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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $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: [email protected]
*
* 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.io.IOException;
import java.util.Map;
import javajs.api.GenericBinaryDocument;
import javajs.api.GenericOutputChannel;
/* a basic binary file reader (extended by CompoundDocument).
*
* 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;
protected boolean isBigEndian = true;
protected BufferedInputStream bis;
protected long nBytes;
protected GenericOutputChannel out;
@Override
public void close() {
if (stream != null)
try {
stream.close();
} catch (IOException e) {
// ignore
}
if (out != null)
out.closeChannel();
}
@Override
public BinaryDocument setStream(BufferedInputStream bis, boolean isBigEndian) {
this.bis = bis;
if (bis != null) {
stream = new DataInputStream(bis);
}
this.isBigEndian = isBigEndian;
return this;
}
@Override
public BufferedInputStream getInputStream() {
return bis;
}
@Override
public void setStreamData(DataInputStream stream, boolean isBigEndian) {
if (stream != null)
this.stream = stream;
this.isBigEndian = isBigEndian;
}
@Override
public void setOutputChannel(GenericOutputChannel out) {
this.out = out;
}
public void setRandom(boolean TF) {
isRandom = TF;
//CANNOT be random for web
}
@Override
public byte readByte() throws IOException {
nBytes++;
return ioReadByte();
}
@Override
public int readUInt8() throws IOException {
nBytes++;
int b = stream.readUnsignedByte();
if (out != null)
out.writeByteAsInt(b);
return b;
}
private byte ioReadByte() throws IOException {
byte b = stream.readByte();
if (out != null)
out.writeByteAsInt(b);
return b;
}
@Override
public byte[] readBytes(int n) throws IOException {
byte[] b = new byte[n];
readByteArray(b, 0, n);
return b;
}
@Override
public int readByteArray(byte[] b, int off, int len) throws IOException {
int n = ioRead(b, off, len);
nBytes += n;
return n;
}
private int ioRead(byte[] b, int off, int len) throws IOException {
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 writeString(String s) throws IOException {
byte[] b = s.getBytes();
out.write(b, 0, b.length);
}
public void writeBytes(byte[] b, int off, int n) throws IOException {
out.write(b, off, n);
}
@Override
public String readString(int nChar) throws IOException {
byte[] temp = new byte[nChar];
int n = readByteArray(temp, 0, nChar);
return new String(temp, 0, n, "UTF-8");
}
@Override
public short readShort() throws IOException {
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 IOException {
short b = stream.readShort();
if (out != null)
writeShort(b);
return b;
}
public void writeShort(short i) throws IOException {
if (out.isBigEndian()) {
out.writeByteAsInt(i >> 8);
out.writeByteAsInt(i);
} else {
out.writeByteAsInt(i);
out.writeByteAsInt(i >> 8);
}
}
@Override
public int readIntLE() throws IOException {
nBytes += 4;
return readLEInt();
}
@Override
public int readInt() throws IOException {
nBytes += 4;
return (isBigEndian ? ioReadInt() : readLEInt());
}
private int ioReadInt() throws IOException {
int i = stream.readInt();
if (out != null)
writeInt(i);
return i;
}
public void writeInt(int i) throws IOException {
if (out.isBigEndian()) {
out.writeByteAsInt(i >> 24);
out.writeByteAsInt(i >> 16);
out.writeByteAsInt(i >> 8);
out.writeByteAsInt(i);
} else {
out.writeByteAsInt(i);
out.writeByteAsInt(i >> 8);
out.writeByteAsInt(i >> 16);
out.writeByteAsInt(i >> 24);
}
}
@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 IOException {
nBytes += 2;
int a = (ioReadByte() & 0xff);
int b = (ioReadByte() & 0xff);
return (isBigEndian ? (a << 8) + b : (b << 8) + a);
}
@Override
public long readLong() throws IOException {
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 IOException {
long b = stream.readLong();
if (out != null)
writeLong(b);
return b;
}
public void writeLong(long b) throws IOException {
if (out.isBigEndian()) {
writeInt((int) ((b >> 32) & 0xFFFFFFFFl));
writeInt((int) (b & 0xFFFFFFFFl));
} else {
out.writeByteAsInt((int) (b >> 56));
out.writeByteAsInt((int) (b >> 48));
out.writeByteAsInt((int) (b >> 40));
out.writeByteAsInt((int) (b >> 32));
out.writeByteAsInt((int) (b >> 24));
out.writeByteAsInt((int) (b >> 16));
out.writeByteAsInt((int) (b >> 8));
out.writeByteAsInt((int) b);
}
}
private int readLEInt() throws IOException {
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 IOException {
/**
*
* 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 IOException {
double d = stream.readDouble();
if (out != null)
writeLong(Double.doubleToRawLongBits(d));
return d;
}
private long readLELong() throws IOException {
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 (IOException e) {
System.out.println(e.toString());
}
}
@Override
public long getPosition() {
return nBytes;
}
@Override
public SB getAllDataFiles(String binaryFileList, String firstFile) {
return null;
}
@Override
public void getAllDataMapped(String replace, String string,
Map fileData) {
}
/* random access -- application only:
*
void seekFile(long offset) {
try {
file.seek(offset);
} catch (IOException e) {
System.out.println(e.getMessage());
}
}
*/
}