Package htsjdk.samtools.util

Class BinaryCodec

java.lang.Object
htsjdk.samtools.util.BinaryCodec
All Implemented Interfaces:
Closeable, AutoCloseable
public class BinaryCodec extends Object implements Closeable
Encapsulates file representation of various primitive data types. Forces little-endian disk representation. Note that this class is currently not very efficient. There are plans to increase the size of the ByteBuffer, and move data between the ByteBuffer and the underlying input or output stream in larger chunks. All the read methods throw RuntimeEOFException if the input stream is exhausted before the required number of bytes are read.

  • Field Details

  • Constructor Details

    • BinaryCodec

      public BinaryCodec(Path path, boolean writing)
      Constructs BinaryCodec from a file and set its mode to writing or not
      Parameters:
      path - file to be written to or read from
      writing - whether the file is being written to

    • BinaryCodec

      public BinaryCodec(File file, boolean writing)
      Constructs BinaryCodec from a file and set its mode to writing or not
      Parameters:
      file - file to be written to or read from
      writing - whether the file is being written to

    • BinaryCodec

      public BinaryCodec(String fileName, boolean writing)
      Constructs BinaryCodec from a file name and set its mode to writing or not
      Parameters:
      fileName - name of the file to be written to or read from
      writing - writing whether the file is being written to

    • BinaryCodec

      public BinaryCodec(OutputStream outputStream)
      Constructs BinaryCodec from an output stream
      Parameters:
      outputStream - Stream to write to, since it's an output stream we know that isWriting should be set to true

    • BinaryCodec

      public BinaryCodec(InputStream inputStream)
      Constructs BinaryCodec from an input stream
      Parameters:
      inputStream - Stream to read from, since we are reading isWriting is set to false

    • BinaryCodec

      public BinaryCodec()
      Ambiguous whether reading or writing until set{In,Out}putStream is called

  • Method Details

    • writeByte

      public void writeByte(byte bite)
      Writes a byte to the output buffer
      Parameters:
      bite - byte array to write

    • writeByte

      public void writeByte(int b)

    • writeBytes

      public void writeBytes(byte[] bytes)
      Writes a byte array to the output buffer
      Parameters:
      bytes - value to write

    • writeBytes

      public void writeBytes(byte[] bytes, int startOffset, int numBytes)

    • writeInt

      public void writeInt(int value)
      Write a 32-bit int to the output stream
      Parameters:
      value - int to write

    • writeDouble

      public void writeDouble(double value)
      Write a double (8 bytes) to the output stream
      Parameters:
      value - double to write

    • writeLong

      public void writeLong(long value)
      Write a 64-bit long to the output stream
      Parameters:
      value - long to write

    • writeShort

      public void writeShort(short value)
      Write a 16-bit short to output stream

    • writeFloat

      public void writeFloat(float value)
      Write a float (4 bytes) to the output stream
      Parameters:
      value - float to write

    • writeBoolean

      public void writeBoolean(boolean value)
      Writes a boolean (1 byte) to the output buffer
      Parameters:
      value - boolean to write

    • writeString

      public void writeString(String value, boolean writeLength, boolean appendNull)
      Writes a string to the buffer as ASCII bytes
      Parameters:
      value - string to write to buffer
      writeLength - prefix the string with the length as a 32-bit int
      appendNull - add a null byte to the end of the string

    • writeUByte

      public void writeUByte(short val)
      Write an 8-bit unsigned byte. NOTE: This method will break if we change to big-endian.

    • writeUShort

      public void writeUShort(int val)
      Write a 16-bit unsigned short. NOTE: This method will break if we change to big-endian.

    • writeUInt

      public void writeUInt(long val)
      Write a 32-bit unsigned int. NOTE: This method will break if we change to big-endian.

    • readBytes

      public void readBytes(byte[] buffer)
      Read a byte array from the input stream.
      Throws:
      RuntimeEOFException - if fewer than buffer.length bytes to read

    • readBytes

      public void readBytes(byte[] buffer, int offset, int length)
      Read a byte array from the input stream
      Parameters:
      buffer - where to put bytes read
      offset - offset to start putting bytes into buffer
      length - number of bytes to read
      Throws:
      RuntimeEOFException - if fewer than length bytes to read

    • readBytesOrFewer

      public int readBytesOrFewer(byte[] buffer, int offset, int length)
      Reads a byte array from the input stream.
      Parameters:
      buffer - where to put bytes read
      offset - offset to start putting bytes into buffer
      length - number of bytes to read. Fewer bytes may be read if EOF is reached before length bytes have been read.
      Returns:
      the total number of bytes read into the buffer, or -1 if there is no more data because the end of the stream has been reached.

    • readByte

      public byte readByte()
      Returns:
      a single byte read from the input stream.

    • knownAtEof

      public boolean knownAtEof()
      Returns:
      true if it is possible to know for sure if at EOF, and it is known for sure. If the input stream is a ByteArrayInputStream, this is faster than causing a RuntimeEOFException to be thrown.

    • readString

      public String readString(int length)
      Read a string off the input stream, as ASCII bytes
      Parameters:
      length - length of string to read
      Returns:
      String read from stream

    • readNullTerminatedString

      public String readNullTerminatedString()
      Read ASCII bytes from the input stream until a null byte is read
      Returns:
      String constructed from the ASCII bytes read

    • readLengthAndString

      public String readLengthAndString(boolean devourNull)
      Read an int length, and then a String of that length
      Parameters:
      devourNull - if true, the length include a null terminator, which is read and discarded

    • readInt

      public int readInt()
      Read an int off the input stream
      Returns:
      int from input stream

    • readDouble

      public double readDouble()
      Reads a double off the input stream
      Returns:
      double

    • readLong

      public long readLong()
      Reads a long off the input stream
      Returns:
      long

    • readShort

      public short readShort()

    • readFloat

      public float readFloat()
      Reads a float off the input stream
      Returns:
      float

    • readBoolean

      public boolean readBoolean()
      Reads a boolean off the input stream, represented as a byte with value 1 or 0
      Returns:
      boolean

    • readUByte

      public short readUByte()
      Reads an 8-bit unsigned byte from the input stream. This method assumes little-endianness.

    • readUShort

      public int readUShort()
      Reads a 16-bit unsigned short from the input stream. This method assumes little-endianness.

    • readUInt

      public long readUInt()
      Reads a 32-bit unsigned int from the input stream. This method assumes little-endianness.

    • close

      public void close()
      Close the appropriate stream
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable

    • getInputFileName

      public String getInputFileName()

    • getOutputFileName

      public String getOutputFileName()

    • setOutputFileName

      public void setOutputFileName(String outputFileName)

    • setInputFileName

      public void setInputFileName(String inputFileName)

    • isWriting

      public boolean isWriting()

    • getOutputStream

      public OutputStream getOutputStream()

    • getInputStream

      public InputStream getInputStream()

    • setInputStream

      public void setInputStream(InputStream is)

    • setOutputStream

      public void setOutputStream(OutputStream os)