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java.lang.Objectcom.compomics.util.nucleotide.NucleotideSequenceImpl
public class NucleotideSequenceImpl
This class represents a nucleotide sequence (RNA or DNA).
Constructor Summary | |
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NucleotideSequenceImpl(String aSequence)
This constructor allows the construction of an Object, wrapping a nucleotidesequence. |
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NucleotideSequenceImpl(String aSequence,
Properties aCodonUsageTable)
This constructor allows the construction of an Object, wrapping a nucleotidesequence. |
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NucleotideSequenceImpl(String aSequence,
String aCodonUsageTable)
This constructor allows the construction of an Object, wrapping a nucleotidesequence. |
Method Summary | |
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int |
getLength()
This method reports on the length of the current sequence. |
double |
getMass()
This method will return the mass for the sequence. |
String |
getReverseComplementary()
This method returns the reverse complementary strand for the sequence. |
String |
getSequence()
This method will retrieve the sequence. |
void |
setSequence(String aSequence)
This method will set the sequence. |
AASequenceImpl[] |
translate()
This method translates the specified nucleotidesequence into the six reading frames. |
Vector |
translateToStopCodonSeparatedEntries(String aDatabaseIdentifier,
String aShortOrganism)
This method translates the specified nucleotidesequence into the six reading frames. |
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 NucleotideSequenceImpl(String aSequence)
aSequence
- String with the nucleotide sequence.public NucleotideSequenceImpl(String aSequence, Properties aCodonUsageTable)
aSequence
- String with the nucleotide sequence.aCodonUsageTable
- Properties instance with the codon usage table
(triplet is key, single-letter amino acid is value).public NucleotideSequenceImpl(String aSequence, String aCodonUsageTable)
aSequence
- String with the nucleotide sequence.aCodonUsageTable
- Properties instance with the codon usage table
(triplet is key, single-letter amino acid is value).Method Detail |
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public void setSequence(String aSequence)
setSequence
in interface Sequence
aSequence
- String with the sequence.public int getLength()
getLength
in interface Sequence
public double getMass()
getMass
in interface Sequence
public String getSequence()
getSequence
in interface Sequence
public AASequenceImpl[] translate()
public Vector translateToStopCodonSeparatedEntries(String aDatabaseIdentifier, String aShortOrganism)
aDatabaseIdentifier
- String to include the database origin in the protein entry annotation.aShortOrganism
- String to include the organism origin in the protein entry annotation.
public String getReverseComplementary()
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