X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FBlosum62ColourScheme.js;h=87c4a514c31ccb879b09d5d63810c0b0f7e1ebb5;hp=3268bc77670368e75217062ae75bce6451dcafde;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/schemes/Blosum62ColourScheme.js b/site/j2s/jalview/schemes/Blosum62ColourScheme.js
index 3268bc7..87c4a51 100644
--- a/site/j2s/jalview/schemes/Blosum62ColourScheme.js
+++ b/site/j2s/jalview/schemes/Blosum62ColourScheme.js
@@ -1,37 +1,37 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.Blosum62ColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () {
-c$ = Clazz.declareType (jalview.schemes, "Blosum62ColourScheme", jalview.schemes.ResidueColourScheme);
-Clazz.defineMethod (c$, "findColour", 
-function (res, j, seq) {
-if ('a' <= res && res <= 'z') {
-res = String.fromCharCode (res.charCodeAt (0) - (32));
-}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null || (this.threshold != 0 && !this.aboveThreshold (res, j))) {
-return java.awt.Color.white;
-}var currentColour;
-if (!jalview.util.Comparison.isGap (res)) {
-var max = this.consensus[j].get ("R");
-if (max.indexOf (res) > -1) {
-currentColour =  new java.awt.Color (154, 154, 255);
-} else {
-var c = 0;
-var max_aa = 0;
-var n = max.length;
-do {
-c += jalview.schemes.ResidueProperties.getBLOSUM62 (max.charAt (max_aa), res);
-} while (++max_aa < n);
-if (c > 0) {
-currentColour =  new java.awt.Color (204, 204, 255);
-} else {
-currentColour = java.awt.Color.white;
-}}if (this.conservationColouring) {
-currentColour = this.applyConservation (currentColour, j);
-}} else {
-return java.awt.Color.white;
-}return currentColour;
-}, "~S,~N,jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "applyTo", 
-function (sg, hiddenRepSequences) {
-var newcs = Clazz.superCall (this, jalview.schemes.Blosum62ColourScheme, "applyTo", [sg, hiddenRepSequences]);
-return newcs;
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.Blosum62ColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () {
+c$ = Clazz.declareType (jalview.schemes, "Blosum62ColourScheme", jalview.schemes.ResidueColourScheme);
+Clazz.defineMethod (c$, "findColour", 
+function (res, j, seq) {
+if ('a' <= res && res <= 'z') {
+res = String.fromCharCode (res.charCodeAt (0) - (32));
+}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null || (this.threshold != 0 && !this.aboveThreshold (res, j))) {
+return java.awt.Color.white;
+}var currentColour;
+if (!jalview.util.Comparison.isGap (res)) {
+var max = this.consensus[j].get ("R");
+if (max.indexOf (res) > -1) {
+currentColour =  new java.awt.Color (154, 154, 255);
+} else {
+var c = 0;
+var max_aa = 0;
+var n = max.length;
+do {
+c += jalview.schemes.ResidueProperties.getBLOSUM62 (max.charAt (max_aa), res);
+} while (++max_aa < n);
+if (c > 0) {
+currentColour =  new java.awt.Color (204, 204, 255);
+} else {
+currentColour = java.awt.Color.white;
+}}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}} else {
+return java.awt.Color.white;
+}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "applyTo", 
+function (sg, hiddenRepSequences) {
+var newcs = Clazz.superCall (this, jalview.schemes.Blosum62ColourScheme, "applyTo", [sg, hiddenRepSequences]);
+return newcs;
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+});