org.biojava3.core.sequence.views
Class RnaSequenceView

java.lang.Object
  extended by org.biojava3.core.sequence.template.SequenceProxyView<NucleotideCompound>
      extended by org.biojava3.core.sequence.views.RnaSequenceView
All Implemented Interfaces:
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
RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
           
RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)
           
 
Method Summary
protected  void buildTranslators()
           
 NucleotideCompound getCompoundAt(int position)
          Returns the Compound at the given biological index
 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
 Map<NucleotideCompound,NucleotideCompound> getRnaToDna()
           
 String getSequenceAsString()
          Returns the String representation of the Sequence
 void setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)
           
 void setContents(String sequence)
           
 
Methods inherited from class org.biojava3.core.sequence.template.SequenceProxyView
countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getInverse, getLength, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava3.core.sequence.template.Sequence
countCompounds, getAsList, getCompoundSet, getInverse, getLength, getSubSequence
 
Methods inherited from interface java.lang.Iterable
iterator
 
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned
getAccession
 

Constructor Detail

RnaSequenceView

public RnaSequenceView(Sequence<NucleotideCompound> sourceDna)

RnaSequenceView

public RnaSequenceView(Sequence<NucleotideCompound> sourceDna,
                       CompoundSet<NucleotideCompound> rnaCompounds)
Method Detail

getSequenceAsString

public 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 Map<NucleotideCompound,NucleotideCompound> getRnaToDna()

getDnaToRna

public 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(String sequence)
Specified by:
setContents in interface SequenceReader<NucleotideCompound>