+ int theChar = symbols[i];
+ int charCount = values[i];
+
+ rtnval[nextArrayPos++] = theChar;
+ final int percentage = (charCount * 100) / divisor;
+ rtnval[nextArrayPos++] = percentage;
+ totalPercentage += percentage;
+ }
+ rtnval[0] = symbols.length;
+ rtnval[1] = totalPercentage;
+ int[] result = new int[rtnval.length + 1];
+ result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+
+ return result;
+ }
+
+ /**
+ * Extract a sorted extract of cDNA codon profile data. The returned array
+ * contains
+ *
+ * <pre>
+ * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value, where the character values encode codon triplets
+ * </pre>
+ *
+ * @param hashtable
+ * @return
+ */
+ public static int[] extractCdnaProfile(Hashtable hashtable,
+ boolean ignoreGaps)
+ {
+ // this holds #seqs, #ungapped, and then codon count, indexed by encoded
+ // codon triplet
+ int[] codonCounts = (int[]) hashtable.get(PROFILE);
+ int[] sortedCounts = new int[codonCounts.length - 2];
+ System.arraycopy(codonCounts, 2, sortedCounts, 0,
+ codonCounts.length - 2);
+
+ int[] result = new int[3 + 2 * sortedCounts.length];
+ // first value is just the type of profile data
+ result[0] = AlignmentAnnotation.CDNA_PROFILE;
+
+ char[] codons = new char[sortedCounts.length];
+ for (int i = 0; i < codons.length; i++)
+ {
+ codons[i] = (char) i;
+ }
+ QuickSort.sort(sortedCounts, codons);
+ int totalPercentage = 0;
+ int distinctValuesCount = 0;
+ int j = 3;
+ int divisor = ignoreGaps ? codonCounts[1] : codonCounts[0];
+ for (int i = codons.length - 1; i >= 0; i--)
+ {
+ final int codonCount = sortedCounts[i];
+ if (codonCount == 0)