1 Clazz.declarePackage ("jalview.analysis.scoremodels");
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2 Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PairwiseSeqScoreModel", ["jalview.util.Comparison"], function () {
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3 c$ = Clazz.declareType (jalview.analysis.scoremodels, "PairwiseSeqScoreModel", 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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10 var end = sequenceString[0].length;
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11 for (var i = 0; i < (noseqs - 1); i++) {
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12 for (var j = i; j < noseqs; j++) {
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14 for (var k = 0; k < end; k++) {
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16 score += this.getPairwiseScore (sequenceString[i].charAt (k), sequenceString[j].charAt (k));
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18 if (Clazz.exceptionOf (ex, Exception)) {
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19 System.err.println ("err creating " + this.getName () + " tree");
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20 ex.printStackTrace ();
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26 distance[i][j] = score;
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27 if (score > maxscore) {
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31 for (var i = 0; i < (noseqs - 1); i++) {
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32 for (var j = i; j < noseqs; j++) {
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33 distance[i][j] = maxscore - distance[i][j];
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34 distance[j][i] = distance[i][j];
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38 }, "jalview.datamodel.AlignmentView");
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