JoiningSequenceReader (biojava 5.3.0 API)

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

Type Parameters:

C - Tyoe of compound to hold

All Implemented Interfaces:

Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>
```
public class JoiningSequenceReader<C extends Compound>
extends Object
implements ProxySequenceReader<C>
```
This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence. The code takes in any number of sequences, records the minimum and maximum bounds each sequence covers with respect to 1 position indexing and then binary searches these when a position is requested. Because of this 0 length Sequences are excluded during construction. Performance is not as good as if you are using a flat sequence however the speed of lookup is more than adaquate for most situations. Using the iterator gives the best performance as this does not rely on the binary search mechanism instead iterating through each sequence in turn.

Author:

ayates

Constructor Summary

Constructors
Constructor and Description
`JoiningSequenceReader(CompoundSet<C> compoundSet, List<Sequence<C>> sequences)`
`JoiningSequenceReader(CompoundSet<C> compoundSet, Sequence<C>... sequences)`
`JoiningSequenceReader(List<Sequence<C>> sequences)` Allows creation of the store from List>.
`JoiningSequenceReader(Sequence<C>... sequences)` Allows creation of the store from Vargs Sequence objects.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`countCompounds(C... compounds)` Returns the number of times we found a compound in the Sequence
`boolean`	`equals(Object o)`
`AccessionID`	`getAccession()` Returns the AccessionID this location is currently bound with
`List<C>`	`getAsList()` Returns the Sequence as a List of compounds
`C`	`getCompoundAt(int position)` Returns the Compound at the given biological index
`CompoundSet<C>`	`getCompoundSet()` Gets the compound set used to back this Sequence
`int`	`getIndexOf(C compound)` Scans through the Sequence looking for the first occurrence of the given compound
`SequenceView<C>`	`getInverse()` Does the right thing to get the inverse of the current Sequence.
`int`	`getLastIndexOf(C compound)` Scans through the Sequence looking for the last occurrence of the given compound
`int`	`getLength()` Returns the length of the Sequence
`String`	`getSequenceAsString()` Returns the String representation of the Sequence
`SequenceView<C>`	`getSubSequence(Integer start, Integer end)` Returns a portion of the sequence from the different positions.
`int`	`hashCode()`
`Iterator<C>`	`iterator()` Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
`void`	`setCompoundSet(CompoundSet<C> compoundSet)`
`void`	`setContents(String sequence)`

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
  - JoiningSequenceReader
```
public JoiningSequenceReader(Sequence<C>... sequences)
```
    Allows creation of the store from Vargs Sequence objects. CompoundSet defaults to the first element of the array (assuming there are elements available during construction otherwise we will throw an illegal state exception).
  - JoiningSequenceReader
```
public JoiningSequenceReader(List<Sequence<C>> sequences)
```
    Allows creation of the store from List>. CompoundSet defaults to the first element of the List (assuming there are elements available during construction otherwise we will throw an illegal state exception).
  - JoiningSequenceReader
```
public JoiningSequenceReader(CompoundSet<C> compoundSet,
                             Sequence<C>... sequences)
```
  - JoiningSequenceReader
```
public JoiningSequenceReader(CompoundSet<C> compoundSet,
                             List<Sequence<C>> sequences)
```
- Method Detail
  - getCompoundAt
```
public C getCompoundAt(int position)
```
    Description copied from interface: Sequence
    
    Returns the Compound at the given 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()
```
    Description copied from interface: Sequence
    
    Gets the compound set used to back this Sequence
    
    Specified by:
    
    getCompoundSet in interface Sequence<C extends Compound>
  - getLength
```
public int getLength()
```
    Description copied from interface: Sequence
    
    Returns the length of the Sequence
    
    Specified by:
    
    getLength in interface Sequence<C extends Compound>
  - iterator
```
public Iterator<C> iterator()
```
    Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
    
    Specified by:
    
    iterator in interface Iterable<C extends Compound>
  - setCompoundSet
```
public void setCompoundSet(CompoundSet<C> compoundSet)
```
    Specified by:
    
    setCompoundSet in interface SequenceReader<C extends Compound>
  - setContents
```
public void setContents(String sequence)
                 throws CompoundNotFoundException
```
    Specified by:
    
    setContents in interface SequenceReader<C extends Compound>
    
    Throws:
    
    CompoundNotFoundException
  - countCompounds
```
public int countCompounds(C... compounds)
```
    Description copied from interface: Sequence
    
    Returns the number of times we found a compound in the Sequence
    
    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()
                         throws UnsupportedOperationException
```
    Description copied from interface: Accessioned
    
    Returns the AccessionID this location is currently bound with
    
    Specified by:
    
    getAccession in interface Accessioned
    
    Throws:
    
    UnsupportedOperationException
  - getAsList
```
public List<C> getAsList()
```
    Description copied from interface: Sequence
    
    Returns the Sequence as a List of compounds
    
    Specified by:
    
    getAsList in interface Sequence<C extends Compound>
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - getIndexOf
```
public int getIndexOf(C compound)
```
    Description copied from interface: Sequence
    
    Scans through the Sequence looking for the first occurrence of the given compound
    
    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)
```
    Description copied from interface: Sequence
    
    Scans through the Sequence looking for the last occurrence of the given compound
    
    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)
  - getSequenceAsString
```
public String getSequenceAsString()
```
    Description copied from interface: Sequence
    
    Returns the String representation of the Sequence
    
    Specified by:
    
    getSequenceAsString in interface Sequence<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>

Class JoiningSequenceReader<C extends Compound>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Detail

JoiningSequenceReader

JoiningSequenceReader

JoiningSequenceReader

JoiningSequenceReader

Method Detail

getCompoundAt

getCompoundSet

getLength

iterator

setCompoundSet

setContents

countCompounds

getAccession

getAsList

equals

hashCode

getIndexOf

getLastIndexOf

getSequenceAsString

getSubSequence

getInverse