RnaSequenceView

java.lang.Object
- org.biojava.nbio.core.sequence.template.SequenceProxyView<NucleotideCompound>
- - org.biojava.nbio.core.sequence.views.RnaSequenceView

All Implemented Interfaces:

java.lang.Iterable<NucleotideCompound>, Accessioned, ProxySequenceReader<NucleotideCompound>, Sequence<NucleotideCompound>, SequenceReader<NucleotideCompound>, SequenceView<NucleotideCompound>
```
public class RnaSequenceView
extends SequenceProxyView<NucleotideCompound>
implements ProxySequenceReader<NucleotideCompound>
```
Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

Author:

ayates

Constructor Summary

Constructors
Constructor	Description
`RnaSequenceView(Sequence<NucleotideCompound> sourceDna)`
`RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`buildTranslators()`
`NucleotideCompound`	`getCompoundAt(int position)`	Returns the Compound at the given biological index
`java.util.Map<NucleotideCompound,NucleotideCompound>`	`getDnaToRna()`
`int`	`getIndexOf(NucleotideCompound compound)`	Scans through the Sequence looking for the first occurrence of the given compound
`int`	`getLastIndexOf(NucleotideCompound compound)`	Scans through the Sequence looking for the last occurrence of the given compound
`java.util.Map<NucleotideCompound,NucleotideCompound>`	`getRnaToDna()`
`java.lang.String`	`getSequenceAsString()`	Returns the String representation of the Sequence
`void`	`setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)`
`void`	`setContents(java.lang.String sequence)`

Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned
getAccession

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

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

Methods inherited from interface org.biojava.nbio.core.sequence.template.Sequence
countCompounds, getAsList, getCompoundSet, getInverse, getLength, getSubSequence

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
  - RnaSequenceView
```
public RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
```
  - RnaSequenceView
```
public RnaSequenceView(Sequence<NucleotideCompound> sourceDna,
                       CompoundSet<NucleotideCompound> rnaCompounds)
```
- 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<NucleotideCompound>
    
    Overrides:
    
    getSequenceAsString in class SequenceProxyView<NucleotideCompound>
  - getCompoundAt
```
public NucleotideCompound getCompoundAt(int position)
```
    Description copied from interface: Sequence
    
    Returns the Compound at the given biological index
    
    Specified by:
    
    getCompoundAt in interface Sequence<NucleotideCompound>
    
    Overrides:
    
    getCompoundAt in class SequenceProxyView<NucleotideCompound>
    
    Parameters:
    
    position - Biological index (1 to n)
    
    Returns:
    
    Compound at the specified position
  - getIndexOf
```
public int getIndexOf(NucleotideCompound 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<NucleotideCompound>
    
    Overrides:
    
    getIndexOf in class SequenceProxyView<NucleotideCompound>
    
    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(NucleotideCompound 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<NucleotideCompound>
    
    Overrides:
    
    getLastIndexOf in class SequenceProxyView<NucleotideCompound>
    
    Parameters:
    
    compound - Compounds to look for
    
    Returns:
    
    Index of the last position of the compound in the sequence (1 to n)
  - getRnaToDna
```
public java.util.Map<NucleotideCompound,NucleotideCompound> getRnaToDna()
```
  - getDnaToRna
```
public java.util.Map<NucleotideCompound,NucleotideCompound> getDnaToRna()
```
  - buildTranslators
```
protected void buildTranslators()
```
  - setCompoundSet
```
public void setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)
```
    Specified by:
    
    setCompoundSet in interface SequenceReader<NucleotideCompound>
  - setContents
```
public void setContents(java.lang.String sequence)
                 throws CompoundNotFoundException
```
    Specified by:
    
    setContents in interface SequenceReader<NucleotideCompound>
    
    Throws:
    
    CompoundNotFoundException

Class RnaSequenceView

Constructor Summary

Method Summary

Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned

Methods inherited from interface java.lang.Iterable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.nbio.core.sequence.template.Sequence

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

Constructor Detail

RnaSequenceView

RnaSequenceView

Method Detail

getSequenceAsString

getCompoundAt

getIndexOf

getLastIndexOf

getRnaToDna

getDnaToRna

buildTranslators

setCompoundSet

setContents