1 package jalview.analysis.scoremodels;
3 import jalview.api.analysis.ScoreModelI;
4 import jalview.datamodel.AlignmentView;
5 import jalview.util.Comparison;
7 public class PIDScoreModel implements ScoreModelI
11 public float[][] findDistances(AlignmentView seqData)
13 String[] sequenceString = seqData
14 .getSequenceStrings(Comparison.GapChars.charAt(0));
15 int noseqs = sequenceString.length;
16 float[][] distance = new float[noseqs][noseqs];
17 for (int i = 0; i < (noseqs - 1); i++)
19 for (int j = i; j < noseqs; j++)
27 distance[i][j] = 100 - Comparison.PID(sequenceString[i],
30 distance[j][i] = distance[i][j];
38 public String getName()
44 public boolean isDNA()
50 public boolean isProtein()