java.lang.Object
- org.jmol.adapter.readers.cif.MessagePackReader

```
public class MessagePackReader
extends java.lang.Object
```
A simple MessagePack reader. See https://github.com/msgpack/msgpack/blob/master/spec.md with very few dependencies. Nuances: Does not implement unsigned int32 or int64 (delivers simple integers in all cases). Does not use doubles; just floats Note: homogeneousArrays == true will deliver null for empty array. Use in MMTF: BufferedInputStream bs = [whatever] GenericBinaryDocument binaryDoc = new javajs.util.BinaryDocument(); binaryDoc.setStream(bs, true); map = (new MessagePackReader(binaryDoc, true)).readMap(); entities = (Object[]) map.get("entityList"); float[] x = (float[]) decode((byte[]) map.get("xCoordList"))

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields
Modifier and Type	Field	Description
`private static int`	`ARRAY16`
`private static int`	`ARRAY32`
`private static int`	`BIN16`
`private static int`	`BIN32`
`private static int`	`BIN8`
`private static int`	`DEFINITE_xE0`
`private javajs.api.GenericBinaryDocument`	`doc`
`private static int`	`EXT16`
`private static int`	`EXT32`
`private static int`	`EXT8`
`private static int`	`FALSE`
`private static int`	`FIXEXT1`
`private static int`	`FIXEXT16`
`private static int`	`FIXEXT2`
`private static int`	`FIXEXT4`
`private static int`	`FIXEXT8`
`private static int`	`FIXMAP_xF0`
`private static int`	`FIXSTR_xE0`
`private static int`	`FLOAT32`
`private static int`	`FLOAT64`
`private static int`	`INT16`
`private static int`	`INT32`
`private static int`	`INT64`
`private static int`	`INT8`
`private boolean`	`isHomo`
`private static int`	`MAP16`
`private static int`	`MAP32`
`private static int`	`NEGATIVEFIXINT_xE0`
`private static int`	`NIL`
`private static int`	`POSITIVEFIXINT_x80`
`private static int`	`STR16`
`private static int`	`STR32`
`private static int`	`STR8`
`private static int`	`TRUE`
`private static int`	`UINT16`
`private static int`	`UINT32`
`private static int`	`UINT64`
`private static int`	`UINT8`

Constructor Summary

Constructors
Constructor Description

MessagePackReader(javajs.api.GenericBinaryDocument binaryDoc, boolean isHomogeneousArrays)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static java.lang.Object`	`decode(byte[] b)`	This single method takes care of all MMTF needs.
`private java.lang.Object`	`getArray(int n)`
`static float[]`	`getFloats(byte[] b, int n, float divisor)`	mmtf type 1 and 11 byte[4] to float32
`static int[]`	`getInts(byte[] b, int n)`	mmtf types 2-4 Decode a byte array into a byte, short, or int array.
`private java.lang.Object`	`getMap(int n)`
`java.lang.Object`	`getNext(java.lang.Object array, int pt)`
`java.util.Map<java.lang.String,java.lang.Object>`	`readMap()`
`static int[]`	`rldecode32(byte[] b, int n)`	mmtf type 7 Decode an array of int32 using run-length decoding.
`static int[]`	`rldecode32Delta(byte[] b, int n)`	mmtf type 8 Decode an array of int32 using run-length decoding of a difference array.
`static char[]`	`rldecode32ToChar(byte[] b, int n)`	mmtf type 6 Decode an array of int32 using run-length decoding to one char per int.
`static java.lang.String[]`	`rldecode32ToStr(byte[] b)`	mmtf type 5 Decode each four bytes as a 1- to 4-character string label where a 0 byte indicates end-of-string.
`static float[]`	`rldecodef(byte[] b, int n, float divisor)`	mmtf type 9 Decode an array of int32 using run-length decoding and divide by a divisor to give a float32.
`static int[]`	`unpack(byte[] b, int nBytes, int n)`	mmtf type 14 and 15 Unpack an array of int8 or int16 to int32.
`static float[]`	`unpack16Deltaf(byte[] b, int n, float divisor)`	mmtf type 10 Decode an array of int16 using run-length decoding of a difference array.
`static float[]`	`unpackf(byte[] b, int nBytes, int n, float divisor)`	mmtf type 12 and 13 Unpack an array of int8 or int16 to int32 and divide to give a float32.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - doc
```
private javajs.api.GenericBinaryDocument doc
```
  - isHomo
```
private boolean isHomo
```
  - POSITIVEFIXINT_x80
```
private static final int POSITIVEFIXINT_x80
```
    See Also:
    
    Constant Field Values
  - FIXMAP_xF0
```
private static final int FIXMAP_xF0
```
    See Also:
    
    Constant Field Values
  - FIXSTR_xE0
```
private static final int FIXSTR_xE0
```
    See Also:
    
    Constant Field Values
  - NEGATIVEFIXINT_xE0
```
private static final int NEGATIVEFIXINT_xE0
```
    See Also:
    
    Constant Field Values
  - DEFINITE_xE0
```
private static final int DEFINITE_xE0
```
    See Also:
    
    Constant Field Values
  - NIL
```
private static final int NIL
```
    See Also:
    
    Constant Field Values
  - FALSE
```
private static final int FALSE
```
    See Also:
    
    Constant Field Values
  - TRUE
```
private static final int TRUE
```
    See Also:
    
    Constant Field Values
  - BIN8
```
private static final int BIN8
```
    See Also:
    
    Constant Field Values
  - BIN16
```
private static final int BIN16
```
    See Also:
    
    Constant Field Values
  - BIN32
```
private static final int BIN32
```
    See Also:
    
    Constant Field Values
  - EXT8
```
private static final int EXT8
```
    See Also:
    
    Constant Field Values
  - EXT16
```
private static final int EXT16
```
    See Also:
    
    Constant Field Values
  - EXT32
```
private static final int EXT32
```
    See Also:
    
    Constant Field Values
  - FLOAT32
```
private static final int FLOAT32
```
    See Also:
    
    Constant Field Values
  - FLOAT64
```
private static final int FLOAT64
```
    See Also:
    
    Constant Field Values
  - UINT8
```
private static final int UINT8
```
    See Also:
    
    Constant Field Values
  - UINT16
```
private static final int UINT16
```
    See Also:
    
    Constant Field Values
  - UINT32
```
private static final int UINT32
```
    See Also:
    
    Constant Field Values
  - UINT64
```
private static final int UINT64
```
    See Also:
    
    Constant Field Values
  - INT8
```
private static final int INT8
```
    See Also:
    
    Constant Field Values
  - INT16
```
private static final int INT16
```
    See Also:
    
    Constant Field Values
  - INT32
```
private static final int INT32
```
    See Also:
    
    Constant Field Values
  - INT64
```
private static final int INT64
```
    See Also:
    
    Constant Field Values
  - FIXEXT1
```
private static final int FIXEXT1
```
    See Also:
    
    Constant Field Values
  - FIXEXT2
```
private static final int FIXEXT2
```
    See Also:
    
    Constant Field Values
  - FIXEXT4
```
private static final int FIXEXT4
```
    See Also:
    
    Constant Field Values
  - FIXEXT8
```
private static final int FIXEXT8
```
    See Also:
    
    Constant Field Values
  - FIXEXT16
```
private static final int FIXEXT16
```
    See Also:
    
    Constant Field Values
  - STR8
```
private static final int STR8
```
    See Also:
    
    Constant Field Values
  - STR16
```
private static final int STR16
```
    See Also:
    
    Constant Field Values
  - STR32
```
private static final int STR32
```
    See Also:
    
    Constant Field Values
  - ARRAY16
```
private static final int ARRAY16
```
    See Also:
    
    Constant Field Values
  - ARRAY32
```
private static final int ARRAY32
```
    See Also:
    
    Constant Field Values
  - MAP16
```
private static final int MAP16
```
    See Also:
    
    Constant Field Values
  - MAP32
```
private static final int MAP32
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MessagePackReader
```
public MessagePackReader(javajs.api.GenericBinaryDocument binaryDoc,
                         boolean isHomogeneousArrays)
```
- Method Detail
  - readMap
```
public java.util.Map<java.lang.String,java.lang.Object> readMap()
                                                               throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - getNext
```
public java.lang.Object getNext(java.lang.Object array,
                                int pt)
                         throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - getArray
```
private java.lang.Object getArray(int n)
                           throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - getMap
```
private java.lang.Object getMap(int n)
                         throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - decode
```
public static java.lang.Object decode(byte[] b)
```
    This single method takes care of all MMTF needs. See https://github.com/rcsb/mmtf/blob/master/spec.md
    
    Parameters:
    
    b -
    
    Returns:
    
    array of int, char, or float, depending upon the type
  - getFloats
```
public static float[] getFloats(byte[] b,
                                int n,
                                float divisor)
```
    mmtf type 1 and 11 byte[4] to float32
    
    Parameters:
    
    b -
    
    n -
    
    divisor -
    
    Returns:
    
    array of floats
  - getInts
```
public static int[] getInts(byte[] b,
                            int n)
```
    mmtf types 2-4 Decode a byte array into a byte, short, or int array.
    
    Parameters:
    
    b -
    
    n -
    
    Returns:
    
    array of integers
  - rldecode32ToStr
```
public static java.lang.String[] rldecode32ToStr(byte[] b)
```
    mmtf type 5 Decode each four bytes as a 1- to 4-character string label where a 0 byte indicates end-of-string.
    
    Parameters:
    
    b - a byte array
    
    Returns:
    
    String[]
  - rldecode32ToChar
```
public static char[] rldecode32ToChar(byte[] b,
                                      int n)
```
    mmtf type 6 Decode an array of int32 using run-length decoding to one char per int.
    
    Parameters:
    
    b -
    
    n -
    
    Returns:
    
    array of characters
  - rldecode32
```
public static int[] rldecode32(byte[] b,
                               int n)
```
    mmtf type 7 Decode an array of int32 using run-length decoding.
    
    Parameters:
    
    b -
    
    n -
    
    Returns:
    
    array of integers
  - rldecode32Delta
```
public static int[] rldecode32Delta(byte[] b,
                                    int n)
```
    mmtf type 8 Decode an array of int32 using run-length decoding of a difference array.
    
    Parameters:
    
    b -
    
    n -
    
    Returns:
    
    array of integers
  - rldecodef
```
public static float[] rldecodef(byte[] b,
                                int n,
                                float divisor)
```
    mmtf type 9 Decode an array of int32 using run-length decoding and divide by a divisor to give a float32.
    
    Parameters:
    
    b -
    
    n -
    
    divisor -
    
    Returns:
    
    array of floats
  - unpack16Deltaf
```
public static float[] unpack16Deltaf(byte[] b,
                                     int n,
                                     float divisor)
```
    mmtf type 10 Decode an array of int16 using run-length decoding of a difference array.
    
    Parameters:
    
    b -
    
    n -
    
    divisor -
    
    Returns:
    
    array of floats
  - unpackf
```
public static float[] unpackf(byte[] b,
                              int nBytes,
                              int n,
                              float divisor)
```
    mmtf type 12 and 13 Unpack an array of int8 or int16 to int32 and divide to give a float32. untested
    
    Parameters:
    
    b -
    
    nBytes -
    
    n -
    
    divisor -
    
    Returns:
    
    array of floats
  - unpack
```
public static int[] unpack(byte[] b,
                           int nBytes,
                           int n)
```
    mmtf type 14 and 15 Unpack an array of int8 or int16 to int32. untested
    
    Parameters:
    
    b -
    
    nBytes -
    
    n -
    
    Returns:
    
    array of integers

Class MessagePackReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

doc

isHomo

POSITIVEFIXINT_x80

FIXMAP_xF0

FIXSTR_xE0

NEGATIVEFIXINT_xE0

DEFINITE_xE0

NIL

FALSE

TRUE

BIN8

BIN16

BIN32

EXT8

EXT16

EXT32

FLOAT32

FLOAT64

UINT8

UINT16

UINT32

UINT64

INT8

INT16

INT32

INT64

FIXEXT1

FIXEXT2

FIXEXT4

FIXEXT8

FIXEXT16

STR8

STR16

STR32

ARRAY16

ARRAY32

MAP16

MAP32

Constructor Detail

MessagePackReader

Method Detail

readMap

getNext

getArray

getMap

decode

getFloats

getInts

rldecode32ToStr

rldecode32ToChar

rldecode32

rldecode32Delta

rldecodef

unpack16Deltaf

unpackf

unpack