1 package jalview.analysis.scoremodels;
3 import jalview.api.analysis.ScoreModelI;
4 import jalview.datamodel.AlignmentView;
5 import jalview.schemes.ScoreMatrix;
6 import jalview.util.Comparison;
8 public abstract class PairwiseSeqScoreModel implements ScoreModelI
10 abstract public int getPairwiseScore(char c, char d);
12 public float[][] findDistances(AlignmentView seqData)
14 String[] sequenceString = seqData
15 .getSequenceStrings(Comparison.GapChars.charAt(0));
16 int noseqs = sequenceString.length;
17 float[][] distance = new float[noseqs][noseqs];
20 int end = sequenceString[0].length();
21 for (int i = 0; i < (noseqs - 1); i++)
23 for (int j = i; j < noseqs; j++)
27 for (int k = 0; k < end; k++)
31 score += getPairwiseScore(sequenceString[i].charAt(k),
32 sequenceString[j].charAt(k));
33 } catch (Exception ex)
35 System.err.println("err creating " + getName() + " tree");
40 distance[i][j] = (float) score;
49 for (int i = 0; i < (noseqs - 1); i++)
51 for (int j = i; j < noseqs; j++)
53 distance[i][j] = (float) maxscore - distance[i][j];
54 distance[j][i] = distance[i][j];
60 abstract public int[][] getMatrix();