JAL-1807 still testing

[jalviewjs.git] / bin / jalview / analysis / scoremodels / PairwiseSeqScoreModel.js

diff --git a/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js b/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js
index 4c1456f..6cfe67a 100644 (file)
--- a/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js
+++ b/bin/jalview/analysis/scoremodels/PairwiseSeqScoreModel.js
@@ -1,39 +1,39 @@
-Clazz.declarePackage ("jalview.analysis.scoremodels");
-Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PairwiseSeqScoreModel", ["jalview.util.Comparison"], function () {
-c$ = Clazz.declareType (jalview.analysis.scoremodels, "PairwiseSeqScoreModel", null, jalview.api.analysis.ScoreModelI);
-Clazz.overrideMethod (c$, "findDistances", 
-function (seqData) {
-var sequenceString = seqData.getSequenceStrings (jalview.util.Comparison.GapChars.charAt (0));
-var noseqs = sequenceString.length;
-var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);
-var maxscore = 0;
-var end = sequenceString[0].length;
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-var score = 0;
-for (var k = 0; k < end; k++) {
-try {
-score += this.getPairwiseScore (sequenceString[i].charAt (k), sequenceString[j].charAt (k));
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-System.err.println ("err creating " + this.getName () + " tree");
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-}
-distance[i][j] = score;
-if (score > maxscore) {
-maxscore = score;
-}}
-}
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-distance[i][j] = maxscore - distance[i][j];
-distance[j][i] = distance[i][j];
-}
-}
-return distance;
-}, "jalview.datamodel.AlignmentView");
-});
+Clazz.declarePackage ("jalview.analysis.scoremodels");\r
+Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.PairwiseSeqScoreModel", ["jalview.util.Comparison"], function () {\r
+c$ = Clazz.declareType (jalview.analysis.scoremodels, "PairwiseSeqScoreModel", 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
+var maxscore = 0;\r
+var end = sequenceString[0].length;\r
+for (var i = 0; i < (noseqs - 1); i++) {\r
+for (var j = i; j < noseqs; j++) {\r
+var score = 0;\r
+for (var k = 0; k < end; k++) {\r
+try {\r
+score += this.getPairwiseScore (sequenceString[i].charAt (k), sequenceString[j].charAt (k));\r
+} catch (ex) {\r
+if (Clazz.exceptionOf (ex, Exception)) {\r
+System.err.println ("err creating " + this.getName () + " tree");\r
+ex.printStackTrace ();\r
+} else {\r
+throw ex;\r
+}\r
+}\r
+}\r
+distance[i][j] = score;\r
+if (score > maxscore) {\r
+maxscore = score;\r
+}}\r
+}\r
+for (var i = 0; i < (noseqs - 1); i++) {\r
+for (var j = i; j < noseqs; j++) {\r
+distance[i][j] = maxscore - distance[i][j];\r
+distance[j][i] = distance[i][j];\r
+}\r
+}\r
+return distance;\r
+}, "jalview.datamodel.AlignmentView");\r
+});\r