Merge branch 'master' of https://source.jalview.org/git/jalviewjs.git

[jalviewjs.git] / site / j2s / jalview / analysis / scoremodels / PIDScoreModel.js

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