Examples of com.affymetrix.genometryImpl.span.SimpleSeqSpan

Package com.affymetrix.genometryImpl.span

Examples of com.affymetrix.genometryImpl.span.SimpleSeqSpan

com.affymetrix.genometryImpl.span.SimpleSeqSpan


        int acount = gseq.getAnnotationCount();


        SeqSymmetry[] path2view = new SeqSymmetry[1];
        MutableSeqSymmetry viewSym = new SimpleMutableSeqSymmetry();
        viewSym.addSpan(new SimpleSeqSpan(gseq.getMin(), gseq.getMax(), gseq));
        vseq = new BioSeq("view seq", null, gseq.getLength());
        vseq.setBounds(gseq.getMin(), gseq.getMax());


        viewSym.addSpan(new SimpleSeqSpan(vseq.getMin(), vseq.getMax(), vseq));


        path2view[0] = viewSym;


        for (int i = 0; i < acount; i++) {
            SeqSymmetry asym = gseq.getAnnotation(i);

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        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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        if (DEBUG) {
            System.err.println("mrna:  start = " + start + "  end = " + end);
        }
        NodeList children = elem.getChildNodes();
        SeqSpan span = new SimpleSeqSpan(start, end, genomic);


        TypeContainerAnnot m2gSym = new TypeContainerAnnot(elem.getAttribute("method"));
        m2gSym.addSpan(span);
        addDescriptors(elem, m2gSym);
        m2gSym.setProperty(TYPESTR, "mRNA");
        boolean forward = (span.isForward());




    transCheckExons = new ArrayList<int[]>();
        List<SeqSymmetry> exon_list = new ArrayList<SeqSymmetry>();
        List<Node> exon_insert_list = new ArrayList<Node>();

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    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();
      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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            // split out exon seg between last insert (or start of exon) and current insert
            //   [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;
            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
            genStart = istart;
            transStart = transEnd;


        }


        // if last insert is not _exactly_ at end of exon, then need to add last exon seg
        //   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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        int start = Integer.parseInt(elem.getAttribute(STARTSTR));
        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));

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        checkTranslationLength(transCheckExons,start,end);


        // 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.");
    }


        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("");

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Related Classes of com.affymetrix.genometryImpl.span.SimpleSeqSpan

org.bioviz.protannot.GenomeView

org.bioviz.protannot.Xml2GenometryParser

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