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java.lang.Objectcom.compomics.util.nucleotide.NucleotideSequence
public class NucleotideSequence
This class combines a protein Header with a nucleotide sequence. Header is in Protein package for historical reasons.
Constructor Summary | |
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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. |
Method Summary | |
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Header |
getHeader()
This method reports on the nucleotide header. |
long |
getLength()
This method reports on the length of the sequence for the current nucleotide sequence. |
double |
getMass()
This method returns the nucleotide sequence weight in Da. |
NucleotideSequenceImpl |
getSequence()
This method reports on the nucleotide sequence. |
void |
setHeader(Header aHeader)
This method sets the header. |
void |
setSequence(NucleotideSequenceImpl aSequence)
This method allows the setting of a sequence. |
Protein[] |
translate()
This method translates the nucleotide sequence in six reading frames. |
void |
writeToFASTAFile(PrintWriter aOut)
This method can be used to append this nucleotide sequence to the FASTA DB flatfile the PrintWriter points to. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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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.Method Detail |
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public NucleotideSequenceImpl getSequence()
public void setSequence(NucleotideSequenceImpl aSequence)
aSequence
- NucleotideSequenceImpl with the sequence.public Header getHeader()
public void setHeader(Header aHeader)
public 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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