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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava3.core.sequence.RNASequence
public class RNASequence
RNASequence where RNACompoundSet are the allowed values
Nested Class Summary |
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Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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AbstractSequence.AnnotationType |
Constructor Summary | |
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RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader)
Create a RNA aequence from a proxy reader |
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RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader,
CompoundSet<NucleotideCompound> compoundSet)
Create a RNA sequence from a proxy reader and user defined RNA compound set |
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RNASequence(String seqString)
Create a RNA sequence from a String |
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RNASequence(String seqString,
CompoundSet<NucleotideCompound> compoundSet)
Create a RNA sequence from a string with a user defined RNA compound set |
Method Summary | |
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SequenceView<NucleotideCompound> |
getComplement()
Get the complement view of the RNA sequence |
double |
getGC()
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SequenceView<NucleotideCompound> |
getInverse()
Get the inverse view of the sequence. |
ProteinSequence |
getProteinSequence()
Get the ProteinSequence from the RNA sequence |
ProteinSequence |
getProteinSequence(TranscriptionEngine engine)
Get the ProteinSequene from the RNA sequence with user defined transcription engine |
SequenceView<NucleotideCompound> |
getReverseComplement()
Get reverse complement view of the sequence |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public RNASequence(String seqString)
seqString
- public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader)
proxyLoader
- public RNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)
seqString
- compoundSet
- public RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
proxyLoader
- compoundSet
- Method Detail |
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public SequenceView<NucleotideCompound> getReverseComplement()
public SequenceView<NucleotideCompound> getInverse()
getInverse
in interface Sequence<NucleotideCompound>
getInverse
in class AbstractSequence<NucleotideCompound>
public SequenceView<NucleotideCompound> getComplement()
public ProteinSequence getProteinSequence()
public ProteinSequence getProteinSequence(TranscriptionEngine engine)
engine
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public double getGC()
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