Examples of Polymorphism

org.hibernate.annotations.Polymorphism
org.moltools.apps.probemaker.seq.Polymorphism

Title: Polymorphism

Description: An interface to be implemented by classes that wish to represent Sequence polymorphisms (like SNPs or InDels)

Copyright: Copyright (c) 2002
@author Johan Stenberg @version 1.0

Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

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Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

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Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

View Full Code Here

Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

View Full Code Here

Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

View Full Code Here

Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

View Full Code Here

Examples of org.hibernate.annotations.Polymorphism

          ? ( hibAnn == null ? OptimisticLockType.VERSION : hibAnn.optimisticLock() )
          : optimisticLockingAnn.type();
    }


    {
      final Polymorphism polymorphismAnn = annotatedClass.getAnnotation( Polymorphism.class );
      this.polymorphismType = polymorphismAnn == null
          ? ( hibAnn == null ? PolymorphismType.IMPLICIT : hibAnn.polymorphism() )
          : polymorphismAnn.type();
    }


    if ( hibAnn != null ) {
      // used later in bind for logging
      explicitHibernateEntityAnnotation = true;

View Full Code Here

Examples of org.moltools.apps.probemaker.seq.Polymorphism

    if (targetPoly == 0) { //No poly
      template = new SimpleSubSequenceTemplate(this, "Template for 3' arm", getType(), //$NON-NLS-1$
                             getTargetPosition(), length(), getID());
    }
    else { //Target is Poly
      Polymorphism poly = getPolys()[targetPoly - 1];
      if (poly instanceof SNP) {


        Nucleotide n = (Nucleotide) poly.getVariants()[variantIndex];
        if (n == null) {
          throw new UnsupportedOperationException("No target nucleotide found"); //$NON-NLS-1$
        }


        String seq = subsequence(getTargetPosition()+1, length());
        String nt = String.valueOf(n.getChar());
        String full = nt + seq;
        
        template = new SimpleSubSequenceTemplate(tempID, full, getType(),
                               getTargetPosition(), length(), getID());
      }
      else if (poly instanceof InDel) {
        switch (variantIndex) {
          case InDel.INS:
            template = new SimpleSubSequenceTemplate(this, tempID, getType(),
                                   getTargetPosition(), length(), getID());
            break;
          case InDel.DEL:
            template = new SimpleSubSequenceTemplate(this,tempID, getType(), 
                                   getTargetPosition() + poly.length(), length(), getID());
            break;
          default:
            throw new UnsupportedOperationException(
                "Invalid InDel mode specified"); //$NON-NLS-1$
        }
      }
      else {
        throw new UnsupportedOperationException(
            "Unsupported Polymorphism type: " + poly.getClass()); //$NON-NLS-1$
      }
    }
    pat3 = template;
  }

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Examples of org.moltools.apps.probemaker.seq.Polymorphism

    else {
      throw new IllegalArgumentException("Invalid variant type"); //$NON-NLS-1$
    }
    if (targetPoly > 0) {
      //Get the target position
      Polymorphism poly = getPolys()[targetPoly - 1];
      int pos = getPolyPosition(targetPoly);
      int length = poly.length();
      String f = seqString().substring(0, pos - 1);
      String t = seqString().substring(pos + length - 1);
      String p = ""; //$NON-NLS-1$
      if (poly instanceof SNP) {
        p = String.valueOf( ( (Nucleotide) ( (SNP) poly).getVariants()[

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Examples of org.moltools.apps.probemaker.seq.Polymorphism

    else {
      l.add(this);
    }
    if (polyIndex >= 0) {
      Variant[] varGroup = this.getVariant().getVariantGroup();
      Polymorphism poly = polys[polyIndex];
      for (int varno = 0; varno < varGroup.length; varno++) {
        AlleleSpecificPadlockTarget vt = new AlleleSpecificPadlockTarget(this);
        vt.setVariant(varGroup[varno]);
        Object var = poly.getVariants()[varno];
        String appendage =  var instanceof Symbol ? String.valueOf(((Symbol) var).getChar()) : var.toString();
        vt.setID(getID() + "|" + appendage); //$NON-NLS-1$
        vt.setName((getName() == null ? getID() : getName()) + "|"  + appendage); //$NON-NLS-1$
        l.add(vt);
      }

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