org.jmol.io2

Class BinaryDocument

java.lang.Object

org.jmol.io2.BinaryDocument

All Implemented Interfaces:

JmolDocument

Direct Known Subclasses:

CompoundDocument

public class BinaryDocument
extends java.lang.Object
implements JmolDocument

Field Summary

Fields

Modifier and Type	Field and Description
private static float[]	fracIEEE
protected boolean	isBigEndian
protected boolean	isRandom
(package private) long	nBytes
(package private) java.io.OutputStream	os
protected java.io.DataInputStream	stream
(package private) byte[]	t8

Constructor Summary

Constructors

Constructor and Description
BinaryDocument()

Method Summary

Methods

Modifier and Type	Method and Description
static float	bytesToDoubleToFloat(byte[] bytes, int j, boolean isBigEndian) see http://en.wikipedia.org/wiki/Binary64 not concerning ourselves with very small or very large numbers and getting this exactly right.
void	close()
SB	getAllDataFiles(java.lang.String binaryFileList, java.lang.String firstFile)
void	getAllDataMapped(java.lang.String replace, java.lang.String string, java.util.Map<java.lang.String,java.lang.String> fileData)
long	getPosition()
private int	ioRead(byte[] b, int off, int len)
private byte	ioReadByte()
private double	ioReadDouble()
private int	ioReadInt()
private long	ioReadLong()
private short	ioReadShort()
byte	readByte()
int	readByteArray(byte[] b, int off, int len)
double	readDouble()
float	readFloat()
int	readInt()
int	readIntLE()
private int	readLEInt()
private long	readLELong()
long	readLong()
short	readShort()
java.lang.String	readString(int nChar)
int	readUnsignedShort()
void	seek(long offset)
(package private) static void	setFracIEEE()
void	setOutputStream(java.io.OutputStream os, Viewer viewer, double privateKey)
void	setRandom(boolean TF)
void	setStream(java.io.BufferedInputStream bis, boolean isBigEndian)
void	setStreamData(java.io.DataInputStream stream, boolean isBigEndian)
(package private) static double	shiftIEEE(double f, int i) only concerned about reasonable float values here
int	swapBytesI(int n)
short	swapBytesS(short n)
void	writeBytes(byte[] b, int off, int n)
void	writeInt(int i)
void	writeLong(long b)
void	writeShort(short i)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

stream

protected java.io.DataInputStream stream

isRandom

protected boolean isRandom

isBigEndian

protected boolean isBigEndian

t8

byte[] t8

fracIEEE

private static float[] fracIEEE

nBytes

long nBytes

os

java.io.OutputStream os

Constructor Detail

BinaryDocument

public BinaryDocument()

Method Detail

close

public void close()

Specified by:

close in interface JmolDocument

setStream

public void setStream(java.io.BufferedInputStream bis,
             boolean isBigEndian)

Specified by:

setStream in interface JmolDocument

setStreamData

public void setStreamData(java.io.DataInputStream stream,
                 boolean isBigEndian)

Specified by:

setStreamData in interface JmolDocument

setRandom

public void setRandom(boolean TF)

readByte

public byte readByte()
              throws java.lang.Exception

Specified by:

readByte in interface JmolDocument

Throws:

java.lang.Exception

ioReadByte

private byte ioReadByte()
                 throws java.lang.Exception

Throws:

java.lang.Exception

readByteArray

public int readByteArray(byte[] b,
                int off,
                int len)
                  throws java.lang.Exception

Specified by:

readByteArray in interface JmolDocument

Throws:

java.lang.Exception

ioRead

private int ioRead(byte[] b,
         int off,
         int len)
            throws java.lang.Exception

Throws:

java.lang.Exception

writeBytes

public void writeBytes(byte[] b,
              int off,
              int n)
                throws java.lang.Exception

Throws:

java.lang.Exception

readString

public java.lang.String readString(int nChar)
                            throws java.lang.Exception

Specified by:

readString in interface JmolDocument

Throws:

java.lang.Exception

readShort

public short readShort()
                throws java.lang.Exception

Specified by:

readShort in interface JmolDocument

Throws:

java.lang.Exception

ioReadShort

private short ioReadShort()
                   throws java.lang.Exception

Throws:

java.lang.Exception

writeShort

public void writeShort(short i)
                throws java.lang.Exception

Throws:

java.lang.Exception

readIntLE

public int readIntLE()
              throws java.lang.Exception

Specified by:

readIntLE in interface JmolDocument

Throws:

java.lang.Exception

readInt

public int readInt()
            throws java.lang.Exception

Specified by:

readInt in interface JmolDocument

Throws:

java.lang.Exception

ioReadInt

private int ioReadInt()
               throws java.lang.Exception

Throws:

java.lang.Exception

writeInt

public void writeInt(int i)
              throws java.lang.Exception

Throws:

java.lang.Exception

swapBytesI

public int swapBytesI(int n)

Specified by:

swapBytesI in interface JmolDocument

swapBytesS

public short swapBytesS(short n)

Specified by:

swapBytesS in interface JmolDocument

readUnsignedShort

public int readUnsignedShort()
                      throws java.lang.Exception

Specified by:

readUnsignedShort in interface JmolDocument

Throws:

java.lang.Exception

readLong

public long readLong()
              throws java.lang.Exception

Specified by:

readLong in interface JmolDocument

Throws:

java.lang.Exception

ioReadLong

private long ioReadLong()
                 throws java.lang.Exception

Throws:

java.lang.Exception

writeLong

public void writeLong(long b)
               throws java.lang.Exception

Throws:

java.lang.Exception

readFloat

public float readFloat()
                throws java.lang.Exception

Specified by:

readFloat in interface JmolDocument

Throws:

java.lang.Exception

readLEInt

private int readLEInt()
               throws java.lang.Exception

Throws:

java.lang.Exception

readDouble

public double readDouble()
                  throws java.lang.Exception

Specified by:

readDouble in interface JmolDocument

Throws:

java.lang.Exception

bytesToDoubleToFloat

public static float bytesToDoubleToFloat(byte[] bytes,
                         int j,
                         boolean isBigEndian)

see http://en.wikipedia.org/wiki/Binary64 not concerning ourselves with very small or very large numbers and getting this exactly right. Just need a float here.

Parameters:

bytes -

j -

isBigEndian -

Returns:

float

setFracIEEE

static void setFracIEEE()

shiftIEEE

static double shiftIEEE(double f,
               int i)

only concerned about reasonable float values here

Parameters:

f -

i -

Returns:

f * 2^i

ioReadDouble

private double ioReadDouble()
                     throws java.lang.Exception

Throws:

java.lang.Exception

readLELong

private long readLELong()
                 throws java.lang.Exception

Throws:

java.lang.Exception

seek

public void seek(long offset)

Specified by:

seek in interface JmolDocument

getPosition

public long getPosition()

Specified by:

getPosition in interface JmolDocument

setOutputStream

public void setOutputStream(java.io.OutputStream os,
                   Viewer viewer,
                   double privateKey)

Specified by:

setOutputStream in interface JmolDocument

getAllDataFiles

public SB getAllDataFiles(java.lang.String binaryFileList,
                 java.lang.String firstFile)

Specified by:

getAllDataFiles in interface JmolDocument

getAllDataMapped

public void getAllDataMapped(java.lang.String replace,
                    java.lang.String string,
                    java.util.Map<java.lang.String,java.lang.String> fileData)

Specified by:

getAllDataMapped in interface JmolDocument