Package org.moltools.lib.seq.impl

Examples of org.moltools.lib.seq.impl.SimpleNucleotideSequence

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    t1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    pm.setProject(proj);
  }
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    pm.setProject(new Project("test project")); //$NON-NLS-1$
    pm.getProject().getSettings().addCandidateModuleStage1(tom);
    pm.getProject().getTargets().addSequence(t1);
    pm.getProject().getTargets().addSequence(t2);
    pm.getProject().getTagAllocationTable().clearUsed();
    lib1.addSequence(new SimpleNucleotideSequence("TAG_A","AAAAAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    lib1.addSequence(new SimpleNucleotideSequence("TAG_T","TTTTTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    lib1.setMode(TagLibrary.USE_UNIQUE_TAG);
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {lib1}));

    pm.getProbeDesignTask(false,true, null, new DefaultNamingScheme(), new GoodFairAcceptor(),new NoSelector(),pd,new DefaultTSSPairDesigner(new DefaultTSSConstructor()),null).run();
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    project.getTargets().addSequence(t1);
    project.getTargets().addSequence(t2);
    project.getTargets().addSequence(t3);
    ListSequenceDB<NucleotideSequence> tags1 = new ListSequenceDB<NucleotideSequence>();
    ListSequenceDB<NucleotideSequence> tags2 = new ListSequenceDB<NucleotideSequence>();
    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);
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    //Add one target
    pm.getProject().getTargets().clear();
    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}));
   
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    //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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  protected NucleotideSequence getTag(Element tagE) {
    String id = tagE.getAttributeValue(ID,ns);
    String typeStr = tagE.getChildText(TYPE,ns);
    String seqStr = tagE.getChildText(SEQUENCE,ns);

    NucleotideSequence seq = new SimpleNucleotideSequence(id,seqStr,Byte.parseByte(typeStr));
    return seq;
  }
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        String tssID = tssE.getAttributeValue(ID,ns);
        String tssTypeStr = tssE.getChildText(TYPE,ns);
        String tssSeqStr = tssE.getChildText(SEQUENCE,ns);
        String tmStr = tssE.getChildText(TM,ns);
        PropertyAcceptorNucleotideSequence tss = ProbeMakerSequenceFactory.createTSS(
            new SimpleNucleotideSequence(tssID, tssSeqStr, Byte.parseByte(tssTypeStr)),
            targetID);
        ProbeMakerPropertyUtils.setHybridizationTemp(tss,Float.parseFloat(tmStr));       
        addMessagesFromElement(tss,tssE.getChild("messageList",ns)); //$NON-NLS-1$
        tssMap.put(key,tss);       
      } 
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  public void testTagSelector() {
    ListSequenceDB<NucleotideSequence> db1 = new ListSequenceDB<NucleotideSequence>();
    ListSequenceDB<NucleotideSequence> db2 = new ListSequenceDB<NucleotideSequence>();
    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"); //$NON-NLS-1$
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            String temp = ""; //$NON-NLS-1$
            //Add a new nucleotide until the correct length is achieved
            for (int i = 0; i < spacerLength; i++) {
              temp += spacerString.charAt(i % spacerString.length());
            }
            spacer = new SimpleNucleotideSequence("Spacer " + temp, temp, p.getType()); //$NON-NLS-1$
          }
          else {
            //Create a new spacer lib for the spacer position and get the first tag
            taglibraries[spacerPosition] = new SpacerLibrary(spacerLength,
                p.getType());
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      String armDesc, 
      int minlength, double preftemp,
      byte acidType, byte fixedEnd) {

    //Create a new TSS.   
    PropertyAcceptorNucleotideSequence pa = ProbeMakerSequenceFactory.createTSS(new SimpleNucleotideSequence(armDesc,"",acidType),temp == null ? "" : DesignUtils.getTargetID(temp)); //$NON-NLS-1$ //$NON-NLS-2$
    ChangeableNucleotideSequence cns = (ChangeableNucleotideSequence) pa;
    if (temp == null) return pa;

    //Set the probe arm sequence to the reverse complement of the template
    try {
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Related Classes of org.moltools.lib.seq.impl.SimpleNucleotideSequence

  • org.moltools.apps.probemaker.calculators.PadlockLigationCalculator
  • org.moltools.apps.probemaker.design.SpacerLibrary
  • org.moltools.apps.probemaker.ext.mod.FalsePrimingModule
  • org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator
  • org.moltools.apps.probemaker.ext.tc.DefaultTSSConstructor
  • org.moltools.apps.probemaker.ext.tc.NoTSSConstructor
  • org.moltools.apps.probemaker.ext.tc.TemplateTSSConstructor
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
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