Package org.moltools.design.data.impl

Examples of org.moltools.design.data.impl.SimpleProperty

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  /**Set the TSSPair of this probe*/
  protected void setTSSPair(TSSPair pair) {
    tssPair = pair;
    String targetID = pair == null ? null : DesignUtils.getTargetID(pair);
    mps.setProperty(new SimpleProperty(KEY_TARGET_ID,targetID,false));
    sequence.replace(0,sequence.length(),composeSequence());
  }
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  public TSSPair(PropertyAcceptorNucleotideSequence five, PropertyAcceptorNucleotideSequence three, ProbeMakerTarget t) {
    super(KEY_SET, t == null ? null : t.getID(),"TSS_PAIR|" + (t == null ? null : t.getID())); //$NON-NLS-1$
    fivePrime = five;
    threePrime = three;
    target = t;   
    mps.setProperty(new SimpleProperty(KEY_TARGET_ID,target == null ? null : target.getID(),true));
  }
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/**Factory class for creating certain kinds of ProbeMaker-specific sequence types*/
public class ProbeMakerSequenceFactory {
 
  public static PropertyAcceptorNucleotideSequence createTSS(NucleotideSequence seq, String targetID) {
    PropertyAcceptorNucleotideSequence tss = new DefaultChangeablePropertyNucleotideSequence(seq.getID(),seq.seqString(),seq.getType());       
    tss.getMutablePropertySet().setProperty(new SimpleProperty(Targetted.KEY_TARGET_ID,targetID,false));
    return tss;
  }
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  /**Set the TSSPair of this probe*/
  protected void setTSSPair(TSSPair pair) {
    tssPair = pair;
    String targetID = pair == null ? null : DesignUtils.getTargetID(pair);
    mps.setProperty(new SimpleProperty(KEY_TARGET_ID,targetID,false));
    sequence.replace(0,sequence.length(),composeSequence());
  }
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  public static final String KEY_MESSAGE = "message"; //$NON-NLS-1$
  public static final String KEY_TM = "tm_complement";   //$NON-NLS-1$
 
  /**Add a message to a MessageHolder*/
  public static void addMessage(PropertyAcceptor pa, Message m) {
    pa.getMutablePropertySet().addProperty(new SimpleProperty(KEY_MESSAGE,m,true));
  }
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    return tmValue.floatValue();
  }
 
  /**Set the hybridization temp of a TSS*/
  public static void setHybridizationTemp(PropertyAcceptor pa, float temp) {
    pa.getMutablePropertySet().setProperty(new SimpleProperty(KEY_TM,new Float(temp),false));
  }
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    return rankValue.shortValue();
  }
 
  /**Set the rank value for a candidate*/
  public static void setRank(PropertyAcceptor c, short rank) {
    c.getMutablePropertySet().setProperty(new SimpleProperty(KEY_RANK,new Short(rank),false));   
  }
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/**Factory class for creating certain kinds of ProbeMaker-specific sequence types*/
public class ProbeMakerSequenceFactory {
 
  public static PropertyAcceptorNucleotideSequence createTSS(NucleotideSequence seq, String targetID) {
    PropertyAcceptorNucleotideSequence tss = new DefaultChangeablePropertyNucleotideSequence(seq.getID(),seq.seqString(),seq.getType());       
    tss.getMutablePropertySet().setProperty(new SimpleProperty(Targetted.KEY_TARGET_ID,targetID,false));
    return tss;
  }
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Related Classes of org.moltools.design.data.impl.SimpleProperty

  • org.moltools.apps.probemaker.seq.impl.AbstractProbe
  • org.moltools.apps.probemaker.seq.impl.TSSPair
  • org.moltools.apps.probemaker.seq.ProbeMakerPropertyUtils
  • org.moltools.apps.probemaker.seq.ProbeMakerSequenceFactory
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