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