X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FNucleotideColourScheme.js;h=6594167936244f9c802325b7c2555ccaf9bd8c9e;hp=1345bc688b010beb92dc757aaee67674dd09c049;hb=36d803e4a1f98728e91e80de5fa0b95e0cadb0d4;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/site/j2s/jalview/schemes/NucleotideColourScheme.js b/site/j2s/jalview/schemes/NucleotideColourScheme.js
index 1345bc6..6594167 100644
--- a/site/j2s/jalview/schemes/NucleotideColourScheme.js
+++ b/site/j2s/jalview/schemes/NucleotideColourScheme.js
@@ -1,31 +1,31 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.NucleotideColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () {
-c$ = Clazz.declareType (jalview.schemes, "NucleotideColourScheme", jalview.schemes.ResidueColourScheme);
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.schemes.NucleotideColourScheme, [jalview.schemes.ResidueProperties.nucleotideIndex, jalview.schemes.ResidueProperties.nucleotide, 0]);
-});
-Clazz.defineMethod (c$, "findColour", 
-function (c) {
-return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]];
-}, "~S");
-Clazz.defineMethod (c$, "findColour", 
-function (c, j, seq) {
-var currentColour;
-if ((this.threshold == 0) || this.aboveThreshold (c, j)) {
-try {
-currentColour = this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]];
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-return java.awt.Color.white;
-} else {
-throw ex;
-}
-}
-} else {
-return java.awt.Color.white;
-}if (this.conservationColouring) {
-currentColour = this.applyConservation (currentColour, j);
-}return currentColour;
-}, "~S,~N,jalview.datamodel.SequenceI");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.NucleotideColourScheme", ["jalview.schemes.ResidueProperties", "java.awt.Color"], function () {
+c$ = Clazz.declareType (jalview.schemes, "NucleotideColourScheme", jalview.schemes.ResidueColourScheme);
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.schemes.NucleotideColourScheme, [jalview.schemes.ResidueProperties.nucleotideIndex, jalview.schemes.ResidueProperties.nucleotide, 0]);
+});
+Clazz.overrideMethod (c$, "findColour", 
+function (c) {
+return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]];
+}, "~S");
+Clazz.overrideMethod (c$, "findColourSeq", 
+function (c, j, seq) {
+var currentColour;
+if ((this.threshold == 0) || this.aboveThreshold (c, j)) {
+try {
+currentColour = this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[c.charCodeAt (0)]];
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+return java.awt.Color.white;
+} else {
+throw ex;
+}
+}
+} else {
+return java.awt.Color.white;
+}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+});