Class RnaSequenceView
- java.lang.Object
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- org.biojava.nbio.core.sequence.template.SequenceProxyView<NucleotideCompound>
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- org.biojava.nbio.core.sequence.views.RnaSequenceView
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- 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
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Constructor Summary
Constructors Constructor Description RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)
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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 indexMap<NucleotideCompound,NucleotideCompound>
getDnaToRna()
int
getIndexOf(NucleotideCompound compound)
Scans through the Sequence looking for the first occurrence of the given compoundint
getLastIndexOf(NucleotideCompound compound)
Scans through the Sequence looking for the last occurrence of the given compoundMap<NucleotideCompound,NucleotideCompound>
getRnaToDna()
String
getSequenceAsString()
Returns the String representation of the Sequencevoid
setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)
void
setContents(String sequence)
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Methods inherited from class org.biojava.nbio.core.sequence.template.SequenceProxyView
countCompounds, equals, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getInverse, getLength, getSubSequence, getViewedSequence, hashCode, iterator, setBioEnd, setBioStart
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned
getAccession
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Methods inherited from interface java.lang.Iterable
forEach, iterator, spliterator
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Methods inherited from interface org.biojava.nbio.core.sequence.template.Sequence
countCompounds, getAsList, getCompoundSet, getInverse, getLength, getSubSequence
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Constructor Detail
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RnaSequenceView
public RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
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RnaSequenceView
public RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)
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Method Detail
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getSequenceAsString
public String getSequenceAsString()
Description copied from interface:Sequence
Returns the String representation of the Sequence- Specified by:
getSequenceAsString
in interfaceSequence<NucleotideCompound>
- Overrides:
getSequenceAsString
in classSequenceProxyView<NucleotideCompound>
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getCompoundAt
public NucleotideCompound getCompoundAt(int position)
Description copied from interface:Sequence
Returns the Compound at the given biological index- Specified by:
getCompoundAt
in interfaceSequence<NucleotideCompound>
- Overrides:
getCompoundAt
in classSequenceProxyView<NucleotideCompound>
- Parameters:
position
- Biological index (1 to n)- Returns:
- Compound at the specified position
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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 interfaceSequence<NucleotideCompound>
- Overrides:
getIndexOf
in classSequenceProxyView<NucleotideCompound>
- Parameters:
compound
- Compounds to look for- Returns:
- Index of the first position of the compound in the sequence (1 to n)
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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 interfaceSequence<NucleotideCompound>
- Overrides:
getLastIndexOf
in classSequenceProxyView<NucleotideCompound>
- Parameters:
compound
- Compounds to look for- Returns:
- Index of the last position of the compound in the sequence (1 to n)
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getRnaToDna
public Map<NucleotideCompound,NucleotideCompound> getRnaToDna()
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getDnaToRna
public Map<NucleotideCompound,NucleotideCompound> getDnaToRna()
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buildTranslators
protected void buildTranslators()
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setCompoundSet
public void setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)
- Specified by:
setCompoundSet
in interfaceSequenceReader<NucleotideCompound>
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setContents
public void setContents(String sequence) throws CompoundNotFoundException
- Specified by:
setContents
in interfaceSequenceReader<NucleotideCompound>
- Throws:
CompoundNotFoundException
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