Examples of com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps.addSpan()

Package com.affymetrix.genometryImpl.symmetry

Class com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps

Examples of com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps.addSpan()

com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps.addSpan()

        spanSym.setProperty(AA_END, prop);
        prop = (Integer.valueOf(end - start)).toString();
        spanSym.setProperty(AA_LENGTH, prop);
    //Multiplying start and end by 3. Because three letters forms one amino acid.
        SeqSpan qspan = new SimpleSeqSpan((start*3)+query_seq.getMin(), (end*3)+query_seq.getMin(), query_seq);
        spanSym.addSpan(qspan);
        return spanSym;
    }


    /**
     *

View Full Code Here

      SeqSpan gspan = esym.getSpan(genomic);
      end = start + gspan.getLength();
      List<Element> hit_inserts = new ArrayList<Element>();
      end = determineOverlappingExons(exon_insert_list, gspan, hit_inserts, end);
      SeqSpan tspan = new SimpleSeqSpan(start, end, mrna);
      esym.addSpan(tspan);
      if (!hit_inserts.isEmpty()) {
        processExonInsert((MutableSeqSymmetry) esym, hit_inserts, genomic, mrna);
      }
      start = end;
    }

View Full Code Here

        SimpleSymWithProps exonsym = new SimpleSymWithProps();
        addDescriptors(elem, exonsym);
        exonsym.setProperty(STARTSTR, elem.getAttribute(STARTSTR));
        exonsym.setProperty(ENDSTR, elem.getAttribute(ENDSTR));
    exonsym.setProperty("length", String.valueOf(end - start));
        exonsym.addSpan(span);
        return exonsym;
    }


  private void processCDS(NodeList children, BioSeq genomic, TypeContainerAnnot m2gSym, BioSeq mrna, String protein_id, String amino_acid) {
    for (int i = 0; i < children.getLength(); i++) {

View Full Code Here

        // could just do this as a single seq span (start, end, seq), but then would end up recreating
        //   the cds segments, which will get ignored afterwards...
        SeqSpan gstart_point = new SimpleSeqSpan(start, start, genomic);
        SeqSpan gend_point = new SimpleSeqSpan(end, end, genomic);
        SimpleSymWithProps result = new SimpleSymWithProps();
        result.addSpan(gstart_point);
        SeqSymmetry[] m2gPath = new SeqSymmetry[]{m2gSym};
        SeqUtils.transformSymmetry((MutableSeqSymmetry) result, m2gPath);
        SeqSpan mstart_point = result.getSpan(mrna);


    if(mstart_point == null) {

View Full Code Here

      throw new NullPointerException("Conflict with start and end in processCDS.");
    }


        result = new SimpleSymWithProps();


        result.addSpan(gend_point);
        SeqUtils.transformSymmetry((MutableSeqSymmetry) result, m2gPath);
        SeqSpan mend_point = result.getSpan(mrna);


    if(mend_point == null) {
      throw new NullPointerException("Conflict with start and end in processCDS.");

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.