uk.ac.roslin.ensembl.model.compara

Class HomologyAlignmentProperties

java.lang.Object

uk.ac.roslin.ensembl.model.compara.HomologyAlignmentProperties

All Implemented Interfaces:

Serializable

public class HomologyAlignmentProperties
extends Object
implements Serializable

Utility class used to hold properties of an aligned homology object (gene) in a HomologyPairRelationship. The compara database doesnt hold enough info to instantiate objects fully. Because a DAHomologyPairRelationship is typically instantiated from the compara databases - the target gene in particular is likely to not be a core-datasource aware object, and therefore species & and mapping details are only simple fields grabbed from compara: these are held in properties objects

Author:

tpaterso

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
HomologyAlignmentProperties()

Method Summary

Methods

Modifier and Type	Method and Description
String	getCigarLine()
Coordinate	getCoords()
String	getGeneID()
String	getPeptideID()
Integer	getPercentCovered()
Integer	getPercentIdentity()
Integer	getPercentSimilar()
String	getSequenceName()
String	getSpeciesName()
void	setCigarLine(String cigarLine)
void	setCoords(Coordinate coords)
void	setGeneID(String geneID)
void	setPeptideID(String peptideID)
void	setPercentCovered(Integer percentCovered)
void	setPercentIdentity(Integer percentIdentity)
void	setPercentSimilar(Integer percentSimilar)
void	setSequenceName(String seqName)
void	setSpeciesName(String speciesName)

Methods inherited from class java.lang.Object

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

Constructor Detail

HomologyAlignmentProperties

public HomologyAlignmentProperties()

Method Detail

getCigarLine

public String getCigarLine()

setCigarLine

public void setCigarLine(String cigarLine)

getGeneID

public String getGeneID()

setGeneID

public void setGeneID(String geneID)

getPeptideID

public String getPeptideID()

setPeptideID

public void setPeptideID(String peptideID)

getPercentCovered

public Integer getPercentCovered()

setPercentCovered

public void setPercentCovered(Integer percentCovered)

getPercentIdentity

public Integer getPercentIdentity()

setPercentIdentity

public void setPercentIdentity(Integer percentIdentity)

getPercentSimilar

public Integer getPercentSimilar()

setPercentSimilar

public void setPercentSimilar(Integer percentSimilar)

getSpeciesName

public String getSpeciesName()

setSpeciesName

public void setSpeciesName(String speciesName)

getSequenceName

public String getSequenceName()

setSequenceName

public void setSequenceName(String seqName)

getCoords

public Coordinate getCoords()

setCoords

public void setCoords(Coordinate coords)