Examples of BioSeq

      throws NumberFormatException {
    int exoncount = m2gSym.getChildCount();
    int mrnalength = determinemRNALength(exoncount, m2gSym, genomic, exon_insert_list);
    int end = 0;
    String mrna_id = MRNASTR;
    BioSeq mrna = new BioSeq(mrna_id, null, mrnalength);
    mrna.setBounds(start, start+mrnalength);
    mrna_hash.put(mrna_id, mrna);
    SeqSpan mrna_span = new SimpleSeqSpan(mrna.getMin(), mrna.getMax(), mrna); 
    m2gSym.addSpan(mrna_span);
    for (int i = 0; i < exoncount; i++) {
      SimpleSymWithProps esym = (SimpleSymWithProps) m2gSym.getChild(i);
      SeqSpan gspan = esym.getSpan(genomic);
      end = start + gspan.getLength();

    }


        TypeContainerAnnot m2pSym = new TypeContainerAnnot(elem.getAttribute(METHODSTR));


        SeqSpan mspan = new SimpleSeqSpan(mstart_point.getStart(), mend_point.getEnd(), mrna);
        BioSeq protein = new BioSeq(protein_id, null, mspan.getLength());
    protein.setResidues(processAminoAcid(amino_acid));
    protein.setBounds(mspan.getMin(), mspan.getMin() + mspan.getLength());


        prot_hash.put(protein_id, protein);
        SeqSpan pspan = new SimpleSeqSpan(protein.getMin(), protein.getMax(), protein); 
        if (DEBUG) {
            System.err.println("protein: length = " + pspan.getLength());
        }
        m2pSym.addSpan(mspan);
        m2pSym.addSpan(pspan);


        m2pSym.setID("");
        protein.addAnnotation(m2pSym);
        mrna.addAnnotation(m2pSym);


        // Use genometry manipulations to map cds start/end on genome to cds start/end on transcript
        //    (so that cds becomes mrna2protein symmetry on mrna (and on protein...)

Examples of com.affymetrix.genometryImpl.BioSeq

Examples of com.affymetrix.genometryImpl.BioSeq