotideSequence("T12","")); //$NON-NLS-1$ //$NON-NLS-2$
    db2.addSequence(new SimpleNucleotideSequence("T21",""));  //$NON-NLS-1$//$NON-NLS-2$
    db2.addSequence(new SimpleNucleotideSequence("T21","")); //$NON-NLS-1$ //$NON-NLS-2$
    
    TagAllocationTable tat = new TagAllocationTable();
    
    TagLibrary lib1 = new DefaultTagLibrary(db1,"lib 1"); //$NON-NLS-1$
    TagLibrary lib2 = new DefaultTagLibrary(db2,"lib 2"); //$NON-NLS-1$
    TagLibrary[] libs = new TagLibrary[] { lib1, lib2 };
    int[] tagorder = new int[] {0,1};

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