int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
: ResidueProperties.maxProteinIndex;
- dbinary = new double[getSequence().length * nores];
+ dbinary = new double[getLength() * nores];
return nores;
}
{
int nores = initMatrixGetNoRes();
final int[] sindex = getSymbolmatrix();
- for (int i = 0; i < getSequence().length; i++)
+ for (int i = 0; i < getLength(); i++)
{
int aanum = nores - 1;
{
int nores = initMatrixGetNoRes();
- for (int i = 0, iSize = getSequence().length; i < iSize; i++)
+ for (int i = 0, iSize = getLength(); i < iSize; i++)
{
int aanum = nores - 1;
for (int i = 0; i < binary.length; i++)
{
- out += (new Integer(binary[i])).toString();
+ out += (Integer.valueOf(binary[i])).toString();
if (i < (binary.length - 1))
{