BitSequenceReader (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.core.sequence.storage.BitSequenceReader<C>

Type Parameters:

C - Type of compound; must extend NucleotideCompound

All Implemented Interfaces:

Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

Direct Known Subclasses:

FourBitSequenceReader, TwoBitSequenceReader
```
public class BitSequenceReader<C extends Compound>
extends Object
implements ProxySequenceReader<C>
```
An implementation of the popular bit encodings. This class provides the Sequence view over what is actually carried out in the BitSequenceReader.BitArrayWorker instances. These are the objects that carry out array storage as well as indexing into those arrays. New bit encodings can be written by extending this class and a worker class. There are a number of issues with this type of storage engine:
- We can only support a finite number of Compounds; 2 bit allows no N compounds
- For real savings you must read the sequence in using your own Reader and a BitSequenceReader.BitArrayWorker instance
Author:

ayates

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`BitSequenceReader.BitArrayWorker<C extends Compound>` The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code.

Constructor Summary

Constructors
Constructor and Description
`BitSequenceReader(BitSequenceReader.BitArrayWorker<C> worker, AccessionID accession)` Instance which allows you to supply a different @{BitArrayWorker} object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`countCompounds(C... compounds)` Counts the number of times a compound appears in this sequence store
`boolean`	`equals(Object o)`
`AccessionID`	`getAccession()` Returns the AccessionID this location is currently bound with
`List<C>`	`getAsList()` Returns this Sequence store as a List
`C`	`getCompoundAt(int position)` Returns the compound at the specified biological index
`CompoundSet<C>`	`getCompoundSet()` Returns the compound set backing this store
`int`	`getIndexOf(C compound)` Returns the first occurrence of the given compound in this store; performs a linear search
`SequenceView<C>`	`getInverse()` Does the right thing to get the inverse of the current Sequence.
`int`	`getLastIndexOf(C compound)` Returns the last occurrence of the given compound in this store; performs a linear search
`int`	`getLength()` Returns the length of the sequence
`String`	`getSequenceAsString()` Returns the sequence as a String
`SequenceView<C>`	`getSubSequence(Integer start, Integer end)` Returns a portion of the sequence from the different positions.
`SequenceView<C>`	`getSubSequence(int start, int end)` Returns a sub sequence view
`int`	`hashCode()`
`Iterator<C>`	`iterator()` Provides basic iterable access to this class
`void`	`setCompoundSet(CompoundSet<C> compoundSet)` Class is immutable & so this is unsupported
`void`	`setContents(String sequence)` Class is immutable & so this is unsupported

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Constructor Detail
  - BitSequenceReader
```
public BitSequenceReader(BitSequenceReader.BitArrayWorker<C> worker,
                         AccessionID accession)
```
    Instance which allows you to supply a different @{BitArrayWorker} object.
- Method Detail
  - setCompoundSet
```
public void setCompoundSet(CompoundSet<C> compoundSet)
```
    Class is immutable & so this is unsupported
    
    Specified by:
    
    setCompoundSet in interface SequenceReader<C extends Compound>
  - setContents
```
public void setContents(String sequence)
                 throws CompoundNotFoundException
```
    Class is immutable & so this is unsupported
    
    Specified by:
    
    setContents in interface SequenceReader<C extends Compound>
    
    Throws:
    
    CompoundNotFoundException
  - countCompounds
```
public int countCompounds(C... compounds)
```
    Counts the number of times a compound appears in this sequence store
    
    Specified by:
    
    countCompounds in interface Sequence<C extends Compound>
    
    Parameters:
    
    compounds - Vargs of the compounds to count
    
    Returns:
    
    Number of times a compound was found
  - getAccession
```
public AccessionID getAccession()
```
    Description copied from interface: Accessioned
    
    Returns the AccessionID this location is currently bound with
    
    Specified by:
    
    getAccession in interface Accessioned
  - getAsList
```
public List<C> getAsList()
```
    Returns this Sequence store as a List
    
    Specified by:
    
    getAsList in interface Sequence<C extends Compound>
  - getCompoundAt
```
public C getCompoundAt(int position)
```
    Returns the compound at the specified biological index
    
    Specified by:
    
    getCompoundAt in interface Sequence<C extends Compound>
    
    Parameters:
    
    position - Biological index (1 to n)
    
    Returns:
    
    Compound at the specified position
  - getCompoundSet
```
public CompoundSet<C> getCompoundSet()
```
    Returns the compound set backing this store
    
    Specified by:
    
    getCompoundSet in interface Sequence<C extends Compound>
  - getIndexOf
```
public int getIndexOf(C compound)
```
    Returns the first occurrence of the given compound in this store; performs a linear search
    
    Specified by:
    
    getIndexOf in interface Sequence<C extends Compound>
    
    Parameters:
    
    compound - Compounds to look for
    
    Returns:
    
    Index of the first position of the compound in the sequence (1 to n)
  - getLastIndexOf
```
public int getLastIndexOf(C compound)
```
    Returns the last occurrence of the given compound in this store; performs a linear search
    
    Specified by:
    
    getLastIndexOf in interface Sequence<C extends Compound>
    
    Parameters:
    
    compound - Compounds to look for
    
    Returns:
    
    Index of the last position of the compound in the sequence (1 to n)
  - getLength
```
public int getLength()
```
    Returns the length of the sequence
    
    Specified by:
    
    getLength in interface Sequence<C extends Compound>
  - getSequenceAsString
```
public String getSequenceAsString()
```
    Returns the sequence as a String
    
    Specified by:
    
    getSequenceAsString in interface Sequence<C extends Compound>
  - getSubSequence
```
public SequenceView<C> getSubSequence(int start,
                                      int end)
```
    Returns a sub sequence view
  - iterator
```
public Iterator<C> iterator()
```
    Provides basic iterable access to this class
    
    Specified by:
    
    iterator in interface Iterable<C extends Compound>
  - getSubSequence
```
public SequenceView<C> getSubSequence(Integer start,
                                      Integer end)
```
    Description copied from interface: Sequence
    
    Returns a portion of the sequence from the different positions. This is indexed from 1
    
    Specified by:
    
    getSubSequence in interface Sequence<C extends Compound>
    
    Parameters:
    
    start - Biological index start; must be greater than 0
    
    end - Biological end; must be less than length + 1
    
    Returns:
    
    A SequenceView of the offset
  - getInverse
```
public SequenceView<C> getInverse()
```
    Description copied from interface: Sequence
    
    Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.
    
    Specified by:
    
    getInverse in interface Sequence<C extends Compound>
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object

Class BitSequenceReader<C extends Compound>

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

BitSequenceReader

Method Detail

setCompoundSet

setContents

countCompounds

getAccession

getAsList

getCompoundAt

getCompoundSet

getIndexOf

getLastIndexOf

getLength

getSequenceAsString

getSubSequence

iterator

getSubSequence

getInverse

hashCode

equals