public AlignSeq(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- seqInit(s1, string1.toUpperCase(Locale.ROOT), s2, string2.toUpperCase(Locale.ROOT), type);
+ seqInit(s1, string1.toUpperCase(Locale.ROOT), s2,
+ string2.toUpperCase(Locale.ROOT), type);
}
/**
for (int j = 1; j < m; j++)
{
// What should these values be? 0 maybe
- E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST, E[0][j - 1] - GAP_EXTEND_COST);
+ E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST,
+ E[0][j - 1] - GAP_EXTEND_COST);
F[0][j] = -GAP_EXTEND_COST;
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
s2str.charAt(j));
- score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST, -GAP_EXTEND_COST);
+ score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST,
+ -GAP_EXTEND_COST);
traceback[0][j] = 1;
}
for (int i = 1; i < n; i++)
{
E[i][0] = -GAP_OPEN_COST;
- F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST, F[i - 1][0] - GAP_EXTEND_COST);
+ F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST,
+ F[i - 1][0] - GAP_EXTEND_COST);
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(0));
{
for (int j = 1; j < m; j++)
{
- E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST, E[i][j - 1] - GAP_EXTEND_COST);
- F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST, F[i - 1][j] - GAP_EXTEND_COST);
+ E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST,
+ E[i][j - 1] - GAP_EXTEND_COST);
+ F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST,
+ F[i - 1][j] - GAP_EXTEND_COST);
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(j));