JAL-1807 test

[jalviewjs.git] / bin / jalview / analysis / CodingUtils.js

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