-/* $RCSfile$\r
- * $Author: egonw $\r
- * $Date: 2006-03-18 15:59:33 -0600 (Sat, 18 Mar 2006) $\r
- * $Revision: 4652 $\r
- *\r
- * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org\r
- *\r
- * Contact: hansonr@stolaf.edu\r
- *\r
- * This library is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU Lesser General Public\r
- * License as published by the Free Software Foundation; either\r
- * version 2.1 of the License, or (at your option) any later version.\r
- *\r
- * This library is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
- * Lesser General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU Lesser General Public\r
- * License along with this library; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.\r
- */\r
-package javajs.util;\r
-\r
-\r
-import java.io.BufferedInputStream;\r
-import java.io.DataInputStream;\r
-import java.util.Map;\r
-\r
-\r
-import javajs.api.GenericBinaryDocument;\r
-import javajs.api.GenericZipTools;\r
-\r
-\r
-//import java.io.RandomAccessFile;\r
-\r
-/* a basic binary file reader (extended by CompoundDocument). \r
- * \r
- * random access file info: \r
- * http://java.sun.com/docs/books/tutorial/essential/io/rafs.html\r
- * \r
- * SHOOT! random access is only for applications, not applets!\r
- * \r
- * Note that YOU are responsible for determining whether a file\r
- * is bigEndian or littleEndian; the default is bigEndian.\r
- * \r
- * JavaScript note: readShort() malfunctioned because (short) (xx << 8) \r
- * isn't the same as (int) (xx << 8); same problem in java.io.DataStream\r
- * \r
- * \r
- */\r
-\r
-public class BinaryDocument extends BC implements GenericBinaryDocument {\r
-\r
- /**\r
- * @j2sIgnore\r
- */\r
- public BinaryDocument() { \r
- }\r
-\r
-\r
- // called by reflection\r
- \r
- protected DataInputStream stream;\r
- protected boolean isRandom = false;\r
- public boolean isBigEndian = true;\r
- protected GenericZipTools jzt;\r
-\r
- @Override\r
- public void close() {\r
- if (stream != null)\r
- try {\r
- stream.close();\r
- } catch (Exception e) {\r
- // ignore\r
- }\r
- if (out != null)\r
- out.closeChannel();\r
- }\r
- \r
- @Override\r
- public void setStream(GenericZipTools jzt, BufferedInputStream bis, boolean isBigEndian) {\r
- if (jzt != null)\r
- this.jzt = jzt;\r
- if (bis != null)\r
- stream = new DataInputStream(bis);\r
- this.isBigEndian = isBigEndian;\r
- }\r
- \r
- @Override\r
- public void setStreamData(DataInputStream stream, boolean isBigEndian) {\r
- if (stream != null)\r
- this.stream = stream;\r
- this.isBigEndian = isBigEndian;\r
- }\r
- \r
- public void setRandom(boolean TF) {\r
- isRandom = TF;\r
- //CANNOT be random for web \r
- }\r
- \r
- @Override\r
- public byte readByte() throws Exception {\r
- nBytes++;\r
- return ioReadByte();\r
- }\r
-\r
- private byte ioReadByte() throws Exception {\r
- byte b = stream.readByte();\r
- if (out != null)\r
- out.writeByteAsInt(b);\r
- return b;\r
- }\r
-\r
- @Override\r
- public int readByteArray(byte[] b, int off, int len) throws Exception {\r
- int n = ioRead(b, off, len);\r
- nBytes += n;\r
- return n;\r
- }\r
-\r
- private int ioRead(byte[] b, int off, int len) throws Exception {\r
- int m = 0;\r
- while (len > 0) {\r
- int n = stream.read(b, off, len);\r
- m += n;\r
- if (n > 0 && out != null)\r
- writeBytes(b, off, n);\r
- if (n >= len)\r
- break;\r
- off += n;\r
- len -= n;\r
- }\r
- return m;\r
- }\r
-\r
- public void writeBytes(byte[] b, int off, int n) throws Exception {\r
- out.write(b, off, n);\r
- }\r
-\r
- @Override\r
- public String readString(int nChar) throws Exception {\r
- byte[] temp = new byte[nChar];\r
- int n = readByteArray(temp, 0, nChar);\r
- return new String(temp, 0, n, "UTF-8");\r
- }\r
- \r
- @Override\r
- public short readShort() throws Exception {\r
- nBytes += 2;\r
- short n = (isBigEndian ? ioReadShort()\r
- : (short) ((ioReadByte() & 0xff) \r
- | (ioReadByte() & 0xff) << 8));\r
- /**\r
- * @j2sNative\r
- *\r
- * return (n > 0x7FFF ? n - 0x10000 : n);\r
- */\r
- {\r
- return n;\r
- }\r
- }\r
-\r
- private short ioReadShort() throws Exception {\r
- short b = stream.readShort();\r
- if (out != null)\r
- writeShort(b);\r
- return b;\r
- }\r
-\r
-\r
- public void writeShort(short i) throws Exception {\r
- out.writeByteAsInt(i >> 8);\r
- out.writeByteAsInt(i);\r
- }\r
-\r
- @Override\r
- public int readIntLE() throws Exception {\r
- nBytes += 4;\r
- return readLEInt();\r
- }\r
- \r
- @Override\r
- public int readInt() throws Exception {\r
- nBytes += 4;\r
- return (isBigEndian ? ioReadInt() : readLEInt());\r
- }\r
- \r
- private int ioReadInt() throws Exception {\r
- int i = stream.readInt();\r
- if (out != null)\r
- writeInt(i);\r
- return i;\r
- }\r
-\r
- public void writeInt(int i) throws Exception {\r
- out.writeByteAsInt(i >> 24);\r
- out.writeByteAsInt(i >> 16);\r
- out.writeByteAsInt(i >> 8);\r
- out.writeByteAsInt(i);\r
- }\r
-\r
- @Override\r
- public int swapBytesI(int n) {\r
- return (((n >> 24) & 0xff)\r
- | ((n >> 16) & 0xff) << 8\r
- | ((n >> 8) & 0xff) << 16 \r
- | (n & 0xff) << 24);\r
- }\r
-\r
- @Override\r
- public short swapBytesS(short n) {\r
- return (short) ((((n >> 8) & 0xff)\r
- | (n & 0xff) << 8));\r
- }\r
-\r
- \r
- @Override\r
- public int readUnsignedShort() throws Exception {\r
- nBytes += 2;\r
- int a = (ioReadByte() & 0xff);\r
- int b = (ioReadByte() & 0xff);\r
- return (isBigEndian ? (a << 8) + b : (b << 8) + a);\r
- }\r
- \r
- @Override\r
- public long readLong() throws Exception {\r
- nBytes += 8;\r
- return (isBigEndian ? ioReadLong()\r
- : ((((long) ioReadByte()) & 0xff)\r
- | (((long) ioReadByte()) & 0xff) << 8\r
- | (((long) ioReadByte()) & 0xff) << 16\r
- | (((long) ioReadByte()) & 0xff) << 24\r
- | (((long) ioReadByte()) & 0xff) << 32\r
- | (((long) ioReadByte()) & 0xff) << 40\r
- | (((long) ioReadByte()) & 0xff) << 48 \r
- | (((long) ioReadByte()) & 0xff) << 54));\r
- }\r
-\r
- private long ioReadLong() throws Exception {\r
- long b = stream.readLong();\r
- if (out != null)\r
- writeLong(b);\r
- return b;\r
- }\r
-\r
- public void writeLong(long b) throws Exception {\r
- writeInt((int)((b >> 32) & 0xFFFFFFFFl));\r
- writeInt((int)(b & 0xFFFFFFFFl));\r
- }\r
-\r
- private int readLEInt() throws Exception {\r
- ioRead(t8, 0, 4);\r
- return bytesToInt(t8, 0, false);\r
- }\r
-\r
- byte[] t8 = new byte[8];\r
- \r
- @Override\r
- public float readFloat() throws Exception {\r
- return intToFloat(readInt());\r
- }\r
-\r
- @Override\r
- public double readDouble() throws Exception {\r
- /**\r
- * \r
- * reading the float equivalent here in JavaScript\r
- * \r
- * @j2sNative\r
- * \r
- * this.readByteArray(this.t8, 0, 8);\r
- * return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian);\r
- * \r
- */\r
- {\r
- nBytes += 8;\r
- return (isBigEndian ? ioReadDouble() : Double.longBitsToDouble(readLELong())); \r
- }\r
- }\r
- \r
- private double ioReadDouble() throws Exception {\r
- double d = stream.readDouble();\r
- if (out != null)\r
- writeLong(Double.doubleToRawLongBits(d));\r
- return d;\r
- }\r
-\r
- private long readLELong() throws Exception {\r
- return ((((long) ioReadByte()) & 0xff)\r
- | (((long) ioReadByte()) & 0xff) << 8\r
- | (((long) ioReadByte()) & 0xff) << 16 \r
- | (((long) ioReadByte()) & 0xff) << 24\r
- | (((long) ioReadByte()) & 0xff) << 32\r
- | (((long) ioReadByte()) & 0xff) << 40\r
- | (((long) ioReadByte()) & 0xff) << 48\r
- | (((long) ioReadByte()) & 0xff) << 56);\r
- }\r
-\r
- @Override\r
- public void seek(long offset) {\r
- // slower, but all that is available using the applet\r
- try {\r
- if (offset == nBytes)\r
- return;\r
- if (offset < nBytes) {\r
- stream.reset();\r
- if (out != null && nBytes != 0)\r
- out.reset();\r
- nBytes = 0;\r
- } else {\r
- offset -= nBytes;\r
- }\r
- if (out == null) {\r
- stream.skipBytes((int)offset);\r
- } else {\r
- readByteArray(new byte[(int)offset], 0, (int) offset);\r
- }\r
- nBytes += offset;\r
- } catch (Exception e) {\r
- System.out.println(e.toString());\r
- }\r
- }\r
-\r
- long nBytes;\r
- \r
- @Override\r
- public long getPosition() {\r
- return nBytes;\r
- }\r
-\r
- OC out;\r
- @Override\r
- public void setOutputChannel(OC out) {\r
- this.out = out;\r
- }\r
-\r
- @Override\r
- public SB getAllDataFiles(String binaryFileList, String firstFile) {\r
- return null;\r
- }\r
-\r
- @Override\r
- public void getAllDataMapped(String replace, String string,\r
- Map<String, String> fileData) {\r
- }\r
-\r
-\r
-/* random access -- application only:\r
- * \r
- void seekFile(long offset) {\r
- try {\r
- file.seek(offset);\r
- } catch (Exception e) {\r
- System.out.println(e.getMessage());\r
- }\r
- }\r
-*/\r
-}\r
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2006-03-18 15:59:33 -0600 (Sat, 18 Mar 2006) $
+ * $Revision: 4652 $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: hansonr@stolaf.edu
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package javajs.util;
+
+
+import java.io.BufferedInputStream;
+import java.io.DataInputStream;
+import java.util.Map;
+
+
+import javajs.api.GenericBinaryDocument;
+import javajs.api.GenericZipTools;
+
+
+//import java.io.RandomAccessFile;
+
+/* a basic binary file reader (extended by CompoundDocument).
+ *
+ * random access file info:
+ * http://java.sun.com/docs/books/tutorial/essential/io/rafs.html
+ *
+ * SHOOT! random access is only for applications, not applets!
+ *
+ * Note that YOU are responsible for determining whether a file
+ * is bigEndian or littleEndian; the default is bigEndian.
+ *
+ * JavaScript note: readShort() malfunctioned because (short) (xx << 8)
+ * isn't the same as (int) (xx << 8); same problem in java.io.DataStream
+ *
+ *
+ */
+
+public class BinaryDocument extends BC implements GenericBinaryDocument {
+
+ /**
+ * @j2sIgnore
+ */
+ public BinaryDocument() {
+ }
+
+
+ // called by reflection
+
+ protected DataInputStream stream;
+ protected boolean isRandom = false;
+ public boolean isBigEndian = true;
+ protected GenericZipTools jzt;
+
+ @Override
+ public void close() {
+ if (stream != null)
+ try {
+ stream.close();
+ } catch (Exception e) {
+ // ignore
+ }
+ if (out != null)
+ out.closeChannel();
+ }
+
+ @Override
+ public void setStream(GenericZipTools jzt, BufferedInputStream bis, boolean isBigEndian) {
+ if (jzt != null)
+ this.jzt = jzt;
+ if (bis != null)
+ stream = new DataInputStream(bis);
+ this.isBigEndian = isBigEndian;
+ }
+
+ @Override
+ public void setStreamData(DataInputStream stream, boolean isBigEndian) {
+ if (stream != null)
+ this.stream = stream;
+ this.isBigEndian = isBigEndian;
+ }
+
+ public void setRandom(boolean TF) {
+ isRandom = TF;
+ //CANNOT be random for web
+ }
+
+ @Override
+ public byte readByte() throws Exception {
+ nBytes++;
+ return ioReadByte();
+ }
+
+ private byte ioReadByte() throws Exception {
+ byte b = stream.readByte();
+ if (out != null)
+ out.writeByteAsInt(b);
+ return b;
+ }
+
+ @Override
+ public int readByteArray(byte[] b, int off, int len) throws Exception {
+ int n = ioRead(b, off, len);
+ nBytes += n;
+ return n;
+ }
+
+ private int ioRead(byte[] b, int off, int len) throws Exception {
+ int m = 0;
+ while (len > 0) {
+ int n = stream.read(b, off, len);
+ m += n;
+ if (n > 0 && out != null)
+ writeBytes(b, off, n);
+ if (n >= len)
+ break;
+ off += n;
+ len -= n;
+ }
+ return m;
+ }
+
+ public void writeBytes(byte[] b, int off, int n) throws Exception {
+ out.write(b, off, n);
+ }
+
+ @Override
+ public String readString(int nChar) throws Exception {
+ byte[] temp = new byte[nChar];
+ int n = readByteArray(temp, 0, nChar);
+ return new String(temp, 0, n, "UTF-8");
+ }
+
+ @Override
+ public short readShort() throws Exception {
+ nBytes += 2;
+ short n = (isBigEndian ? ioReadShort()
+ : (short) ((ioReadByte() & 0xff)
+ | (ioReadByte() & 0xff) << 8));
+ /**
+ * @j2sNative
+ *
+ * return (n > 0x7FFF ? n - 0x10000 : n);
+ */
+ {
+ return n;
+ }
+ }
+
+ private short ioReadShort() throws Exception {
+ short b = stream.readShort();
+ if (out != null)
+ writeShort(b);
+ return b;
+ }
+
+
+ public void writeShort(short i) throws Exception {
+ out.writeByteAsInt(i >> 8);
+ out.writeByteAsInt(i);
+ }
+
+ @Override
+ public int readIntLE() throws Exception {
+ nBytes += 4;
+ return readLEInt();
+ }
+
+ @Override
+ public int readInt() throws Exception {
+ nBytes += 4;
+ return (isBigEndian ? ioReadInt() : readLEInt());
+ }
+
+ private int ioReadInt() throws Exception {
+ int i = stream.readInt();
+ if (out != null)
+ writeInt(i);
+ return i;
+ }
+
+ public void writeInt(int i) throws Exception {
+ out.writeByteAsInt(i >> 24);
+ out.writeByteAsInt(i >> 16);
+ out.writeByteAsInt(i >> 8);
+ out.writeByteAsInt(i);
+ }
+
+ @Override
+ public int swapBytesI(int n) {
+ return (((n >> 24) & 0xff)
+ | ((n >> 16) & 0xff) << 8
+ | ((n >> 8) & 0xff) << 16
+ | (n & 0xff) << 24);
+ }
+
+ @Override
+ public short swapBytesS(short n) {
+ return (short) ((((n >> 8) & 0xff)
+ | (n & 0xff) << 8));
+ }
+
+
+ @Override
+ public int readUnsignedShort() throws Exception {
+ nBytes += 2;
+ int a = (ioReadByte() & 0xff);
+ int b = (ioReadByte() & 0xff);
+ return (isBigEndian ? (a << 8) + b : (b << 8) + a);
+ }
+
+ @Override
+ public long readLong() throws Exception {
+ nBytes += 8;
+ return (isBigEndian ? ioReadLong()
+ : ((((long) ioReadByte()) & 0xff)
+ | (((long) ioReadByte()) & 0xff) << 8
+ | (((long) ioReadByte()) & 0xff) << 16
+ | (((long) ioReadByte()) & 0xff) << 24
+ | (((long) ioReadByte()) & 0xff) << 32
+ | (((long) ioReadByte()) & 0xff) << 40
+ | (((long) ioReadByte()) & 0xff) << 48
+ | (((long) ioReadByte()) & 0xff) << 54));
+ }
+
+ private long ioReadLong() throws Exception {
+ long b = stream.readLong();
+ if (out != null)
+ writeLong(b);
+ return b;
+ }
+
+ public void writeLong(long b) throws Exception {
+ writeInt((int)((b >> 32) & 0xFFFFFFFFl));
+ writeInt((int)(b & 0xFFFFFFFFl));
+ }
+
+ private int readLEInt() throws Exception {
+ ioRead(t8, 0, 4);
+ return bytesToInt(t8, 0, false);
+ }
+
+ byte[] t8 = new byte[8];
+
+ @Override
+ public float readFloat() throws Exception {
+ return intToFloat(readInt());
+ }
+
+ @Override
+ public double readDouble() throws Exception {
+ /**
+ *
+ * reading the float equivalent here in JavaScript
+ *
+ * @j2sNative
+ *
+ * this.readByteArray(this.t8, 0, 8);
+ * return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian);
+ *
+ */
+ {
+ nBytes += 8;
+ return (isBigEndian ? ioReadDouble() : Double.longBitsToDouble(readLELong()));
+ }
+ }
+
+ private double ioReadDouble() throws Exception {
+ double d = stream.readDouble();
+ if (out != null)
+ writeLong(Double.doubleToRawLongBits(d));
+ return d;
+ }
+
+ private long readLELong() throws Exception {
+ return ((((long) ioReadByte()) & 0xff)
+ | (((long) ioReadByte()) & 0xff) << 8
+ | (((long) ioReadByte()) & 0xff) << 16
+ | (((long) ioReadByte()) & 0xff) << 24
+ | (((long) ioReadByte()) & 0xff) << 32
+ | (((long) ioReadByte()) & 0xff) << 40
+ | (((long) ioReadByte()) & 0xff) << 48
+ | (((long) ioReadByte()) & 0xff) << 56);
+ }
+
+ @Override
+ public void seek(long offset) {
+ // slower, but all that is available using the applet
+ try {
+ if (offset == nBytes)
+ return;
+ if (offset < nBytes) {
+ stream.reset();
+ if (out != null && nBytes != 0)
+ out.reset();
+ nBytes = 0;
+ } else {
+ offset -= nBytes;
+ }
+ if (out == null) {
+ stream.skipBytes((int)offset);
+ } else {
+ readByteArray(new byte[(int)offset], 0, (int) offset);
+ }
+ nBytes += offset;
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+ }
+
+ long nBytes;
+
+ @Override
+ public long getPosition() {
+ return nBytes;
+ }
+
+ OC out;
+ @Override
+ public void setOutputChannel(OC out) {
+ this.out = out;
+ }
+
+ @Override
+ public SB getAllDataFiles(String binaryFileList, String firstFile) {
+ return null;
+ }
+
+ @Override
+ public void getAllDataMapped(String replace, String string,
+ Map<String, String> fileData) {
+ }
+
+
+/* random access -- application only:
+ *
+ void seekFile(long offset) {
+ try {
+ file.seek(offset);
+ } catch (Exception e) {
+ System.out.println(e.getMessage());
+ }
+ }
+*/
+}
git://source.jalview.org / jalviewjs.git / blobdiff