Examples of com.affymetrix.genoviz.glyph.FillRectGlyph

             *    and y = FLOAT_MIN/2 and height = FLOAT_MAX (???)
             */
            int segStart = unique_transitions[i];
            int segEnd = unique_transitions[i + 1];


            GlyphI newgl = new FillRectGlyph();
            newgl.setColor(glyph_color);


      int hitCount = determineGlyphHits(glyphsToSummarize, segEnd, segStart);


            /**
             * reset y = 0 and height = # of hits
             */
            //      newgl.setCoords(segStart, 0, segEnd - segStart, hitCount);
            // just hardwiring height multiple till get normalization code implemented
            //      newgl.setCoords(segStart, 0, segEnd - segStart, hitCount*10);
            // if want to filter out regions with no hits, uncomment out conditional
            newgl.setCoords(segStart, -hitCount * scale_factor, segEnd - segStart, hitCount * scale_factor);
      summaryGlyph.addChild(newgl);
        }


        /**
         * 5) normalize height somehow...

    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.
      cglyph.setCoords(gSpan.getMin(), 0, gSpan.getLength(), 20);
      aGlyph.addChild(cglyph);
      if (amino_acid != null) {
        SequenceGlyph sg = new ColoredResiduesGlyph(false);
        int start = prev_amino_end;
        int end = start + gSpan.getLength();
        String sub_amino_acid = amino_acid.substring(start, end);
        prev_amino_end += gSpan.getLength();
        sg.setResidues(sub_amino_acid);
        sg.setCoords(gSpan.getMin(), 0, gSpan.getLength(), 20);
        sg.setForegroundColor(col_amino_acid);
        sg.setBackgroundColor(cglyph.getBackgroundColor());
        aGlyph.addChild(sg);
      }
    }
  }

Examples of com.affymetrix.genoviz.glyph.FillRectGlyph

Related Classes of com.affymetrix.genoviz.glyph.FillRectGlyph