com.compomics.util
Class BinaryArrayImpl

java.lang.Object
  extended by com.compomics.util.BinaryArrayImpl

public class BinaryArrayImpl
extends Object

Persistence independent object model implementation class:

Implements a binary array of the kind found in mzData/spectrumList/spectrum/mzArrayBinary or mzData/spectrumList/spectrum/intenArrayBinary.  Holds both the data itself and meta data describing the encoding of the data.

Author:
Philip Jones

Field Summary
static String BIG_ENDIAN_LABEL
          Defines the valid String indicating big endian byte order.
static int BYTES_TO_HOLD_DOUBLE
          Defines the number of bytes required in an UNENCODED byte array to hold a dingle double value.
static int BYTES_TO_HOLD_FLOAT
          Defines the number of bytes required in an UNENCODED byte array to hold a single float value.
static String DOUBLE_PRECISION
          Defines the valid String indicating the correct precision for encoded doubles.
static String FLOAT_PRECISION
          Defines the valid String indicating the correct precision for encoded floats.
protected  String iBase64String
          Represents the binary contents of the array as an array of bytes.
protected  String iDataEndian
          Represents the endian value of the binary array (mzData element .../data/endian).
protected  long iDataLength
          Represents the length of the binary array (mzData element .../data/length).
protected  String iDataPrecision
          Represents the precision of the binary array (mzData element .../data/precision).
static String LITTLE_ENDIAN_LABEL
          Defines the valid String indicating little endian byte order.
 
Constructor Summary
protected BinaryArrayImpl()
          Default constructor with protected access.
  BinaryArrayImpl(double[] doubleArray, String aDataEndian)
          Constructor that allows the creation of a BinaryArray object using an array of double values.
  BinaryArrayImpl(float[] floatArray, String aDataEndian)
          Constructor that allows the creation of a BinaryArray object using an array of float values.
  BinaryArrayImpl(String aBase64String, long aDataLength, String aDataEndian, String aDataPrecision)
          Creates an instance of this BinaryArray object, setting all fields as per description below.
 
Method Summary
 boolean equals(Object o)
          Performs equals methods dependent on values of instance variables and class of Object o.
 String getBase64String()
           
 String getDataEndian()
          Returns the endian value of the binary array (mzData element .../data/endian).
 long getDataLength()
          Returns the length of the binary array (mzData element .../data/length).
 String getDataPrecision()
          Returns the precision of the binary array (mzData element .../data/precision).
 byte[] getDecodedByteArray()
          Returns the contents of the binary array decoded using the Base64 algorithm.
 double[] getDoubleArray()
          Checks if all the necessary information is provided and then converts the decoded binary array into an array of double values (that for example could be used to draw a spectra).
 int hashCode()
           
 String toString()
          Returns a useful String representation of this Imlplementation instance that includes details of all fields.
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

BIG_ENDIAN_LABEL

public static final String BIG_ENDIAN_LABEL
Defines the valid String indicating big endian byte order.

See Also:
Constant Field Values

LITTLE_ENDIAN_LABEL

public static final String LITTLE_ENDIAN_LABEL
Defines the valid String indicating little endian byte order.

See Also:
Constant Field Values

FLOAT_PRECISION

public static final String FLOAT_PRECISION
Defines the valid String indicating the correct precision for encoded floats.

See Also:
Constant Field Values

DOUBLE_PRECISION

public static final String DOUBLE_PRECISION
Defines the valid String indicating the correct precision for encoded doubles.

See Also:
Constant Field Values

BYTES_TO_HOLD_FLOAT

public static final int BYTES_TO_HOLD_FLOAT
Defines the number of bytes required in an UNENCODED byte array to hold a single float value.

See Also:
Constant Field Values

BYTES_TO_HOLD_DOUBLE

public static final int BYTES_TO_HOLD_DOUBLE
Defines the number of bytes required in an UNENCODED byte array to hold a dingle double value.

See Also:
Constant Field Values

iBase64String

protected String iBase64String

Represents the binary contents of the array as an array of bytes. (mzData element .../binaryDataGroup.)

Note that the contents of this field can be obtained from a database by calling the java.sql.Blob.getBytes():byte[] method.


iDataLength

protected long iDataLength

Represents the length of the binary array (mzData element .../data/length).


iDataEndian

protected String iDataEndian

Represents the endian value of the binary array (mzData element .../data/endian).


iDataPrecision

protected String iDataPrecision

Represents the precision of the binary array (mzData element .../data/precision).

Constructor Detail

BinaryArrayImpl

protected BinaryArrayImpl()

Default constructor with protected access.


BinaryArrayImpl

public BinaryArrayImpl(String aBase64String,
                       long aDataLength,
                       String aDataEndian,
                       String aDataPrecision)

Creates an instance of this BinaryArray object, setting all fields as per description below.

Parameters:
aBase64String - the binary contents of the array as an array of bytes. (mzData element .../binaryDataGroup.) Note that the contents of this field can be obtained from a database by calling the java.sql.Blob.getBytes():byte[] method.
aDataLength - the length of the binary array (mzData element .../data/length).
aDataEndian - The byte order is used when reading or writing multibyte values stored as mzData element .../data/endian. Only possible values are defined by the static String members of this class 'BIG_ENDIAN_LABEL' (or "big") and 'LITTLE_ENDIAN_LABEL' (or "little").
aDataPrecision - the precision of the binary array (mzData element .../data/precision) that indicates if the array contains encoded double values or encoded float values. Only possible values for this parameter are defined byt he static String members of this class 'FLOAT_PRECISION' (or "32") and 'DOUBLE_PRECISION' (or "64").

BinaryArrayImpl

public BinaryArrayImpl(double[] doubleArray,
                       String aDataEndian)
Constructor that allows the creation of a BinaryArray object using an array of double values.

Parameters:
doubleArray - being the array of double values to be converted to base64 and placed in the mzData element .../binaryDataGroup.
aDataEndian - The byte order is used when reading or writing multibyte values stored as mzData element .../data/endian. Only possible values are defined by the static String members of this class 'BIG_ENDIAN_LABEL' (or "big") and 'LITTLE_ENDIAN_LABEL' (or "little").

BinaryArrayImpl

public BinaryArrayImpl(float[] floatArray,
                       String aDataEndian)
Constructor that allows the creation of a BinaryArray object using an array of float values.

Parameters:
floatArray - being the array of float values to be converted to base64 and placed in the mzData element .../binaryDataGroup.
aDataEndian - The byte order is used when reading or writing multibyte values stored as mzData element .../data/endian. Only possible values are defined by the static String members of this class 'BIG_ENDIAN_LABEL' (or "big") and 'LITTLE_ENDIAN_LABEL' (or "little").
Method Detail

getBase64String

public String getBase64String()

getDecodedByteArray

public byte[] getDecodedByteArray()

Returns the contents of the binary array decoded using the Base64 algorithm.

Returns:
the contents of the binary array decoded using the Base64 algorithm.

getDoubleArray

public double[] getDoubleArray()
Checks if all the necessary information is provided and then converts the decoded binary array into an array of double values (that for example could be used to draw a spectra).

Returns:
the decoded binary array converted into an array of double values.

getDataLength

public long getDataLength()

Returns the length of the binary array (mzData element .../data/length).

Returns:
Returns the length of the binary array (mzData element .../data/length).

getDataEndian

public String getDataEndian()

Returns the endian value of the binary array (mzData element .../data/endian).

Returns:
Returns the endian value of the binary array (mzData element .../data/endian).

getDataPrecision

public String getDataPrecision()

Returns the precision of the binary array (mzData element .../data/precision).

Returns:
Returns the precision of the binary array (mzData element .../data/precision).

toString

public String toString()
Returns a useful String representation of this Imlplementation instance that includes details of all fields.

Overrides:
toString in class Object
Returns:
a useful String representation of this Imlplementation instance.

equals

public boolean equals(Object o)

Performs equals methods dependent on values of instance variables and class of Object o.

Overrides:
equals in class Object
Parameters:
o - Object that this is being compared with.
Returns:
boolean indicating equality of this object with the parameter Object o

hashCode

public int hashCode()
Overrides:
hashCode in class Object


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