X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fanalysis%2FCodingUtils.js;h=69abb90c89317dc013fc22435fb212e35db523cd;hp=08fa0ce217ccb21f0abf29cc8daa8fb575a46794;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/analysis/CodingUtils.js b/bin/jalview/analysis/CodingUtils.js
index 08fa0ce..69abb90 100644
--- a/bin/jalview/analysis/CodingUtils.js
+++ b/bin/jalview/analysis/CodingUtils.js
@@ -1,64 +1,64 @@
-Clazz.declarePackage ("jalview.analysis");
-c$ = Clazz.declareType (jalview.analysis, "CodingUtils");
-c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", 
-function (codon) {
-if (codon == null) {
-return -1;
-}return jalview.analysis.CodingUtils.encodeCodon (codon[2]) + (jalview.analysis.CodingUtils.encodeCodon (codon[1]) << 2) + (jalview.analysis.CodingUtils.encodeCodon (codon[0]) << (4));
-}, "~A");
-c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", 
-function (c) {
-var result = -2147483648;
-switch (c) {
-case 'A':
-case 'a':
-result = 0;
-break;
-case 'C':
-case 'c':
-result = 1;
-break;
-case 'G':
-case 'g':
-result = 2;
-break;
-case 'T':
-case 't':
-case 'U':
-case 'u':
-result = 3;
-break;
-}
-return result;
-}, "~S");
-c$.decodeCodon = Clazz.defineMethod (c$, "decodeCodon", 
-function (encoded) {
-var result =  Clazz.newCharArray (3, '\0');
-result[2] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3);
-encoded = encoded >>> 2;
-result[1] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3);
-encoded = encoded >>> 2;
-result[0] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3);
-return result;
-}, "~N");
-c$.decodeNucleotide = Clazz.defineMethod (c$, "decodeNucleotide", 
-function (i) {
-var result = '0';
-switch (i) {
-case 0:
-result = 'A';
-break;
-case 1:
-result = 'C';
-break;
-case 2:
-result = 'G';
-break;
-case 3:
-result = 'T';
-break;
-}
-return result;
-}, "~N");
-Clazz.defineStatics (c$,
-"CODON_ENCODING_BITSHIFT", 2);
+Clazz.declarePackage ("jalview.analysis");
+c$ = Clazz.declareType (jalview.analysis, "CodingUtils");
+c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", 
+function (codon) {
+if (codon == null) {
+return -1;
+}return jalview.analysis.CodingUtils.encodeCodon (codon[2]) + (jalview.analysis.CodingUtils.encodeCodon (codon[1]) << 2) + (jalview.analysis.CodingUtils.encodeCodon (codon[0]) << (4));
+}, "~A");
+c$.encodeCodon = Clazz.defineMethod (c$, "encodeCodon", 
+function (c) {
+var result = -2147483648;
+switch (c) {
+case 'A':
+case 'a':
+result = 0;
+break;
+case 'C':
+case 'c':
+result = 1;
+break;
+case 'G':
+case 'g':
+result = 2;
+break;
+case 'T':
+case 't':
+case 'U':
+case 'u':
+result = 3;
+break;
+}
+return result;
+}, "~S");
+c$.decodeCodon = Clazz.defineMethod (c$, "decodeCodon", 
+function (encoded) {
+var result =  Clazz.newCharArray (3, '\0');
+result[2] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3);
+encoded = encoded >>> 2;
+result[1] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3);
+encoded = encoded >>> 2;
+result[0] = jalview.analysis.CodingUtils.decodeNucleotide (encoded & 3);
+return result;
+}, "~N");
+c$.decodeNucleotide = Clazz.defineMethod (c$, "decodeNucleotide", 
+function (i) {
+var result = '0';
+switch (i) {
+case 0:
+result = 'A';
+break;
+case 1:
+result = 'C';
+break;
+case 2:
+result = 'G';
+break;
+case 3:
+result = 'T';
+break;
+}
+return result;
+}, "~N");
+Clazz.defineStatics (c$,
+"CODON_ENCODING_BITSHIFT", 2);