Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

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

java.lang.Object
  extended by 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
HomologyAlignmentProperties()
           
 
Method Summary
 Integer getCigarEnd()
           
 String getCigarLine()
           
 Integer getCigarStart()
           
 Coordinate getCoords()
           
 String getGeneID()
           
 String getPeptideID()
           
 Integer getPercentCovered()
           
 Integer getPercentIdentity()
           
 Integer getPercentSimilar()
           
 String getSequenceName()
           
 String getSpeciesName()
           
 void setCigarEnd(Integer cigarEnd)
           
 void setCigarLine(String cigarLine)
           
 void setCigarStart(Integer cigarStart)
           
 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

getCigarEnd

public Integer getCigarEnd()

setCigarEnd

public void setCigarEnd(Integer cigarEnd)

getCigarLine

public String getCigarLine()

setCigarLine

public void setCigarLine(String cigarLine)

getCigarStart

public Integer getCigarStart()

setCigarStart

public void setCigarStart(Integer cigarStart)

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)

Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3