public abstract class PairwiseSeqScoreModel implements ScoreModelI
{
- abstract public int getPairwiseScore(char c, char d);
+ abstract public float getPairwiseScore(char c, char d);
+ @Override
public float[][] findDistances(AlignmentView seqData)
{
String[] sequenceString = seqData
int noseqs = sequenceString.length;
float[][] distance = new float[noseqs][noseqs];
- int maxscore = 0;
+ float maxscore = 0;
int end = sequenceString[0].length();
for (int i = 0; i < (noseqs - 1); i++)
{
for (int j = i; j < noseqs; j++)
{
- int score = 0;
+ float score = 0;
for (int k = 0; k < end; k++)
{
}
}
- distance[i][j] = (float) score;
+ distance[i][j] = score;
if (score > maxscore)
{
{
for (int j = i; j < noseqs; j++)
{
- distance[i][j] = (float) maxscore - distance[i][j];
+ distance[i][j] = maxscore - distance[i][j];
distance[j][i] = distance[i][j];
}
}
return distance;
}
- abstract public int[][] getMatrix();
+ abstract public float[][] getMatrix();
}