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java.lang.Objectorg.biojava3.core.sequence.template.AbstractSequence<NucleotideCompound>
org.biojava3.core.sequence.DNASequence
public class DNASequence
This is class should model the attributes associated with a DNA sequence
Nested Class Summary | |
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static class |
DNASequence.DNAType
The type of DNA sequence |
Nested classes/interfaces inherited from class org.biojava3.core.sequence.template.AbstractSequence |
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AbstractSequence.AnnotationType |
Constructor Summary | |
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DNASequence()
Shouldn't be used but makes it bean happy |
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DNASequence(SequenceReader<NucleotideCompound> proxyLoader)
Create a sequence where the actual storage of the sequence data is somewhere else |
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DNASequence(SequenceReader<NucleotideCompound> proxyLoader,
CompoundSet<NucleotideCompound> compoundSet)
Create a sequence from a ProxySequencereader and user defined compound set |
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DNASequence(String seqString)
String is king and create a sequence from DNA with default DNA compound set |
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DNASequence(String seqString,
CompoundSet<NucleotideCompound> compoundSet)
Create a sequence from a string with user defined compound set |
Method Summary | |
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SequenceView<NucleotideCompound> |
getComplement()
Returns a Sequence which will complement every base |
DNASequence.DNAType |
getDNAType()
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int |
getGCCount()
Get the GC count in the DNA Sequence |
SequenceView<NucleotideCompound> |
getReverse()
Returns a Sequence which runs in the current reverse order |
SequenceView<NucleotideCompound> |
getReverseComplement()
Delegates to AbstractSequence.getInverse() for the reverse complement |
RNASequence |
getRNASequence()
Return the RNASequence equivalent of the DNASequence using default Transcription Engine. |
RNASequence |
getRNASequence(Frame frame)
Allows the user to pass in the Frame shift. |
RNASequence |
getRNASequence(TranscriptionEngine engine)
Allow a user to pass in a rules engine to do the DNA to RNA translation |
RNASequence |
getRNASequence(TranscriptionEngine engine,
Frame frame)
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static void |
main(String[] args)
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void |
setDNAType(DNASequence.DNAType dnaType)
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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 DNASequence()
public DNASequence(String seqString)
seqString
- public DNASequence(SequenceReader<NucleotideCompound> proxyLoader)
proxyLoader
- public DNASequence(String seqString, CompoundSet<NucleotideCompound> compoundSet)
seqString
- compoundSet
- public DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
proxyLoader
- compoundSet
- Method Detail |
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public RNASequence getRNASequence()
public RNASequence getRNASequence(TranscriptionEngine engine)
engine
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public RNASequence getRNASequence(Frame frame)
frame
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public RNASequence getRNASequence(TranscriptionEngine engine, Frame frame)
public int getGCCount()
public SequenceView<NucleotideCompound> getReverse()
public SequenceView<NucleotideCompound> getComplement()
public SequenceView<NucleotideCompound> getReverseComplement()
AbstractSequence.getInverse()
for the reverse complement
public DNASequence.DNAType getDNAType()
public void setDNAType(DNASequence.DNAType dnaType)
dnaType
- the dnaType to setpublic static void main(String[] args)
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