/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
+ *
* @author gmcarstairs
*
*/
* fast lookup tables holding the index into our count
* arrays of each symbol; index 0 is reserved for gap counting
*/
- private static int[] NUC_INDEX = new int[26];
+ private final static int[] NUC_INDEX = new int[26];
+
+ private final static int[] AA_INDEX = new int[26];
- private static int[] AA_INDEX = new int[26];
static
{
for (int i = 0; i < NUCS.length(); i++)
{
if (intCounts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
{
if (counts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
*
* @return
*/
- public int size() {
+ public int size()
+ {
int size = 0;
if (useIntCounts)
{
{
if (intCounts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = intCounts[i];
j++;
{
if (counts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = counts[i];
j++;