+ // System.out.println("Quality " + s);
+ qualityRange[0] = new Double(0);
+ qualityRange[1] = new Double(newmax);
+ }
+
+ /**
+ * complete the given consensus and quuality annotation rows.
+ * Note: currently this method will enlarge the given annotation row if it is too small, otherwise will leave its length unchanged.
+ * @param conservation conservation annotation row
+ * @param quality2 (optional - may be null)
+ * @param istart first column for conservation
+ * @param alWidth extent of conservation
+ */
+ public void completeAnnotations(AlignmentAnnotation conservation,
+ AlignmentAnnotation quality2, int istart, int alWidth)
+ {
+ char[] sequence = getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and
+ // Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ if (conservation.annotations !=null && conservation.annotations.length<alWidth)
+ { conservation.annotations = new Annotation[alWidth]; }
+
+
+ if (quality2 != null)
+ {
+ quality2.graphMax = qualityRange[1].floatValue();
+ if (quality2.annotations!=null && quality2.annotations.length<alWidth) {
+ quality2.annotations = new Annotation[alWidth];
+ }
+ qmin = qualityRange[0].floatValue();
+ qmax = qualityRange[1].floatValue();
+ }