SeekableStream (htsjdk 2.14.3 API)

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 Summary

Fields
Modifier and Type Field Description

protected OptionalLong mark
If the stream is marked with mark(int) this represents the position() where the stream was; otherwise, this is empty.

Fields
Modifier and Type	Field	Description
`protected OptionalLong`	`mark`	If the stream is marked with `mark(int)` this represents the `position()` where the stream was; otherwise, this is empty.

Constructor Summary

Constructors
Constructor Description

SeekableStream()

Constructors
Constructor	Description
`SeekableStream()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`available()`	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
`abstract void`	`close()`
`abstract boolean`	`eof()`
`abstract String`	`getSource()`
`abstract long`	`length()`
`void`	`mark(int readlimit)`	Mark the current position of the stream.
`boolean`	`markSupported()`	Mark is always supported by any `SeekableStream`.
`abstract long`	`position()`
`abstract int`	`read(byte[] buffer, int offset, int length)`
`void`	`readFully(byte[] b)`	Read enough bytes to fill the input buffer.
`void`	`reset()`	Seeks to the marked position if set; otherwise to the beginning of the stream.
`abstract void`	`seek(long position)`	Seeks the stream to the provided position.

Methods inherited from class java.io.InputStream
read, read, readAllBytes, readNBytes, skip, transferTo

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

- Field Detail
  - mark
```
protected OptionalLong mark
```
    If the stream is marked with mark(int) this represents the position() where the stream was; otherwise, this is empty.
- Constructor Detail
  - SeekableStream
```
public SeekableStream()
```
- Method Detail
  - 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

Class SeekableStream

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.io.InputStream

Methods inherited from class java.lang.Object

Field Detail

mark

Constructor Detail

SeekableStream

Method Detail

length

position

seek

read

close

eof

getSource

readFully

available

mark

reset

markSupported