Package org.moltools.apps.probemaker.design

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

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    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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    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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    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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    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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    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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    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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    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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Related Classes of org.moltools.apps.probemaker.design.TagAllocationTable

  • org.apache.commons.collections.KeyValue
  • org.apache.commons.collections.keyvalue.DefaultKeyValue
  • org.moltools.apps.probemaker.project.Project
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTableTest
  • org.moltools.apps.probemaker.test.TagSelectorTest
  • org.moltools.lib.Identifiable
  • org.moltools.lib.seq.alphabet.Nucleotide
  • org.moltools.lib.seq.NucleotideSequence
  • java.util.LinkedHashSet
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