Package org.moltools.apps.probemaker.design

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

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    tags1.addSequence(new SimpleNucleotideSequence("ZIP|1","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    tags1.addSequence(new SimpleNucleotideSequence("ZIP|2","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    tags1.addSequence(new SimpleNucleotideSequence("ZIP|3","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    tags2.addSequence(new SimpleNucleotideSequence("PRIMER|1","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    project.getSettings().getDesignParameters().put("UPSTREAM_BLOCKS","1"); //$NON-NLS-1$ //$NON-NLS-2$
    TagLibrary lib1 = new DefaultTagLibrary(tags1,"Lib 1"); //$NON-NLS-1$
    TagLibrary lib2 = new DefaultTagLibrary(tags2,"Lib 2"); //$NON-NLS-1$
    lib1.setMode(TagLibrary.USE_UNIQUE_TAG);
    lib2.setMode(TagLibrary.USE_SAME_TAG);
    project.setTagSettings(new DefaultTagSettings(new TagLibrary[] { lib1, lib2 }));
  }
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    pm.getProject().getTargets().addSequence(t1);
   
    ListSequenceDB<NucleotideSequence> db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(new SimpleNucleotideSequence("Tag 1","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 2","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    TagLibrary tl = new DefaultTagLibrary(db,"Unique"); //$NON-NLS-1$
    tl.setMode(TagLibrary.USE_UNIQUE_TAG);
   
    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();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
      
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t1);
    pm.getProject().getTargets().addSequence(t2);
   
    db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(new SimpleNucleotideSequence("Tag 1","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 2","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 3","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 4","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    tl = new DefaultTagLibrary(db,"Unique"); //$NON-NLS-1$
    tl.setMode(TagLibrary.USE_PER_GROUP);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl, tl}));
   
//  Design
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(), new NoSelector(), pd, new DefaultTSSConstructor(), eh).run();   
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    t1.setVariant(t1.getVariants()[0]);
    t2.setVariant(t2.getVariants()[0]);


    //Make tag library with ten tags
    TagLibrary tags10 = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags10.setMode(TagLibrary.USE_UNIQUE_TAG);
    for (int i = 1;i <= 10;i++) {
      tags10.addSequence(new SimpleNucleotideSequence("Tag" + i,"AAAAAAAAAAAAAAAAAAAA", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
    }   

    //Make tag library with one tag
    TagLibrary tags1 = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 1"); //$NON-NLS-1$
    tags1.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags1.addSequence(new SimpleNucleotideSequence("Tag1","AAAAAAAAAAAAAAAAAAAA", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$

    TagLibrary tags1b = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 1b"); //$NON-NLS-1$
    tags1b.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags1b.addSequence(new SimpleNucleotideSequence("Tag1b","AAAAAAAAAAAAAAAAAAAA", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$

    libraries1_10 = new TagLibrary[] { tags10 };
    libraries1_1 = new TagLibrary[] { tags1 };
    libraries2_1_1 = new TagLibrary[] { tags1, tags1b };
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    for (Iterator<?> i2 = tagsE.getChildren().iterator();i2.hasNext();) {
      Element tagE = (Element) i2.next();
      tags.addSequence(getTag(tagE));
    }

    TagLibrary tl = new DefaultTagLibrary(tags,libName);
    tl.setMode(Byte.parseByte(libMode));
    return tl;
  }
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  @Override
  protected void setUp() throws Exception {
    ListSequenceDB<NucleotideSequence> db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(tag1);
    db.addSequence(tag2);
    lib = new DefaultTagLibrary(db,"lib"); //$NON-NLS-1$
    TagLibrary[] libs = new TagLibrary[] {lib};
    c1 = new DefaultProbe(null,0,0,NucleotideSequence.DNA);
    c1.setID("PROBE_1"); //$NON-NLS-1$
    c2 = new DefaultProbe(null,0,0,NucleotideSequence.DNA);
    c2.setID("PROBE_2"); //$NON-NLS-1$
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    while (!(libString = r.readLine()).startsWith(String.valueOf(TITLE_DESCRIPTOR))) {

      String[] substrings = tio.getInStrings(libString);
      if (substrings.length != 4)
        throw new UnsupportedOperationException("Error parsing tag library line: " + libString); //$NON-NLS-1$
      TagLibrary l = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(), substrings[0]);
      l.setMode(Byte.parseByte(substrings[1]));
      libs.add(l);
    }
    TagLibrary[] libraries = new TagLibrary[libs.size()];
    for (int l = 0; l < libraries.length; l++) {
      libraries[l] = libs.get(l);
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    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};
   
    lib1.setMode(TagLibrary.USE_SAME_TAG);
    lib1.setMode(TagLibrary.USE_UNIQUE_TAG);
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Related Classes of org.moltools.apps.probemaker.design.DefaultTagLibrary

  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.swingui.TagSetupPanel
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTableTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
  • org.moltools.apps.probemaker.test.TagSelectorTest
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