X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fschemes%2FConsensus.js;h=45c3c6a22186ca9439084398c9b8177b5a84f9f0;hp=39d8ac95d83d3ae5b03af3307ede90434da191bd;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/schemes/Consensus.js b/bin/jalview/schemes/Consensus.js
index 39d8ac9..45c3c6a 100644
--- a/bin/jalview/schemes/Consensus.js
+++ b/bin/jalview/schemes/Consensus.js
@@ -1,45 +1,45 @@
-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$, "setNums", 
-function (s) {
-var out =  Clazz.newIntArray (s.length, 0);
-var i = 0;
-while (i < s.length) {
-out[i] = jalview.schemes.ResidueProperties.aaIndex[s.charCodeAt (i)];
-i++;
-}
-return out;
-}, "~S");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (null, "jalview.schemes.Consensus", ["jalview.schemes.ResidueProperties"], function () {
+c$ = 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");
+});