Examples of com.affymetrix.genometryImpl.symmetry.SeqSymmetry

Package com.affymetrix.genometryImpl.symmetry

Examples of com.affymetrix.genometryImpl.symmetry.SeqSymmetry

com.affymetrix.genometryImpl.symmetry.SeqSymmetry

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


        path2view[0] = viewSym;


        for (int i = 0; i < acount; i++) {
            SeqSymmetry asym = gseq.getAnnotation(i);
            if (DEBUG_GENOMIC_ANNOTS) {
                SeqUtils.printSymmetry(asym);
            }
            glyphifyMRNA(asym, path2view);
        }

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    seqmap.setDataModel(tGlyph, mrna2genome);
    SeqSpan tSpan = annot2genome.getSpan(vseq);
    tGlyph.setCoords(tSpan.getMin(), 0, tSpan.getLength(), 20);
    tGlyph.setColor(col_ts);
    for (int i = 0; i < childcount; i++) {
      SeqSymmetry exon2genome = annot2genome.getChild(i);
      SeqSpan gSpan = exon2genome.getSpan(vseq);
      GlyphI cglyph = new OutlineRectGlyph();
      seqmap.setDataModel(cglyph, exon2genome);
      // can't give this a type and therefore signal
      // to the selection logic that this is first class selectable
      // object
      // so let's put it in a list
      exonList.add(exon2genome);
      cglyph.setColor(col_ts);
      cglyph.setCoords(gSpan.getMin(), 0, gSpan.getLength(), 20);
      exonGlyphs.add(cglyph);
      tGlyph.addChild(cglyph);
      //  testing display of "exon segments" for transcripts that have
      //     base inserts relative to the genomic sequence
      //  haven't dealt with display of base deletions in transcript relative to genomic yet
      //  if exon is segmented by inserts, then it will have children
      //     that specify this segmentation
      for (int seg_index = 0; seg_index < exon2genome.getChildCount(); seg_index++) {
        SeqSymmetry eseg2genome = exon2genome.getChild(seg_index);
        SeqSpan seg_gspan = eseg2genome.getSpan(vseq);
        if (seg_gspan.getLength() == 0) {
          // only mark the inserts (those whose genomic extent is zero
          GlyphI segGlyph = new OutlineRectGlyph();
          segGlyph.setColor(col_bg);
          segGlyph.setCoords(seg_gspan.getMin(), 0, seg_gspan.getLength(), 25);

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      SeqSymmetry[] new_path2view = new SeqSymmetry[path2view.length + 1];
      System.arraycopy(path2view, 0, new_path2view, 1, path2view.length);
      new_path2view[0] = mrna2genome;
      int acount = mrna.getAnnotationCount();
      for (int i = 0; i < acount; i++) {
        SeqSymmetry annot2mrna = mrna.getAnnotation(i);
        if (annot2mrna != mrna2genome) {
          glyphifyTranscriptAnnots(mrna, annot2mrna, new_path2view, tier, tGlyph);
        }
      }
    }

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      SeqSymmetry[] new_path2view = new SeqSymmetry[path2view.length + 1];
      System.arraycopy(path2view, 0, new_path2view, 1, path2view.length);
      new_path2view[0] = annot2mrna;
      int acount = protein.getAnnotationCount();
      for (int i = 0; i < acount; i++) {
        SeqSymmetry annot2protein = protein.getAnnotation(i);
        if (annot2protein != annot2mrna) {
          glyphifyProteinAnnots(annot2protein, new_path2view, tier);
        }
      }
    }

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      MutableSeqSymmetry annot2genome, BioSeq protein, GlyphI aGlyph, String amino_acid, BioSeq vseq) {
    int cdsCount = annot2genome.getChildCount();
    int prev_amino_end = 0;
    int prev_add = 0;
    for (int j = 0; j < cdsCount; j++) {
      SeqSymmetry cds2genome = annot2genome.getChild(j);
      SeqSpan gSpan = cds2genome.getSpan(vseq);
      GlyphI cglyph = new FillRectGlyph();
      //SeqSpan protSpan = cds2genome.getSpan(protein);
      // coloring based on frame
      colorByFrame(cglyph, gSpan.getMin() + prev_add);
      prev_add += 3 - (gSpan.getLength() % 3);  //Keep a track of no of complete amino acid added.

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        //    eventually will use some sort of flattening method (probably
        //    first set up as part of SeqUtils)
        int count1 = annot2genome.getChildCount();
        for (int i = 0; i < count1; i++) {


            SeqSymmetry child = annot2genome.getChild(i);
            int count2 = child.getChildCount();


            // reach "back" and get actual symmetry (rather than transformed symmetry)
            //   really need some sort of tracking in transform mechanism to associate calculated
            //   symmetries with original symmetries that they map back to...
            SymWithProps original_child = (SymWithProps) annot2protein.getChild(i);


            for (int j = 0; j < count2; j++) {
                SeqSymmetry grandchild = child.getChild(j);
                SeqSpan gSpan = grandchild.getSpan(vseq);
                LabelledRectGlyph cglyph = new LabelledRectGlyph();
        if(i%2 == 0) {
          cglyph.setColor(color);
        }
        else {

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            SeqSpan newspan = new SimpleMutableSeqSpan(span);
            mut.addSpan(newspan);
        }
        int childCount = sym.getChildCount();
        for (int i = 0; i < childCount; i++) {
            SeqSymmetry child = sym.getChild(i);
            MutableSeqSymmetry newchild = new SimpleMutableSeqSymmetry();
            copyToMutable(child, newchild);
            mut.addChild(newchild);
        }
    }

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            Node child = children.item(i);
            String name = child.getNodeName();
            if (child instanceof Element) {
                Element chelem = (Element) child;
                if (name.equalsIgnoreCase("simspan")) {
                    SeqSymmetry spanSym = processSimSpan(query_seq, chelem);
                    ((SymWithProps) spanSym).setProperty(METHODSTR, method);
                    hitSym.addChild(spanSym);
                    SeqSpan spanSpan = spanSym.getSpan(query_seq);
                    if (hitSpan == null) {
                        hitSpan = new SimpleMutableSeqSpan(spanSpan.getMin(), spanSpan.getMax(), query_seq); 
                    } else {
                        SeqUtils.encompass(hitSpan, spanSpan, (MutableSeqSpan) hitSpan);
                    }

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  }


  private static int determinemRNALength(int exoncount, TypeContainerAnnot m2gSym, BioSeq genomic, List exon_insert_list) throws NumberFormatException {
    int mrnalength = 0;
    for (int i = 0; i < exoncount; i++) {
      SeqSymmetry esym = m2gSym.getChild(i);
      SeqSpan gspan = esym.getSpan(genomic);
      mrnalength += gspan.getLength();
    }
    for (int i = 0; i < exon_insert_list.size(); i++) {
      Element iel = (Element) exon_insert_list.get(i);
      int ilength = Integer.parseInt(iel.getAttribute("insert_length"));

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

org.bioviz.protannot.GenomeView

org.bioviz.protannot.Xml2GenometryParser

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