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

[jalviewjs.git] / site / j2s / jalview / schemes / Blosum62ColourScheme.js

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