JAL-1807 still testing

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

diff --git a/bin/jalview/analysis/CodingUtils.js b/bin/jalview/analysis/CodingUtils.js
index 69abb90..08fa0ce 100644 (file)
--- 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$,
-"CODON_ENCODING_BITSHIFT", 2);
+Clazz.declarePackage ("jalview.analysis");\r
+c$ = 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