Package com.affymetrix.genometryImpl

Examples of com.affymetrix.genometryImpl.BioSeq

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      try {
        NormalizeXmlStrand nxs = new NormalizeXmlStrand(bistr);
        //NormalizeXmlStrand.outputXMLToScreen(nxs.doc);
        Xml2GenometryParser parser = new Xml2GenometryParser();

        BioSeq seq = parser.parse(nxs.doc);
        if (seq != null) {
          GenomeView gview = new GenomeView(GenomeView.COLORS.defaultColorList());
          gview.setBioSeq(seq, true);
          return true;
        }
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        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;
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        copyToMutable(mrna2genome, annot2genome);

        SeqUtils.transformSymmetry(annot2genome, path2view);
    GlyphI tGlyph = glyphifyExons(mrna2genome, annot2genome, childcount);
        tier.addChild(tGlyph);
    BioSeq mrna = SeqUtils.getOtherSpan(mrna2genome, mrna2genome.getSpan(gseq)).getBioSeq();
    displayAssociatedmRNAforTranscript(mrna, path2view, mrna2genome, tier, tGlyph);
    }
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        if (DEBUG_TRANSCRIPT_ANNOTS) {
            SeqUtils.printSymmetry(annot2genome);
        }

        SeqSpan pSpan = SeqUtils.getOtherSpan(annot2mrna, mrna_span);
        BioSeq protein = pSpan.getBioSeq();
    String amino_acid = null;

    try{
      amino_acid = protein.getResidues(0, protein.getLength());
    }catch(Exception ex){
      System.out.println("*** Warning: No amino acid found ");
    }

        GlyphI aGlyph = new LineContainerGlyph();
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      NormalizeXmlStrand nxs = new NormalizeXmlStrand(bistr);
      if (DEBUG) {
        NormalizeXmlStrand.outputXMLToScreen(nxs.doc);
      }
      Xml2GenometryParser parser = new Xml2GenometryParser();
      BioSeq genome_seq = parser.parse(nxs.doc);
      gview.setTitle("viewing file: " + filename + "\t genome version: " + genome_seq.getVersion() + "\t sequence: " + genome_seq.getID());
      gview.setBioSeq(genome_seq, true);
      frm.setTitle(" ProtAnnot: " + filename + "\t version: " + genome_seq.getVersion() + "\t id: " + genome_seq.getID());
    } catch (Exception ex) {
      Reporter.report("Couldn't read file: " + filename + "\n"
          + "Error : " + ex.getMessage(),
          ex, false, false, true);
      no_data();
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    BioSeq parse(Document doc) throws Exception{
    mrna_hash = new HashMap<String,BioSeq>();
    prot_hash = new HashMap<String,BioSeq>();

        try {
            BioSeq ret_genomic = processDocument(doc);

      return ret_genomic;

        } catch (Exception ex) {
      ex.printStackTrace();
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      seq = top_element.getAttribute("seq");
    } catch (Exception e) {
      // ignore exception
    }

    BioSeq chrom = buildChromosome(top_element, seq, version);

    processDNASeq(chrom, top_element);

    return chrom;
    }
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    return chrom;
    }

    private static BioSeq buildChromosome(Element top_element, String seq, String version)
            throws DOMException {
        BioSeq chrom = null;
        NodeList children = top_element.getChildNodes();
        for (int i = 0; i < children.getLength(); i++) {
            Node child = children.item(i);
            String cname = child.getNodeName();
            if (cname != null && cname.equalsIgnoreCase(RESIDUESSTR)) {
                Text resnode = (Text) child.getFirstChild();
                String residues = resnode.getData();
                chrom = new BioSeq(seq, version, residues.length());
                chrom.setResidues(residues);
            }
        }
        return chrom;
    }
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     * @param   elem        Node for which protein is to be processed
     * @see     com.affymetrix.genometryImpl.BioSeq
     */
    private static void processProtein(Map<String,BioSeq> prot_hash, Element elem) {
        String pid = elem.getAttribute(IDSTR);
        BioSeq protein = prot_hash.get(pid);
        if (protein == null) {
            System.err.println("Error: no bioseq matching id: " + pid
                    + ". Skipping it.");
            return;
        }
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        Collections.sort(exon_list, new SeqSymStartComparator( genomic, forward));
        for (SeqSymmetry esym : exon_list) {
            m2gSym.addChild(esym);
        }

    BioSeq mrna = addSpans(m2gSym, genomic, exon_insert_list, start);
   
    String protein_id = determineProteinID(children);

    String amino_acid = getAminoAcid(m2gSym);
    processCDS(children, genomic, m2gSym, mrna, protein_id, amino_acid);

        m2gSym.setID("");
        genomic.addAnnotation(m2gSym);
        mrna.addAnnotation(m2gSym);
    }
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Related Classes of com.affymetrix.genometryImpl.BioSeq

  • org.bioviz.protannot.GenomeView
  • org.bioviz.protannot.ProtAnnotMain
  • org.bioviz.protannot.TestSamples
  • org.bioviz.protannot.Xml2GenometryParser
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