Examples of com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps

Package com.affymetrix.genometryImpl.symmetry

Examples of com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps

com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps

            end = Integer.parseInt(elem.getAttribute("query_end"));
        } catch (Exception ex) {
            end = Integer.parseInt(elem.getAttribute("query_stop"));
        }


        SimpleSymWithProps spanSym = new SimpleSymWithProps();
        addDescriptors(elem, spanSym);
        String prop = (Integer.valueOf(start)).toString();
        spanSym.setProperty(AA_START, prop);
        prop = (Integer.valueOf(end)).toString();
        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;
    }

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    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();
      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;
    }

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        int end = Integer.parseInt(elem.getAttribute(ENDSTR));


        transCheckExons.add(new int[]{start,end});


        SeqSpan span = new SimpleSeqSpan(start, end, genomic);
        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;
    }

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) {
      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.");
    }

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Related Classes of com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps

org.bioviz.protannot.Xml2GenometryParser

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