Examples of TSSPair

org.moltools.apps.probemaker.seq.impl.TSSPair
A specialized SequenceCluster, capable of holding two sequences only, namely a 5' and 3' target specific sequence. In addition, the TSSPair is also a candidate, and holds a direct reference to the Target of the TSSPair. @author Johan Stenberg

Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

  }


  public void testTSSPair() {
    PropertyAcceptorNucleotideSequence tss5 = ProbeMakerSequenceFactory.createTSS(seq,target.getID());    
    ProbeMakerPropertyUtils.addMessage(tss5, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR));     //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    TSSPair pair = new TSSPair(tss5,null,target);
    ProbeMakerPropertyUtils.setRank(pair, ProbeMakerConstants.BAD_QUALITY);
    
    assertTrue("Incorrect rank", ProbeMakerConstants.BAD_QUALITY == ProbeMakerPropertyUtils.getRank(pair)); //$NON-NLS-1$
    assertTrue("Incorrect target ID", target.getID().equals(DesignUtils.getTargetID(pair))); //$NON-NLS-1$
    assertTrue("Incorrect message count", 1 == ProbeMakerPropertyUtils.getAllMessages(pair).size()); //$NON-NLS-1$

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

  }


  public void testProbe() {
    PropertyAcceptorNucleotideSequence tss5 = ProbeMakerSequenceFactory.createTSS(seq,target.getID());    
    ProbeMakerPropertyUtils.addMessage(tss5, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR));     //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    TSSPair pair = new TSSPair(tss5,null,target);
    ProbeMakerPropertyUtils.addMessage(pair, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$


    Probe probe = new DefaultProbe(pair,0,0,NucleotideSequence.DNA);


    ProbeMakerPropertyUtils.setRank(probe, ProbeMakerConstants.BAD_QUALITY);
    
    assertTrue("Incorrect rank", ProbeMakerConstants.BAD_QUALITY == ProbeMakerPropertyUtils.getRank(probe)); //$NON-NLS-1$
    
    assertTrue("Incorrect target ID", target.getID().equals(DesignUtils.getTargetID(probe))); //$NON-NLS-1$
    assertTrue("Incorrect target", target.equals(pair.getTarget())); //$NON-NLS-1$
    assertTrue("Incorrect target", target.equals(probe.getTarget())); //$NON-NLS-1$
    assertTrue("Incorrect message count", 2 == ProbeMakerPropertyUtils.getAllMessages(probe).size()); //$NON-NLS-1$
    assertTrue("Wrong tss pair",pair == probe.getTSSPair()); //$NON-NLS-1$
    
    ProbeMakerPropertyUtils.addMessage(probe, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), pd, tsc, new StreamErrorHandler(System.out,true));
    task.run();
    
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
    
    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
    PropertyAcceptorNucleotideSequence tss3 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_THREE_PRIME);
    
    String seq5 = tss5.seqString();
    String seq3 = tss3.seqString();
    
    assertTrue("5' arm sequence failed, expected '" + expect5 + "', got: '" + seq5 + "'", seq5.equals(expect5)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

    
    TSSConstructor con = new DefaultTSSConstructor();
    DefaultTSSPairDesigner tpd = new DefaultTSSPairDesigner(con);
  
    ProbeMakerTarget target = new PadlockTarget("T1","ATACAGTCGTCCGGGTCGAA|AAGAGCATCGACGCGGATCAAGCCTATCGTCACGCGA","Target 1");
    TSSPair pair = tpd.designTSSPair(target);
    
    Probe p = new DefaultProbe(pair,0,0,NucleotideSequence.DNA);
  
    plc.checkTemplatingByTarget(p);

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(tsc), new StreamErrorHandler(System.out,true));
    task.run();
    
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
    
    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
    PropertyAcceptorNucleotideSequence tss3 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_THREE_PRIME);
    
    String seq5 = tss5.seqString();
    String seq3 = tss3.seqString();
    
    assertTrue("5' arm sequence failed, expected '" + expect5 + "', got: '" + seq5 + "'", seq5.equals(expect5)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

    }
    return p;
  }


  public static TSSPair createTSSPair(PropertyAcceptorNucleotideSequence tss5, PropertyAcceptorNucleotideSequence tss3, ProbeMakerTarget target) {
    return new TSSPair(tss5,tss3,target);
  }

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

    if (mh instanceof Probe) {
      Probe probe = (Probe) mh;
      l.addAll(getAllMessages(probe.getTSSPair()));
    }
    else if (mh instanceof TSSPair) {
      TSSPair pair = (TSSPair) mh;
      if (pair.getFivePrime() != null) l.addAll(getAllMessages(pair.getFivePrime()));
      if (pair.getThreePrime() != null) l.addAll(getAllMessages(pair.getThreePrime()));
    }
    l.addAll(getOwnMessages(mh));
    Collection<Message> messages = CollectionUtils.unmodifiableCollection(l);
    return messages;
  }

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

    }
    return p;
  }


  public static TSSPair createTSSPair(PropertyAcceptorNucleotideSequence tss5, PropertyAcceptorNucleotideSequence tss3, ProbeMakerTarget target) {
    return new TSSPair(tss5,tss3,target);
  }

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair

      probeE.addContent(groupE);
    }


    probeE.addContent(new Element(RANK,ns).addContent(String.valueOf(ProbeMakerPropertyUtils.getRank(pr))));


    TSSPair tssPair = pr.getTSSPair();
    Element tssPairE = new Element(TSS_PAIR,ns);
    String targetID = DesignUtils.getTargetID(tssPair);
    tssPairE.setAttribute(TARGET_ID, targetID == null ? "" : targetID ,ns); //$NON-NLS-1$
    Collection<String> tssIDs = new HashSet<String>();
    for (Iterator<String> i2 = tssPair.getKeys().iterator();i2.hasNext();) {
      String key = i2.next();                
      try {
        PropertyAcceptorNucleotideSequence tss = (PropertyAcceptorNucleotideSequence) tssPair.getSequence(key);
        if (tss != null) {
          Element seqE = new Element(TSS,ns);
          seqE.setAttribute("key",key,ns); //$NON-NLS-1$
          seqE.setAttribute(ID,tss.getID(),ns);
          tssIDs.add(tss.getID());

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Examples of org.moltools.apps.probemaker.seq.impl.TSSPair


      PropertyAcceptorNucleotideSequence five = null;
      PropertyAcceptorNucleotideSequence three = null;
      five = tssMap.get(TSSPair.KEY_FIVE_PRIME);
      three = tssMap.get(TSSPair.KEY_THREE_PRIME);      
      TSSPair tssP = ProbeMakerSequenceFactory.createTSSPair(five,three,target);
      addMessagesFromElement(tssP,tssPairE.getChild("messageList",ns)); //$NON-NLS-1$


      //Tags
      int upstream = -1;
      int downstream = -1;

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