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