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

[jalviewjs.git] / site / j2s / jalview / schemes / Consensus.js

diff --git a/site/j2s/jalview/schemes/Consensus.js b/site/j2s/jalview/schemes/Consensus.js
index 39d8ac9..45c3c6a 100644 (file)
--- a/site/j2s/jalview/schemes/Consensus.js
+++ b/site/j2s/jalview/schemes/Consensus.js
@@ -1,45 +1,45 @@
-Clazz.declarePackage ("jalview.schemes");\r
-Clazz.load (null, "jalview.schemes.Consensus", ["jalview.schemes.ResidueProperties"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.mask = null;\r
-this.threshold = 0;\r
-this.maskstr = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.schemes, "Consensus");\r
-Clazz.makeConstructor (c$, \r
-function (mask, threshold) {\r
-this.maskstr = mask;\r
-this.setMask (mask);\r
-this.threshold = threshold;\r
-}, "~S,~N");\r
-Clazz.defineMethod (c$, "setMask", \r
-function (s) {\r
-this.mask = this.setNums (s);\r
-}, "~S");\r
-Clazz.defineMethod (c$, "isConserved", \r
-function (cons2, col, size) {\r
-return this.isConserved (cons2, col, size, true);\r
-}, "~A,~N,~N");\r
-Clazz.defineMethod (c$, "isConserved", \r
-function (cons2, col, size, includeGaps) {\r
-var tot = 0;\r
-if (!includeGaps) {\r
-size -= cons2[col][cons2[col].length - 1];\r
-}for (var i = 0; i < this.mask.length; i++) {\r
-tot += cons2[col][this.mask[i]];\r
-}\r
-if (tot > ((this.threshold * size) / 100)) {\r
-return true;\r
-}return false;\r
-}, "~A,~N,~N,~B");\r
-Clazz.defineMethod (c$, "setNums", \r
-function (s) {\r
-var out =  Clazz.newIntArray (s.length, 0);\r
-var i = 0;\r
-while (i < s.length) {\r
-out[i] = jalview.schemes.ResidueProperties.aaIndex[s.charCodeAt (i)];\r
-i++;\r
-}\r
-return out;\r
-}, "~S");\r
-});\r
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (null, "jalview.schemes.Consensus", ["jalview.schemes.ResidueProperties"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.mask = null;
+this.threshold = 0;
+this.maskstr = null;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "Consensus");
+Clazz.makeConstructor (c$, 
+function (mask, threshold) {
+this.maskstr = mask;
+this.setMask (mask);
+this.threshold = threshold;
+}, "~S,~N");
+Clazz.defineMethod (c$, "setMask", 
+function (s) {
+this.mask = this.setNums (s);
+}, "~S");
+Clazz.defineMethod (c$, "isConserved", 
+function (cons2, col, size) {
+return this.isConserved (cons2, col, size, true);
+}, "~A,~N,~N");
+Clazz.defineMethod (c$, "isConserved", 
+function (cons2, col, size, includeGaps) {
+var tot = 0;
+if (!includeGaps) {
+size -= cons2[col][cons2[col].length - 1];
+}for (var i = 0; i < this.mask.length; i++) {
+tot += cons2[col][this.mask[i]];
+}
+if (tot > ((this.threshold * size) / 100)) {
+return true;
+}return false;
+}, "~A,~N,~N,~B");
+Clazz.defineMethod (c$, "setNums", 
+function (s) {
+var out =  Clazz.newIntArray (s.length, 0);
+var i = 0;
+while (i < s.length) {
+out[i] = jalview.schemes.ResidueProperties.aaIndex[s.charCodeAt (i)];
+i++;
+}
+return out;
+}, "~S");
+});