X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fdatamodel%2FBinarySequence.js;h=e6cf2e570d22f168866d2b002552022ed5715b70;hp=8677473076b156ca6f7c28821235b362debdbafd;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/datamodel/BinarySequence.js b/site/j2s/jalview/datamodel/BinarySequence.js
index 8677473..e6cf2e5 100644
--- a/site/j2s/jalview/datamodel/BinarySequence.js
+++ b/site/j2s/jalview/datamodel/BinarySequence.js
@@ -1,99 +1,99 @@
-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (["jalview.datamodel.Sequence", "java.lang.Exception"], "jalview.datamodel.BinarySequence", ["jalview.schemes.ResidueProperties"], function () {
-c$ = Clazz.decorateAsClass (function () {
-if (!Clazz.isClassDefined ("jalview.datamodel.BinarySequence.InvalidSequenceTypeException")) {
-jalview.datamodel.BinarySequence.$BinarySequence$InvalidSequenceTypeException$ ();
-}
-this.binary = null;
-this.dbinary = null;
-this.isNa = false;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "BinarySequence", jalview.datamodel.Sequence);
-Clazz.makeConstructor (c$, 
-function (s, isNa) {
-Clazz.superConstructor (this, jalview.datamodel.BinarySequence, ["", s, 0, s.length]);
-this.isNa = isNa;
-}, "~S,~B");
-Clazz.defineMethod (c$, "initMatrixGetNoRes", 
- function () {
-var nores = (this.isNa) ? 10 : 23;
-this.dbinary =  Clazz.newDoubleArray (this.getSequence ().length * nores, 0);
-for (var i = 0; i < this.dbinary.length; i++) {
-this.dbinary[i] = 0.0;
-}
-return nores;
-});
-Clazz.defineMethod (c$, "getSymbolmatrix", 
- function () {
-return (this.isNa) ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex;
-});
-Clazz.defineMethod (c$, "encode", 
-function () {
-var nores = this.initMatrixGetNoRes ();
-var sindex = this.getSymbolmatrix ();
-for (var i = 0; i < this.getSequence ().length; i++) {
-var aanum = nores - 1;
-try {
-aanum = sindex[this.getCharAt (i).charCodeAt (0)];
-} catch (e) {
-if (Clazz.exceptionOf (e, NullPointerException)) {
-aanum = nores - 1;
-} else {
-throw e;
-}
-}
-if (aanum >= nores) {
-aanum = nores - 1;
-}this.dbinary[(i * nores) + aanum] = 1.0;
-}
-});
-Clazz.defineMethod (c$, "matrixEncode", 
-function (matrix) {
-if (this.isNa != matrix.isDNA ()) {
-throw Clazz.innerTypeInstance (jalview.datamodel.BinarySequence.InvalidSequenceTypeException, this, null, "matrix " + matrix.getClass ().getCanonicalName () + " is not a valid matrix for " + (this.isNa ? "nucleotide" : "protein") + "sequences");
-}this.matrixEncode (matrix.isDNA () ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex, matrix.getMatrix ());
-}, "jalview.schemes.ScoreMatrix");
-Clazz.defineMethod (c$, "matrixEncode", 
- function (aaIndex, matrix) {
-var nores = this.initMatrixGetNoRes ();
-for (var i = 0, iSize = this.getSequence ().length; i < iSize; i++) {
-var aanum = nores - 1;
-try {
-aanum = aaIndex[this.getCharAt (i).charCodeAt (0)];
-} catch (e) {
-if (Clazz.exceptionOf (e, NullPointerException)) {
-aanum = nores - 1;
-} else {
-throw e;
-}
-}
-if (aanum >= nores) {
-aanum = nores - 1;
-}for (var j = 0; j < nores; j++) {
-this.dbinary[(i * nores) + j] = matrix[aanum][j];
-}
-}
-}, "~A,~A");
-Clazz.defineMethod (c$, "toBinaryString", 
-function () {
-var out = "";
-for (var i = 0; i < this.binary.length; i++) {
-out += ( new Integer (this.binary[i])).toString ();
-if (i < (this.binary.length - 1)) {
-out += " ";
-}}
-return out;
-});
-Clazz.defineMethod (c$, "getDBinary", 
-function () {
-return this.dbinary;
-});
-c$.$BinarySequence$InvalidSequenceTypeException$ = function () {
-Clazz.pu$h(self.c$);
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel.BinarySequence, "InvalidSequenceTypeException", Exception);
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.datamodel");
+Clazz.load (["jalview.datamodel.Sequence", "java.lang.Exception"], "jalview.datamodel.BinarySequence", ["jalview.schemes.ResidueProperties"], function () {
+c$ = Clazz.decorateAsClass (function () {
+if (!Clazz.isClassDefined ("jalview.datamodel.BinarySequence.InvalidSequenceTypeException")) {
+jalview.datamodel.BinarySequence.$BinarySequence$InvalidSequenceTypeException$ ();
+}
+this.binary = null;
+this.dbinary = null;
+this.isNa = false;
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel, "BinarySequence", jalview.datamodel.Sequence);
+Clazz.makeConstructor (c$, 
+function (s, isNa) {
+Clazz.superConstructor (this, jalview.datamodel.BinarySequence, ["", s, 0, s.length]);
+this.isNa = isNa;
+}, "~S,~B");
+Clazz.defineMethod (c$, "initMatrixGetNoRes", 
+ function () {
+var nores = (this.isNa) ? 10 : 23;
+this.dbinary =  Clazz.newDoubleArray (this.getSequence ().length * nores, 0);
+for (var i = 0; i < this.dbinary.length; i++) {
+this.dbinary[i] = 0.0;
+}
+return nores;
+});
+Clazz.defineMethod (c$, "getSymbolmatrix", 
+ function () {
+return (this.isNa) ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex;
+});
+Clazz.defineMethod (c$, "encode", 
+function () {
+var nores = this.initMatrixGetNoRes ();
+var sindex = this.getSymbolmatrix ();
+for (var i = 0; i < this.getSequence ().length; i++) {
+var aanum = nores - 1;
+try {
+aanum = sindex[this.getCharAt (i).charCodeAt (0)];
+} catch (e) {
+if (Clazz.exceptionOf (e, NullPointerException)) {
+aanum = nores - 1;
+} else {
+throw e;
+}
+}
+if (aanum >= nores) {
+aanum = nores - 1;
+}this.dbinary[(i * nores) + aanum] = 1.0;
+}
+});
+Clazz.defineMethod (c$, "matrixEncode", 
+function (matrix) {
+if (this.isNa != matrix.isDNA ()) {
+throw Clazz.innerTypeInstance (jalview.datamodel.BinarySequence.InvalidSequenceTypeException, this, null, "matrix " + matrix.getClass ().getCanonicalName () + " is not a valid matrix for " + (this.isNa ? "nucleotide" : "protein") + "sequences");
+}this.matrixEncode (matrix.isDNA () ? jalview.schemes.ResidueProperties.nucleotideIndex : jalview.schemes.ResidueProperties.aaIndex, matrix.getMatrix ());
+}, "jalview.schemes.ScoreMatrix");
+Clazz.defineMethod (c$, "matrixEncode", 
+ function (aaIndex, matrix) {
+var nores = this.initMatrixGetNoRes ();
+for (var i = 0, iSize = this.getSequence ().length; i < iSize; i++) {
+var aanum = nores - 1;
+try {
+aanum = aaIndex[this.getCharAt (i).charCodeAt (0)];
+} catch (e) {
+if (Clazz.exceptionOf (e, NullPointerException)) {
+aanum = nores - 1;
+} else {
+throw e;
+}
+}
+if (aanum >= nores) {
+aanum = nores - 1;
+}for (var j = 0; j < nores; j++) {
+this.dbinary[(i * nores) + j] = matrix[aanum][j];
+}
+}
+}, "~A,~A");
+Clazz.defineMethod (c$, "toBinaryString", 
+function () {
+var out = "";
+for (var i = 0; i < this.binary.length; i++) {
+out += ( new Integer (this.binary[i])).toString ();
+if (i < (this.binary.length - 1)) {
+out += " ";
+}}
+return out;
+});
+Clazz.defineMethod (c$, "getDBinary", 
+function () {
+return this.dbinary;
+});
+c$.$BinarySequence$InvalidSequenceTypeException$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+Clazz.instantialize (this, arguments);
+}, jalview.datamodel.BinarySequence, "InvalidSequenceTypeException", Exception);
+c$ = Clazz.p0p ();
+};
+});