CachingInputStream (biojava-legacy 1.9.5 API)

java.lang.Object
- java.io.InputStream
- - org.biojava.utils.io.CachingInputStream

All Implemented Interfaces:

Closeable, AutoCloseable, Seekable
```
public class CachingInputStream
extends InputStream
implements Seekable
```
A wrapper around InputStream that provides in-memory caching of the input data. This allows it to provide a seek(long) method, which lets the user use an InputStream like a RandomAccessFile (with appropriate caveats about memory footprint, security, and performance).
This class has not been tested with very long input streams. It might choke.

Author:

Rhett Sutphin (UI CBCB)

Field Summary

Fields
Modifier and Type	Field	Description
`protected byte[]`	`cache`	The byte cache itself.
`protected InputStream`	`in`	The underlying input stream whose data we're caching
`protected int`	`ptr`	The 0-based index into cache of the _next_ byte to return.
`protected int`	`validLen`	A count of the number of bytes in `cache` that contain data read from the stream.

Constructor Summary

Constructors
Constructor Description

CachingInputStream(InputStream in)

Constructors
Constructor	Description
`CachingInputStream(InputStream in)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`expandCache(int additionalBytes)`	Expands the cache to hold some number of `additionalBytes`.
`int`	`read()`
`int`	`read(byte[] b, int start, int len)`
`void`	`seek(long pos)`	Moves the pointer in the inputstream such that the byte starting at `pos` are returned by the next read.
`long`	`skip(long num)`

Methods inherited from class java.io.InputStream
available, close, mark, markSupported, nullInputStream, read, readAllBytes, readNBytes, readNBytes, reset, transferTo

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

- Field Detail
  - cache
```
protected byte[] cache
```
    The byte cache itself.
  - ptr
```
protected int ptr
```
    The 0-based index into cache of the _next_ byte to return. If ptr == validLen, data must be read from the stream into the cache.
  - validLen
```
protected int validLen
```
    A count of the number of bytes in cache that contain data read from the stream.
  - in
```
protected InputStream in
```
    The underlying input stream whose data we're caching
- Constructor Detail
  - CachingInputStream
```
public CachingInputStream(InputStream in)
```
- Method Detail
  - seek
```
public void seek(long pos)
          throws IOException
```
    Description copied from interface: Seekable
    
    Moves the pointer in the inputstream such that the byte starting at pos are returned by the next read.
    
    Specified by:
    
    seek in interface Seekable
    
    Parameters:
    
    pos - the position to which to seek
    
    Throws:
    
    IOException - when there's an I/O problem
  - read
```
public int read()
         throws IOException
```
    Specified by:
    
    read in class InputStream
    
    Throws:
    
    IOException
  - read
```
public int read(byte[] b,
                int start,
                int len)
         throws IOException
```
    Overrides:
    
    read in class InputStream
    
    Throws:
    
    IOException
  - skip
```
public long skip(long num)
          throws IOException
```
    Overrides:
    
    skip in class InputStream
    
    Throws:
    
    IOException
  - expandCache
```
protected void expandCache(int additionalBytes)
```
    Expands the cache to hold some number of additionalBytes. Expansion is done multiplicatively for efficiency. Immediately after calling this method, you must fill the additional bytes from the stream because this method also updates validLen.

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.io.InputStream

Methods inherited from class java.lang.Object

Field Detail

cache

ptr

validLen

in

Constructor Detail

CachingInputStream

Method Detail

seek

read

read

skip

expandCache