1 Clazz.declarePackage ("jalview.analysis.scoremodels");
2 Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PIDScoreModel", ["jalview.util.Comparison"], function () {
3 c$ = Clazz.declareType (jalview.analysis.scoremodels, "PIDScoreModel", null, jalview.api.analysis.ScoreModelI);
4 Clazz.overrideMethod (c$, "findDistances",
6 var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0));
7 var noseqs = sequenceString.length;
8 var distance = Clazz.newFloatArray (noseqs, noseqs, 0);
9 for (var i = 0; i < (noseqs - 1); i++) {
10 for (var j = i; j < noseqs; j++) {
14 distance[i][j] = 100 - jalview.util.Comparison.PID (sequenceString[i], sequenceString[j]);
15 distance[j][i] = distance[i][j];
19 }, "jalview.datamodel.AlignmentView");
20 Clazz.overrideMethod (c$, "getName",
24 Clazz.overrideMethod (c$, "isDNA",
28 Clazz.overrideMethod (c$, "isProtein",