public class NucleotideSequence extends Object
Constructor and Description |
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NucleotideSequence(Header aHeader,
NucleotideSequenceImpl aSequence)
This constructor allows the passing of a Header, as well as an
AASequenceImpl for this Protein.
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NucleotideSequence(NucleotideSequenceImpl aSequence)
This constructor requires a NucleotideSequenceImpl as argument.
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NucleotideSequence(String aFASTAString)
This constructor allows for the construction of a NucleotideSequence instance
by passing a FASTA entry.
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NucleotideSequence(String aHeader,
String aSequence)
This constructor allows for the construction of a NucleotideSequence instance through the
passing of a NucleotideSequence String and a Sequence String.
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Modifier and Type | Method and Description |
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Header |
getHeader()
This method reports on the nucleotide header.
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long |
getLength()
This method reports on the length of the sequence for the current nucleotide sequence.
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double |
getMass()
This method returns the nucleotide sequence weight in Da.
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NucleotideSequenceImpl |
getSequence()
This method reports on the nucleotide sequence.
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void |
setHeader(Header aHeader)
This method sets the header.
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void |
setSequence(NucleotideSequenceImpl aSequence)
This method allows the setting of a sequence.
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Protein[] |
translate()
This method translates the nucleotide sequence in six reading frames.
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void |
writeToFASTAFile(PrintWriter aOut)
This method can be used to append this nucleotide sequence to the
FASTA DB flatfile the PrintWriter points to.
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public NucleotideSequence(NucleotideSequenceImpl aSequence)
aSequence
- NucleotideSequenceImpl around which this NucleotideSequence will be built.public NucleotideSequence(Header aHeader, NucleotideSequenceImpl aSequence)
aHeader
- Header with the header information for this NucleotideSequence.aSequence
- NucleotideSequenceImpl with the sequence for this NucleotideSequence.public NucleotideSequence(String aFASTAString)
aFASTAString
- String with the FASTA representation of the NucleotideSequence.public NucleotideSequence(String aHeader, String aSequence)
aHeader
- String with the header (can be 'null').aSequence
- String with the sequence.public NucleotideSequenceImpl getSequence()
public void setSequence(NucleotideSequenceImpl aSequence)
aSequence
- NucleotideSequenceImpl with the sequence.public Header getHeader()
public void setHeader(Header aHeader)
aHeader
- the headerpublic long getLength()
public double getMass()
public void writeToFASTAFile(PrintWriter aOut) throws IOException
aOut
- PrintWriter to write the file to.IOException
- when the writing failed.public Protein[] translate()
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