Package bacnet.datamodel.sequence

Class Gene

java.lang.Object

bacnet.datamodel.sequence.Sequence

bacnet.datamodel.sequence.Gene

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

NcRNA

public class Gene
extends Sequence

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class bacnet.datamodel.sequence.Sequence

Sequence.SeqType

Field Summary

Fields inherited from class bacnet.datamodel.sequence.Sequence

ANTI_SD_SEQ, DEFAULT_LENGTH

Constructor Summary

Constructors

Constructor	Description
Gene()
Gene(String name, int from, int to, char strand)

Method Summary

Modifier and Type	Method	Description
String	getCog()
Gene	getGeneDownstream()	Return the gene downstream on the + strand
String	getGeneName()
Gene	getGeneUpstream()	Return the gene upstream on the + strand
String	getInfo()	Return a String containing getProduct() and getComment() information
int	getLengthAA()
double	getMolMass()
String	getNewLocusTag()
String	getOldLocusTag()
String	getOperon()
String	getProduct()
String	getProtein_id()
String	getRASTinfo()
static long	getSerialversionuid()
boolean	isPseudogene()
static Gene	load(String fileName)	Load a serialized Gene
void	setCog(String cog)
void	setGeneName(String geneName)
void	setLengthAA(int lengthAA)
void	setMolMass(double molMass)
void	setNewLocusTag(String newLocusTag)
void	setOldLocusTag(String oldLocusTag)
void	setOperon(String operon)
void	setProduct(String product)
void	setProtein_id(String protein_id)
void	setPseudogene(boolean pseudogene)

Methods inherited from class bacnet.datamodel.sequence.Sequence

foundSDSequence, get3UTRSequence, getBegin, getChromosome, getChromosomeID, getComment, getConservation, getConservationHashMap, getEnd, getFeature, getFeatures, getFeaturesText, getFeaturesTextForTable, getGenome, getGenomeName, getId, getLength, getName, getRef, getSDSequence, getSDSequence, getSequence, getSequenceAA, getSequenceAACurated, getSequenceAACurated, getSequenceRNA, getSignatures, getSignaturesToString, getStrand, getSynonym, getSynonymsText, getType, isEqual, isOverlap, isOverlap, isOverlapStart, isSameStrand, isStrand, overlap, save, setBegin, setChromosomeID, setComment, setConservation, setConservationHashMap, setEnd, setFeatures, setGenomeName, setId, setLength, setName, setRef, setSignatures, setStrand, setSynonym, setType, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

Gene

public Gene()

Gene

public Gene(String name,
 int from,
 int to,
 char strand)

Method Details

getGeneDownstream

public Gene getGeneDownstream()

Return the gene downstream on the + strand

Parameters:

gene -

Returns:

getGeneUpstream

public Gene getGeneUpstream()

Return the gene upstream on the + strand

Parameters:

gene -

Returns:

load

public static Gene load(String fileName)

Load a serialized Gene

Parameters:

fileName -

Returns:

getInfo

public String getInfo()

Return a String containing getProduct() and getComment() information

Returns:

getRASTinfo

public String getRASTinfo()

getGeneName

public String getGeneName()

setGeneName

public void setGeneName(String geneName)

getProduct

public String getProduct()

setProduct

public void setProduct(String product)

getProtein_id

public String getProtein_id()

setProtein_id

public void setProtein_id(String protein_id)

getLengthAA

public int getLengthAA()

setLengthAA

public void setLengthAA(int lengthAA)

getOperon

public String getOperon()

setOperon

public void setOperon(String operon)

getCog

public String getCog()

setCog

public void setCog(String cog)

getMolMass

public double getMolMass()

setMolMass

public void setMolMass(double molMass)

getOldLocusTag

public String getOldLocusTag()

setOldLocusTag

public void setOldLocusTag(String oldLocusTag)

getNewLocusTag

public String getNewLocusTag()

setNewLocusTag

public void setNewLocusTag(String newLocusTag)

getSerialversionuid

public static long getSerialversionuid()

isPseudogene

public boolean isPseudogene()

setPseudogene

public void setPseudogene(boolean pseudogene)