JAL-1807 still testing

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

diff --git a/bin/jalview/analysis/scoremodels/SWScoreModel.js b/bin/jalview/analysis/scoremodels/SWScoreModel.js
index e2e0eef..06ef966 100644 (file)
--- a/bin/jalview/analysis/scoremodels/SWScoreModel.js
+++ b/bin/jalview/analysis/scoremodels/SWScoreModel.js
@@ -1,45 +1,45 @@
-Clazz.declarePackage ("jalview.analysis.scoremodels");
-Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.SWScoreModel", ["jalview.analysis.AlignSeq", "jalview.util.Comparison"], function () {
-c$ = Clazz.declareType (jalview.analysis.scoremodels, "SWScoreModel", null, jalview.api.analysis.ScoreModelI);
-Clazz.overrideMethod (c$, "findDistances", 
-function (seqData) {
-var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray ();
-var noseqs = sequenceString.length;
-var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);
-var max = -1;
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-var as =  new jalview.analysis.AlignSeq (sequenceString[i], sequenceString[j], seqData.isNa () ? "dna" : "pep");
-as.calcScoreMatrix ();
-as.traceAlignment ();
-as.printAlignment (System.out);
-distance[i][j] = as.maxscore;
-if (max < distance[i][j]) {
-max = distance[i][j];
-}}
-}
-for (var i = 0; i < (noseqs - 1); i++) {
-for (var j = i; j < noseqs; j++) {
-distance[i][j] = max - distance[i][j];
-distance[j][i] = distance[i][j];
-}
-}
-return distance;
-}, "jalview.datamodel.AlignmentView");
-Clazz.overrideMethod (c$, "getName", 
-function () {
-return "Smith Waterman Score";
-});
-Clazz.overrideMethod (c$, "isDNA", 
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "isProtein", 
-function () {
-return true;
-});
-Clazz.overrideMethod (c$, "toString", 
-function () {
-return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
-});
-});
+Clazz.declarePackage ("jalview.analysis.scoremodels");\r
+Clazz.load (["jalview.api.analysis.ScoreModelI"], "jalview.analysis.scoremodels.SWScoreModel", ["jalview.analysis.AlignSeq", "jalview.util.Comparison"], function () {\r
+c$ = Clazz.declareType (jalview.analysis.scoremodels, "SWScoreModel", null, jalview.api.analysis.ScoreModelI);\r
+Clazz.overrideMethod (c$, "findDistances", \r
+function (seqData) {\r
+var sequenceString = seqData.getVisibleAlignment (jalview.util.Comparison.GapChars.charAt (0)).getSequencesArray ();\r
+var noseqs = sequenceString.length;\r
+var distance =  Clazz.newFloatArray (noseqs, noseqs, 0);\r
+var max = -1;\r
+for (var i = 0; i < (noseqs - 1); i++) {\r
+for (var j = i; j < noseqs; j++) {\r
+var as =  new jalview.analysis.AlignSeq (sequenceString[i], sequenceString[j], seqData.isNa () ? "dna" : "pep");\r
+as.calcScoreMatrix ();\r
+as.traceAlignment ();\r
+as.printAlignment (System.out);\r
+distance[i][j] = as.maxscore;\r
+if (max < distance[i][j]) {\r
+max = distance[i][j];\r
+}}\r
+}\r
+for (var i = 0; i < (noseqs - 1); i++) {\r
+for (var j = i; j < noseqs; j++) {\r
+distance[i][j] = max - distance[i][j];\r
+distance[j][i] = distance[i][j];\r
+}\r
+}\r
+return distance;\r
+}, "jalview.datamodel.AlignmentView");\r
+Clazz.overrideMethod (c$, "getName", \r
+function () {\r
+return "Smith Waterman Score";\r
+});\r
+Clazz.overrideMethod (c$, "isDNA", \r
+function () {\r
+return true;\r
+});\r
+Clazz.overrideMethod (c$, "isProtein", \r
+function () {\r
+return true;\r
+});\r
+Clazz.overrideMethod (c$, "toString", \r
+function () {\r
+return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";\r
+});\r
+});\r