X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fanalysis%2Fscoremodels%2FPIDScoreModel.js;h=09c86e555a39152bc97a82e9a560b722d5f8ca6c;hp=0266c3386cb8da2f84509d1b9e4fe22ee833e51a;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/analysis/scoremodels/PIDScoreModel.js b/site/j2s/jalview/analysis/scoremodels/PIDScoreModel.js
index 0266c33..09c86e5 100644
--- a/site/j2s/jalview/analysis/scoremodels/PIDScoreModel.js
+++ b/site/j2s/jalview/analysis/scoremodels/PIDScoreModel.js
@@ -1,32 +1,32 @@
-Clazz.declarePackage ("jalview.analysis.scoremodels");
-Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PIDScoreModel", ["jalview.util.Comparison"], function () {
-c$ = Clazz.declareType (jalview.analysis.scoremodels, "PIDScoreModel", null, jalview.api.analysis.ScoreModelI);
-Clazz.overrideMethod (c$, "findDistances", 
-function (seqData) {
-var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0));
-var noseqs = sequenceString.length;
-var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-if (j == i) {
-distance[i][i] = 0;
-} else {
-distance[i][j] = 100 - jalview.util.Comparison.PID (sequenceString[i], sequenceString[j]);
-distance[j][i] = distance[i][j];
-}}
-}
-return distance;
-}, "jalview.datamodel.AlignmentView");
-Clazz.overrideMethod (c$, "getName", 
-function () {
-return "PID";
-});
-Clazz.overrideMethod (c$, "isDNA", 
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "isProtein", 
-function () {
-return true;
-});
-});
+Clazz.declarePackage ("jalview.analysis.scoremodels");
+Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PIDScoreModel", ["jalview.util.Comparison"], function () {
+c$ = Clazz.declareType (jalview.analysis.scoremodels, "PIDScoreModel", null, jalview.api.analysis.ScoreModelI);
+Clazz.overrideMethod (c$, "findDistances", 
+function (seqData) {
+var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0));
+var noseqs = sequenceString.length;
+var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);
+for (var i = 0; i < (noseqs - 1); i++) {
+for (var j = i; j < noseqs; j++) {
+if (j == i) {
+distance[i][i] = 0;
+} else {
+distance[i][j] = 100 - jalview.util.Comparison.PID (sequenceString[i], sequenceString[j]);
+distance[j][i] = distance[i][j];
+}}
+}
+return distance;
+}, "jalview.datamodel.AlignmentView");
+Clazz.overrideMethod (c$, "getName", 
+function () {
+return "PID";
+});
+Clazz.overrideMethod (c$, "isDNA", 
+function () {
+return true;
+});
+Clazz.overrideMethod (c$, "isProtein", 
+function () {
+return true;
+});
+});