- // int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
- Profile profile = (Profile) hci.get(AAFrequency.PROFILE);
- if (profile != null && includeAllConsSymbols)
- {
- int sequenceCount = profile.height;// profile[1][0];
- int nonGappedCount = profile.nonGapped;// [1][1];
- int normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount
- : sequenceCount;
- mouseOver.setLength(0);
- // TODO do this sort once only in calculate()?
- // char[][] ca = new char[profile[0].length][];
- // /int length = profile[0].length;
- int length = profile.profile.size();
- char[] ca = new char[length];
- // float[] vl = new float[length];
- int[] vl = new int[length];
- for (int c = 0; c < ca.length; c++)
- {
- int theChar = profile.profile.keyAt(c);
- ca[c] = (char) theChar;// c;
- // ca[c] = new char[]
- // { (char) c };
- vl[c] = profile.profile.get(theChar);// profile[0][c];
- }
-
- /*
- * sort characters into ascending order of their counts
- */
- QuickSort.sort(vl, ca);
+ consensus.annotations[i] = new Annotation(modalResidue, description,
+ ' ', value);
+ }
+ // long elapsed = System.currentTimeMillis() - now;
+ // System.out.println(-elapsed);
+ }