Package htsjdk.samtools.seekablestream

Class SeekableStream

java.lang.Object
java.io.InputStream
htsjdk.samtools.seekablestream.SeekableStream
All Implemented Interfaces:
Closeable, AutoCloseable
Direct Known Subclasses:
ByteArraySeekableStream, SeekableBufferedStream, SeekableFileStream, SeekableFTPStream, SeekableHTTPStream, SeekableMemoryStream, SeekablePathStream
public abstract class SeekableStream extends InputStream
InputStream with random access support (seek).

SeekableStream provides an interface for random access support in InputStream, thought the implementation of seek(long). As a random access stream, it supports mark by design, being able to seek to a concrete position.

  • Field Details

  • Constructor Details

    • SeekableStream

      public SeekableStream()

  • Method Details

    • length

      public abstract long length()
      Returns:
      the length of the stream; 0 if not available or empty.

    • position

      public abstract long position() throws IOException
      Returns:
      the current byte position of the stream.
      Throws:
      IOException

    • seek

      public abstract void seek(long position) throws IOException
      Seeks the stream to the provided position.
      Throws:
      IOException

    • read

      public abstract int read(byte[] buffer, int offset, int length) throws IOException
      Overrides:
      read in class InputStream
      Throws:
      IOException

    • close

      public abstract void close() throws IOException
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Overrides:
      close in class InputStream
      Throws:
      IOException

    • eof

      public abstract boolean eof() throws IOException
      Returns:
      true if the stream is already consumed; false otherwise.
      Throws:
      IOException

    • getSource

      public abstract String getSource()
      Returns:
      String representation of source (e.g. URL, file path, etc.), or null if not available.

    • readFully

      public void readFully(byte[] b) throws IOException
      Read enough bytes to fill the input buffer.
      Parameters:
      b -
      Throws:
      EOFException - If EOF is reached before buffer is filled
      IOException

    • available

      public int available() throws IOException
      The return value of this method is unusable for any purpose, and we are only implementing it because certain Java classes like GZIPInputStream incorrectly rely on it to detect EOF

      If eof() == true, 0 bytes are available. Otherwise, available bytes are the difference between the length of the stream (length()) and the current position (position().

      Overrides:
      available in class InputStream
      Returns:
      0 if the end of the file has been reached or the length cannot be determined; number of bytes remaining in the stream otherwise.
      Throws:
      IOException

    • mark

      public final void mark(int readlimit)
      Mark the current position of the stream.

      Note: there is no limit for reading.

      Overrides:
      mark in class InputStream
      Parameters:
      readlimit - ignored.
      Throws:
      RuntimeIOException - if an IO error occurs other than an already closed stream.

    • reset

      public void reset() throws IOException
      Seeks to the marked position if set; otherwise to the beginning of the stream.
      Overrides:
      reset in class InputStream
      Throws:
      IOException

    • markSupported

      public final boolean markSupported()
      Mark is always supported by any SeekableStream.
      Overrides:
      markSupported in class InputStream