java.lang.Iterable<NucleotideCompound>
, Accessioned
, ProxySequenceReader<NucleotideCompound>
, Sequence<NucleotideCompound>
, SequenceReader<NucleotideCompound>
, SequenceView<NucleotideCompound>
public class RnaSequenceView extends SequenceProxyView<NucleotideCompound> implements ProxySequenceReader<NucleotideCompound>
Constructor | Description |
---|---|
RnaSequenceView(Sequence<NucleotideCompound> sourceDna) |
|
RnaSequenceView(Sequence<NucleotideCompound> sourceDna,
CompoundSet<NucleotideCompound> rnaCompounds) |
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) |
getAccession
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
countCompounds, getAsList, getCompoundSet, getInverse, getLength, getSubSequence
countCompounds, getAccession, getAsList, getBioEnd, getBioStart, getCompoundSet, getInverse, getLength, getSubSequence, getViewedSequence, iterator, setBioEnd, setBioStart
public RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
public RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)
public java.lang.String getSequenceAsString()
Sequence
getSequenceAsString
in interface Sequence<NucleotideCompound>
getSequenceAsString
in class SequenceProxyView<NucleotideCompound>
public NucleotideCompound getCompoundAt(int position)
Sequence
getCompoundAt
in interface Sequence<NucleotideCompound>
getCompoundAt
in class SequenceProxyView<NucleotideCompound>
position
- Biological index (1 to n)public int getIndexOf(NucleotideCompound compound)
Sequence
getIndexOf
in interface Sequence<NucleotideCompound>
getIndexOf
in class SequenceProxyView<NucleotideCompound>
compound
- Compounds to look forpublic int getLastIndexOf(NucleotideCompound compound)
Sequence
getLastIndexOf
in interface Sequence<NucleotideCompound>
getLastIndexOf
in class SequenceProxyView<NucleotideCompound>
compound
- Compounds to look forpublic java.util.Map<NucleotideCompound,NucleotideCompound> getRnaToDna()
public java.util.Map<NucleotideCompound,NucleotideCompound> getDnaToRna()
protected void buildTranslators()
public void setCompoundSet(CompoundSet<NucleotideCompound> compoundSet)
setCompoundSet
in interface SequenceReader<NucleotideCompound>
public void setContents(java.lang.String sequence) throws CompoundNotFoundException
setContents
in interface SequenceReader<NucleotideCompound>
CompoundNotFoundException