List of addSpan() Examples

Examples of addSpan()

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

            //   [unless start of exon and the insert is actually at exact beginning of exon]
            if (istart != genStart) {
                MutableSeqSymmetry segSym = new SimpleMutableSeqSymmetry();
                SeqSpan gSpan = new SimpleSeqSpan(genStart, istart, genomic);  // start of insert is end of exon seg
                SeqSpan tSpan = new SimpleSeqSpan(transStart, transEnd, mrna);
                segSym.addSpan(gSpan);
                segSym.addSpan(tSpan);
                exonSym.addChild(segSym);
            }
            // now add exon seg for the current insert
            transStart = transEnd;

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

            if (istart != genStart) {
                MutableSeqSymmetry segSym = new SimpleMutableSeqSymmetry();
                SeqSpan gSpan = new SimpleSeqSpan(genStart, istart, genomic);  // start of insert is end of exon seg
                SeqSpan tSpan = new SimpleSeqSpan(transStart, transEnd, mrna);
                segSym.addSpan(gSpan);
                segSym.addSpan(tSpan);
                exonSym.addChild(segSym);
            }
            // now add exon seg for the current insert
            transStart = transEnd;
            transEnd += ilength;

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

            transStart = transEnd;
            transEnd += ilength;
            SeqSpan insert_tspan = new SimpleSeqSpan(transStart, transEnd, mrna);
            SeqSpan insert_gspan = new SimpleSeqSpan(istart, istart, genomic);
            MutableSeqSymmetry isegSym = new SimpleMutableSeqSymmetry();
            isegSym.addSpan(insert_tspan);
            // experimenting with adding a zero-length placeholder for exon insert relative to genomic
            isegSym.addSpan(insert_gspan);
            exonSym.addChild(isegSym);


            // set current genomic start point for next loop to location of current insert

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

            SeqSpan insert_tspan = new SimpleSeqSpan(transStart, transEnd, mrna);
            SeqSpan insert_gspan = new SimpleSeqSpan(istart, istart, genomic);
            MutableSeqSymmetry isegSym = new SimpleMutableSeqSymmetry();
            isegSym.addSpan(insert_tspan);
            // experimenting with adding a zero-length placeholder for exon insert relative to genomic
            isegSym.addSpan(insert_gspan);
            exonSym.addChild(isegSym);


            // set current genomic start point for next loop to location of current insert
            genStart = istart;
            transStart = transEnd;

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

        //   after finished looping through inserts
        if (genStart != egSpan.getEnd()) {
            SeqSpan gSpan = new SimpleSeqSpan(genStart, egSpan.getEnd(), genomic);
            SeqSpan tSpan = new SimpleSeqSpan(transStart, etSpan.getEnd(), mrna);
            MutableSeqSymmetry endSym = new SimpleMutableSeqSymmetry();
            endSym.addSpan(gSpan);
            endSym.addSpan(tSpan);
            exonSym.addChild(endSym);
        }
    }

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

        if (genStart != egSpan.getEnd()) {
            SeqSpan gSpan = new SimpleSeqSpan(genStart, egSpan.getEnd(), genomic);
            SeqSpan tSpan = new SimpleSeqSpan(transStart, etSpan.getEnd(), mrna);
            MutableSeqSymmetry endSym = new SimpleMutableSeqSymmetry();
            endSym.addSpan(gSpan);
            endSym.addSpan(tSpan);
            exonSym.addChild(endSym);
        }
    }


    /**

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Examples of 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;
    }


    /**
     *

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

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

        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++) {

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

        // 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) {

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