ComplementSequenceView

java.lang.Object
- org.biojava.nbio.core.sequence.template.SequenceProxyView<C>
- - org.biojava.nbio.core.sequence.views.ComplementSequenceView<C>

Type Parameters:

C - Must be a subtype of @{link ComplementCompound} since only those support complements

All Implemented Interfaces:

java.lang.Iterable<C>, Accessioned, Sequence<C>, SequenceView<C>
```
public class ComplementSequenceView<C extends ComplementCompound>
extends SequenceProxyView<C>
```
For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g. base A will become base T

Author:

Andy Yates

Constructor Summary

Constructors
Constructor Description

ComplementSequenceView(Sequence<C> sequence)

Constructors
Constructor	Description
`ComplementSequenceView(Sequence<C> sequence)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`C`	`getCompoundAt(int position)`	Returns the Compound at the given biological index
`int`	`getIndexOf(C compound)`	Scans through the Sequence looking for the first occurrence of the given compound
`int`	`getLastIndexOf(C compound)`	Scans through the Sequence looking for the last occurrence of the given compound
`java.lang.String`	`getSequenceAsString()`	Returns the String representation of the Sequence

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

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

Methods inherited from class org.biojava.nbio.core.sequence.template.SequenceProxyView
countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getInverse, getLength, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart

- Constructor Detail
  - ComplementSequenceView
```
public ComplementSequenceView(Sequence<C> sequence)
```
- Method Detail
  - getSequenceAsString
```
public java.lang.String getSequenceAsString()
```
    Description copied from interface: Sequence
    
    Returns the String representation of the Sequence
    
    Specified by:
    
    getSequenceAsString in interface Sequence<C extends ComplementCompound>
    
    Overrides:
    
    getSequenceAsString in class SequenceProxyView<C extends ComplementCompound>
  - 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 ComplementCompound>
    
    Overrides:
    
    getCompoundAt in class SequenceProxyView<C extends ComplementCompound>
    
    Parameters:
    
    position - Biological index (1 to n)
    
    Returns:
    
    Compound at the specified position
  - 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 ComplementCompound>
    
    Overrides:
    
    getIndexOf in class SequenceProxyView<C extends ComplementCompound>
    
    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 ComplementCompound>
    
    Overrides:
    
    getLastIndexOf in class SequenceProxyView<C extends ComplementCompound>
    
    Parameters:
    
    compound - Compounds to look for
    
    Returns:
    
    Index of the last position of the compound in the sequence (1 to n)

Class ComplementSequenceView<C extends ComplementCompound>

Constructor Summary

Method Summary

Methods inherited from interface java.lang.Iterable

Methods inherited from class java.lang.Object

Methods inherited from class org.biojava.nbio.core.sequence.template.SequenceProxyView

Constructor Detail

ComplementSequenceView

Method Detail

getSequenceAsString

getCompoundAt

getIndexOf

getLastIndexOf