*/
private void calcSeqNum(int i, ScoreMatrix sm)
{
- int gapIndex = sm.getMatrixIndex(' ');
+ int gapIndex = sm.getGapIndex();
int sSize = sequences.length;
if ((i > -1) && (i < sSize))
calcSeqNum(i, sm);
}
- int gapIndex = sm.getMatrixIndex(' ');
+ int gapIndex = sm.getGapIndex();
if ((cons2 == null) || seqNumsChanged)
{
double max = -Double.MAX_VALUE;
ScoreMatrix blosum62 = ScoreModels.getInstance().getBlosum62();
float[][] blosumScores = blosum62.getMatrix();
- int gapIndex = blosum62.getMatrixIndex(' ');
// Loop over columns // JBPNote Profiling info
// long ts = System.currentTimeMillis();
// todo ? remove '*' (unused?) from score matrix and
// use getSize() here instead of getSize() - 1 ??
final int symbolCount = blosum62.getSize() - 1; // 24;
+ int gapIndex = blosum62.getGapIndex();
for (j = startRes; j <= endRes; j++)
{