com.hfg.bio.seq.translation

Class CodonUsage

java.lang.Object

com.hfg.bio.seq.translation.CodonUsage

public class CodonUsage
extends java.lang.Object

Codon usage data container.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	XML_BIAS_ATT
static java.lang.String	XML_CODON_USAGE
static java.lang.String	XML_FREQ_PER_1000_ATT
static java.lang.String	XML_NUMBER_ATT

Constructor Summary

Constructors

Constructor and Description
CodonUsage()
CodonUsage(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
java.lang.Float	getBias() Returns the bias - the fraction of this codon's use as compared to the other codons that code for the same amino acid.
java.lang.Float	getFreqPer1000() Returns the frequency (per 1000 codons) that this codon was observed in the set of sequences.
java.lang.Integer	getNumber() Returns the number of times this codon was observed in the set of sequences.
CodonUsage	setBias(java.lang.Float inValue) Specifies the bias - the fraction of this codon's use as compared to the other codons that code for the same amino acid.
CodonUsage	setFreqPer1000(java.lang.Float inValue) Specifies the frequency (per 1000 codons) that this codon was observed in the set of sequences.
CodonUsage	setNumber(java.lang.Integer inValue) Specifies the number of times this codon was observed in the set of sequences.
XMLTag	toXMLTag()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

XML_CODON_USAGE

public static final java.lang.String XML_CODON_USAGE

See Also:

Constant Field Values

XML_NUMBER_ATT

public static final java.lang.String XML_NUMBER_ATT

See Also:

Constant Field Values

XML_FREQ_PER_1000_ATT

public static final java.lang.String XML_FREQ_PER_1000_ATT

See Also:

Constant Field Values

XML_BIAS_ATT

public static final java.lang.String XML_BIAS_ATT

See Also:

Constant Field Values

Constructor Detail

CodonUsage

public CodonUsage()

CodonUsage

public CodonUsage(XMLTag inXMLTag)

Method Detail

setNumber

public CodonUsage setNumber(java.lang.Integer inValue)

Specifies the number of times this codon was observed in the set of sequences.

Parameters:

inValue - the number of times this codon was observed in the set of sequences

Returns:

this CodonUsage object (for potential method chaining)

getNumber

public java.lang.Integer getNumber()

Returns the number of times this codon was observed in the set of sequences.

Returns:

the number of times this codon was observed in the set of sequences

setFreqPer1000

public CodonUsage setFreqPer1000(java.lang.Float inValue)

Specifies the frequency (per 1000 codons) that this codon was observed in the set of sequences.

Parameters:

inValue - the frequency (per 1000 codons) that this codon was observed in the set of sequences

Returns:

this CodonUsage object (for potential method chaining)

getFreqPer1000

public java.lang.Float getFreqPer1000()

Returns the frequency (per 1000 codons) that this codon was observed in the set of sequences.

Returns:

the frequency (per 1000 codons) that this codon was observed in the set of sequences

setBias

public CodonUsage setBias(java.lang.Float inValue)

Specifies the bias - the fraction of this codon's use as compared to the other codons that code for the same amino acid.

Parameters:

inValue - the fraction of this codon's use out of the total for all codons coding for the same amino acid

Returns:

this CodonUsage object (for potential method chaining)

getBias

public java.lang.Float getBias()

Returns the bias - the fraction of this codon's use as compared to the other codons that code for the same amino acid.

Returns:

the fraction of this codon's use out of the total for all codons coding for the same amino acid

toXMLTag

public XMLTag toXMLTag()