X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjavajs%2Futil%2FBinaryDocument.js;h=a0edf334fb5486a4ada54c045bc517b36b858857;hp=420db0bb83ab2f7e97f16fba92f237e4f35e28d1;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/javajs/util/BinaryDocument.js b/bin/javajs/util/BinaryDocument.js
index 420db0b..a0edf33 100644
--- a/bin/javajs/util/BinaryDocument.js
+++ b/bin/javajs/util/BinaryDocument.js
@@ -1,218 +1,218 @@
-Clazz.declarePackage ("javajs.util");
-Clazz.load (["javajs.api.GenericBinaryDocument", "javajs.util.BC"], "javajs.util.BinaryDocument", ["java.io.DataInputStream", "java.lang.Double"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.stream = null;
-this.isRandom = false;
-this.isBigEndian = true;
-this.jzt = null;
-this.t8 = null;
-this.nBytes = 0;
-this.out = null;
-Clazz.instantialize (this, arguments);
-}, javajs.util, "BinaryDocument", javajs.util.BC, javajs.api.GenericBinaryDocument);
-Clazz.prepareFields (c$, function () {
-this.t8 =  Clazz.newByteArray (8, 0);
-});
-Clazz.overrideMethod (c$, "close", 
-function () {
-if (this.stream != null) try {
-this.stream.close ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-if (this.out != null) this.out.closeChannel ();
-});
-Clazz.overrideMethod (c$, "setStream", 
-function (jzt, bis, isBigEndian) {
-if (jzt != null) this.jzt = jzt;
-if (bis != null) this.stream =  new java.io.DataInputStream (bis);
-this.isBigEndian = isBigEndian;
-}, "javajs.api.GenericZipTools,java.io.BufferedInputStream,~B");
-Clazz.overrideMethod (c$, "setStreamData", 
-function (stream, isBigEndian) {
-if (stream != null) this.stream = stream;
-this.isBigEndian = isBigEndian;
-}, "java.io.DataInputStream,~B");
-Clazz.defineMethod (c$, "setRandom", 
-function (TF) {
-this.isRandom = TF;
-}, "~B");
-Clazz.overrideMethod (c$, "readByte", 
-function () {
-this.nBytes++;
-return this.ioReadByte ();
-});
-Clazz.defineMethod (c$, "ioReadByte", 
-($fz = function () {
-var b = this.stream.readByte ();
-if (this.out != null) this.out.writeByteAsInt (b);
-return b;
-}, $fz.isPrivate = true, $fz));
-Clazz.overrideMethod (c$, "readByteArray", 
-function (b, off, len) {
-var n = this.ioRead (b, off, len);
-this.nBytes += n;
-return n;
-}, "~A,~N,~N");
-Clazz.defineMethod (c$, "ioRead", 
-($fz = function (b, off, len) {
-var m = 0;
-while (len > 0) {
-var n = this.stream.read (b, off, len);
-m += n;
-if (n > 0 && this.out != null) this.writeBytes (b, off, n);
-if (n >= len) break;
-off += n;
-len -= n;
-}
-return m;
-}, $fz.isPrivate = true, $fz), "~A,~N,~N");
-Clazz.defineMethod (c$, "writeBytes", 
-function (b, off, n) {
-this.out.write (b, off, n);
-}, "~A,~N,~N");
-Clazz.overrideMethod (c$, "readString", 
-function (nChar) {
-var temp =  Clazz.newByteArray (nChar, 0);
-var n = this.readByteArray (temp, 0, nChar);
-return  String.instantialize (temp, 0, n, "UTF-8");
-}, "~N");
-Clazz.overrideMethod (c$, "readShort", 
-function () {
-this.nBytes += 2;
-var n = (this.isBigEndian ? this.ioReadShort () : ((this.ioReadByte () & 0xff) | (this.ioReadByte () & 0xff) << 8));
-{
-return (n > 0x7FFF ? n - 0x10000 : n);
-}});
-Clazz.defineMethod (c$, "ioReadShort", 
-($fz = function () {
-var b = this.stream.readShort ();
-if (this.out != null) this.writeShort (b);
-return b;
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "writeShort", 
-function (i) {
-this.out.writeByteAsInt (i >> 8);
-this.out.writeByteAsInt (i);
-}, "~N");
-Clazz.overrideMethod (c$, "readIntLE", 
-function () {
-this.nBytes += 4;
-return this.readLEInt ();
-});
-Clazz.overrideMethod (c$, "readInt", 
-function () {
-this.nBytes += 4;
-return (this.isBigEndian ? this.ioReadInt () : this.readLEInt ());
-});
-Clazz.defineMethod (c$, "ioReadInt", 
-($fz = function () {
-var i = this.stream.readInt ();
-if (this.out != null) this.writeInt (i);
-return i;
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "writeInt", 
-function (i) {
-this.out.writeByteAsInt (i >> 24);
-this.out.writeByteAsInt (i >> 16);
-this.out.writeByteAsInt (i >> 8);
-this.out.writeByteAsInt (i);
-}, "~N");
-Clazz.overrideMethod (c$, "swapBytesI", 
-function (n) {
-return (((n >> 24) & 0xff) | ((n >> 16) & 0xff) << 8 | ((n >> 8) & 0xff) << 16 | (n & 0xff) << 24);
-}, "~N");
-Clazz.overrideMethod (c$, "swapBytesS", 
-function (n) {
-return ((((n >> 8) & 0xff) | (n & 0xff) << 8));
-}, "~N");
-Clazz.overrideMethod (c$, "readUnsignedShort", 
-function () {
-this.nBytes += 2;
-var a = (this.ioReadByte () & 0xff);
-var b = (this.ioReadByte () & 0xff);
-return (this.isBigEndian ? (a << 8) + b : (b << 8) + a);
-});
-Clazz.overrideMethod (c$, "readLong", 
-function () {
-this.nBytes += 8;
-return (this.isBigEndian ? this.ioReadLong () : (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 54));
-});
-Clazz.defineMethod (c$, "ioReadLong", 
-($fz = function () {
-var b = this.stream.readLong ();
-if (this.out != null) this.writeLong (b);
-return b;
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "writeLong", 
-function (b) {
-this.writeInt (((b >> 32) & 0xFFFFFFFF));
-this.writeInt ((b & 0xFFFFFFFF));
-}, "~N");
-Clazz.defineMethod (c$, "readLEInt", 
-($fz = function () {
-this.ioRead (this.t8, 0, 4);
-return javajs.util.BC.bytesToInt (this.t8, 0, false);
-}, $fz.isPrivate = true, $fz));
-Clazz.overrideMethod (c$, "readFloat", 
-function () {
-return javajs.util.BC.intToFloat (this.readInt ());
-});
-Clazz.overrideMethod (c$, "readDouble", 
-function () {
-{
-this.readByteArray(this.t8, 0, 8);
-return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian);
-}});
-Clazz.defineMethod (c$, "ioReadDouble", 
-($fz = function () {
-var d = this.stream.readDouble ();
-if (this.out != null) this.writeLong (Double.doubleToRawLongBits (d));
-return d;
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "readLELong", 
-($fz = function () {
-return (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 56);
-}, $fz.isPrivate = true, $fz));
-Clazz.overrideMethod (c$, "seek", 
-function (offset) {
-try {
-if (offset == this.nBytes) return;
-if (offset < this.nBytes) {
-this.stream.reset ();
-if (this.out != null && this.nBytes != 0) this.out.reset ();
-this.nBytes = 0;
-} else {
-offset -= this.nBytes;
-}if (this.out == null) {
-this.stream.skipBytes (offset);
-} else {
-this.readByteArray ( Clazz.newByteArray (offset, 0), 0, offset);
-}this.nBytes += offset;
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-System.out.println (e.toString ());
-} else {
-throw e;
-}
-}
-}, "~N");
-Clazz.overrideMethod (c$, "getPosition", 
-function () {
-return this.nBytes;
-});
-Clazz.overrideMethod (c$, "setOutputChannel", 
-function (out) {
-this.out = out;
-}, "javajs.util.OC");
-Clazz.overrideMethod (c$, "getAllDataFiles", 
-function (binaryFileList, firstFile) {
-return null;
-}, "~S,~S");
-Clazz.overrideMethod (c$, "getAllDataMapped", 
-function (replace, string, fileData) {
-}, "~S,~S,java.util.Map");
-});
+Clazz.declarePackage ("javajs.util");
+Clazz.load (["javajs.api.GenericBinaryDocument", "javajs.util.BC"], "javajs.util.BinaryDocument", ["java.io.DataInputStream", "java.lang.Double"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.stream = null;
+this.isRandom = false;
+this.isBigEndian = true;
+this.jzt = null;
+this.t8 = null;
+this.nBytes = 0;
+this.out = null;
+Clazz.instantialize (this, arguments);
+}, javajs.util, "BinaryDocument", javajs.util.BC, javajs.api.GenericBinaryDocument);
+Clazz.prepareFields (c$, function () {
+this.t8 =  Clazz.newByteArray (8, 0);
+});
+Clazz.overrideMethod (c$, "close", 
+function () {
+if (this.stream != null) try {
+this.stream.close ();
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+if (this.out != null) this.out.closeChannel ();
+});
+Clazz.overrideMethod (c$, "setStream", 
+function (jzt, bis, isBigEndian) {
+if (jzt != null) this.jzt = jzt;
+if (bis != null) this.stream =  new java.io.DataInputStream (bis);
+this.isBigEndian = isBigEndian;
+}, "javajs.api.GenericZipTools,java.io.BufferedInputStream,~B");
+Clazz.overrideMethod (c$, "setStreamData", 
+function (stream, isBigEndian) {
+if (stream != null) this.stream = stream;
+this.isBigEndian = isBigEndian;
+}, "java.io.DataInputStream,~B");
+Clazz.defineMethod (c$, "setRandom", 
+function (TF) {
+this.isRandom = TF;
+}, "~B");
+Clazz.overrideMethod (c$, "readByte", 
+function () {
+this.nBytes++;
+return this.ioReadByte ();
+});
+Clazz.defineMethod (c$, "ioReadByte", 
+($fz = function () {
+var b = this.stream.readByte ();
+if (this.out != null) this.out.writeByteAsInt (b);
+return b;
+}, $fz.isPrivate = true, $fz));
+Clazz.overrideMethod (c$, "readByteArray", 
+function (b, off, len) {
+var n = this.ioRead (b, off, len);
+this.nBytes += n;
+return n;
+}, "~A,~N,~N");
+Clazz.defineMethod (c$, "ioRead", 
+($fz = function (b, off, len) {
+var m = 0;
+while (len > 0) {
+var n = this.stream.read (b, off, len);
+m += n;
+if (n > 0 && this.out != null) this.writeBytes (b, off, n);
+if (n >= len) break;
+off += n;
+len -= n;
+}
+return m;
+}, $fz.isPrivate = true, $fz), "~A,~N,~N");
+Clazz.defineMethod (c$, "writeBytes", 
+function (b, off, n) {
+this.out.write (b, off, n);
+}, "~A,~N,~N");
+Clazz.overrideMethod (c$, "readString", 
+function (nChar) {
+var temp =  Clazz.newByteArray (nChar, 0);
+var n = this.readByteArray (temp, 0, nChar);
+return  String.instantialize (temp, 0, n, "UTF-8");
+}, "~N");
+Clazz.overrideMethod (c$, "readShort", 
+function () {
+this.nBytes += 2;
+var n = (this.isBigEndian ? this.ioReadShort () : ((this.ioReadByte () & 0xff) | (this.ioReadByte () & 0xff) << 8));
+{
+return (n > 0x7FFF ? n - 0x10000 : n);
+}});
+Clazz.defineMethod (c$, "ioReadShort", 
+($fz = function () {
+var b = this.stream.readShort ();
+if (this.out != null) this.writeShort (b);
+return b;
+}, $fz.isPrivate = true, $fz));
+Clazz.defineMethod (c$, "writeShort", 
+function (i) {
+this.out.writeByteAsInt (i >> 8);
+this.out.writeByteAsInt (i);
+}, "~N");
+Clazz.overrideMethod (c$, "readIntLE", 
+function () {
+this.nBytes += 4;
+return this.readLEInt ();
+});
+Clazz.overrideMethod (c$, "readInt", 
+function () {
+this.nBytes += 4;
+return (this.isBigEndian ? this.ioReadInt () : this.readLEInt ());
+});
+Clazz.defineMethod (c$, "ioReadInt", 
+($fz = function () {
+var i = this.stream.readInt ();
+if (this.out != null) this.writeInt (i);
+return i;
+}, $fz.isPrivate = true, $fz));
+Clazz.defineMethod (c$, "writeInt", 
+function (i) {
+this.out.writeByteAsInt (i >> 24);
+this.out.writeByteAsInt (i >> 16);
+this.out.writeByteAsInt (i >> 8);
+this.out.writeByteAsInt (i);
+}, "~N");
+Clazz.overrideMethod (c$, "swapBytesI", 
+function (n) {
+return (((n >> 24) & 0xff) | ((n >> 16) & 0xff) << 8 | ((n >> 8) & 0xff) << 16 | (n & 0xff) << 24);
+}, "~N");
+Clazz.overrideMethod (c$, "swapBytesS", 
+function (n) {
+return ((((n >> 8) & 0xff) | (n & 0xff) << 8));
+}, "~N");
+Clazz.overrideMethod (c$, "readUnsignedShort", 
+function () {
+this.nBytes += 2;
+var a = (this.ioReadByte () & 0xff);
+var b = (this.ioReadByte () & 0xff);
+return (this.isBigEndian ? (a << 8) + b : (b << 8) + a);
+});
+Clazz.overrideMethod (c$, "readLong", 
+function () {
+this.nBytes += 8;
+return (this.isBigEndian ? this.ioReadLong () : (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 54));
+});
+Clazz.defineMethod (c$, "ioReadLong", 
+($fz = function () {
+var b = this.stream.readLong ();
+if (this.out != null) this.writeLong (b);
+return b;
+}, $fz.isPrivate = true, $fz));
+Clazz.defineMethod (c$, "writeLong", 
+function (b) {
+this.writeInt (((b >> 32) & 0xFFFFFFFF));
+this.writeInt ((b & 0xFFFFFFFF));
+}, "~N");
+Clazz.defineMethod (c$, "readLEInt", 
+($fz = function () {
+this.ioRead (this.t8, 0, 4);
+return javajs.util.BC.bytesToInt (this.t8, 0, false);
+}, $fz.isPrivate = true, $fz));
+Clazz.overrideMethod (c$, "readFloat", 
+function () {
+return javajs.util.BC.intToFloat (this.readInt ());
+});
+Clazz.overrideMethod (c$, "readDouble", 
+function () {
+{
+this.readByteArray(this.t8, 0, 8);
+return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian);
+}});
+Clazz.defineMethod (c$, "ioReadDouble", 
+($fz = function () {
+var d = this.stream.readDouble ();
+if (this.out != null) this.writeLong (Double.doubleToRawLongBits (d));
+return d;
+}, $fz.isPrivate = true, $fz));
+Clazz.defineMethod (c$, "readLELong", 
+($fz = function () {
+return (((this.ioReadByte ()) & 0xff) | ((this.ioReadByte ()) & 0xff) << 8 | ((this.ioReadByte ()) & 0xff) << 16 | ((this.ioReadByte ()) & 0xff) << 24 | ((this.ioReadByte ()) & 0xff) << 32 | ((this.ioReadByte ()) & 0xff) << 40 | ((this.ioReadByte ()) & 0xff) << 48 | ((this.ioReadByte ()) & 0xff) << 56);
+}, $fz.isPrivate = true, $fz));
+Clazz.overrideMethod (c$, "seek", 
+function (offset) {
+try {
+if (offset == this.nBytes) return;
+if (offset < this.nBytes) {
+this.stream.reset ();
+if (this.out != null && this.nBytes != 0) this.out.reset ();
+this.nBytes = 0;
+} else {
+offset -= this.nBytes;
+}if (this.out == null) {
+this.stream.skipBytes (offset);
+} else {
+this.readByteArray ( Clazz.newByteArray (offset, 0), 0, offset);
+}this.nBytes += offset;
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+System.out.println (e.toString ());
+} else {
+throw e;
+}
+}
+}, "~N");
+Clazz.overrideMethod (c$, "getPosition", 
+function () {
+return this.nBytes;
+});
+Clazz.overrideMethod (c$, "setOutputChannel", 
+function (out) {
+this.out = out;
+}, "javajs.util.OC");
+Clazz.overrideMethod (c$, "getAllDataFiles", 
+function (binaryFileList, firstFile) {
+return null;
+}, "~S,~S");
+Clazz.overrideMethod (c$, "getAllDataMapped", 
+function (replace, string, fileData) {
+}, "~S,~S,java.util.Map");
+});