bioroot.antibody
Class AntibodyBean

java.lang.Object
  bioroot.ReagentBean
      bioroot.antibody.AntibodyBean

All Implemented Interfaces:

java.lang.Comparable

public class AntibodyBean

extends ReagentBean

Author:

nix Container for holding base Antibody information, AntibodyPreps have most of it.

Field Summary

Fields inherited from class bioroot.ReagentBean

log

Constructor Summary

AntibodyBean()

AntibodyBean(int id, DBUtil bioRoot)
Assumes id is not zero

AntibodyBean(java.sql.ResultSet results)

Method Summary

int	compareTo(java.lang.Object obj)
AntibodyPrep[]	getAntibodyPreps(DBUtil bioRoot)
java.lang.String	getAntigen()
java.lang.String	getFileName()
java.lang.String	getGeneId(DBUtil bioRoot)
java.lang.String	getGeneName(DBUtil bioRoot)
java.lang.String	getHotLinkedPlasmids(DBUtil bioRoot) Returns HTML plasmid names for display.
java.lang.String	getHotLinkedStrains(DBUtil bioRoot) Returns HTML strain names for display.
int	getNumberPrepUseLines()
java.lang.String	getOldFileName()
java.lang.String	getPlainTextPlasmid() Returns plain text of plasmid ids for archive.
java.lang.String	getPlainTextStrain() Returns plain text of strain ids for archive.
java.lang.String[]	getPlasmidConcats(DBUtil bioRoot) Returns an array of id: plasmidName, or empty String[]{""} if there are none.
java.lang.String	getSource()
java.lang.String[]	getStrainConcats(DBUtil bioRoot) Returns an array of id: strainName, or empty String[]{""} if there are none.
java.lang.String	getType()
boolean	isAntibodyNameUnique(DBUtil bioRoot) checks to see if antibody name is unique within labgroup, assumes a connection has been made
boolean	isNameChanged()
void	loadAntibodyBean(java.sql.ResultSet results)
boolean	saveNewAntibodyPreps(DBUtil bioRoot)
boolean	savePlasmidIds(DBUtil bioRoot, boolean deleteOld) Can delete old plasmidIds from AntibodyPlasmid table, and add new entries if any are present in the plasmidConcats.
boolean	saveStrainIds(DBUtil bioRoot, boolean deleteOld) Can delete old strainIds from AntibodyStrain table, and add new entries if any are present in the strainConcats.
void	setAntibodyPreps(AntibodyPrep[] antibodyPrepBeans)
void	setAntigen(java.lang.String antigen)
void	setFileName(java.lang.String fileName)
void	setGeneId(int i)
void	setGeneName(java.lang.String geneName)
void	setNameChanged(boolean nameChanged)
void	setNumberPrepUseLines(int numberPrepsUses)
void	setOldFileName(java.lang.String oldFileName)
void	setPlasmidConcats(java.lang.String[] plasmidConcats)
void	setSource(java.lang.String source)
void	setStrainConcats(java.lang.String[] strainConcats)
void	setType(java.lang.String type)
boolean	submitNew(DBUtil bioRoot) Makes a new Antibody table entry, don't forget to save associated strains and plasmids after updating this bean with its new id number.
boolean	updateOld(DBUtil bioRoot, UserBean submitter) Updates a Antibody entry, don't forget to update geneId

Methods inherited from class bioroot.ReagentBean

appendMessages, canModifyAll, canModifyCommon, canView, getAlias, getAvailability, getComments, getEditHistory, getGenericVisibility, getId, getLabGroupId, getLabGroupName, getLastUser, getLocation, getMessages, getName, getNotes, getOrderBy, getOrganismId, getOrganismName, getOrganization, getOwnerId, getOwnerName, getReference, getVisibility, isComplete, isReagentNameUnique, loadReagentBean, setAlias, setAvailability, setComments, setComplete, setEditHistory, setId, setLabGroupId, setLabGroupName, setLastUser, setLocation, setMessages, setName, setNotes, setOrderBy, setOrganismId, setOrganismName, setOwnerId, setOwnerName, setReference, setVisibility, updateCommonAccessFields

Methods inherited from class java.lang.Object

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

Constructor Detail

AntibodyBean

public AntibodyBean()

AntibodyBean

public AntibodyBean(java.sql.ResultSet results)

AntibodyBean

public AntibodyBean(int id,
                    DBUtil bioRoot)

Assumes id is not zero

Method Detail

getAntibodyPreps

public AntibodyPrep[] getAntibodyPreps(DBUtil bioRoot)

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

Overrides:

compareTo in class ReagentBean

loadAntibodyBean

public void loadAntibodyBean(java.sql.ResultSet results)

getGeneName

public java.lang.String getGeneName(DBUtil bioRoot)

getStrainConcats

public java.lang.String[] getStrainConcats(DBUtil bioRoot)

Returns an array of id: strainName, or empty String[]{""} if there are none.

saveStrainIds

public boolean saveStrainIds(DBUtil bioRoot,
                             boolean deleteOld)

Can delete old strainIds from AntibodyStrain table, and add new entries if any are present in the strainConcats.

getHotLinkedStrains

public java.lang.String getHotLinkedStrains(DBUtil bioRoot)

Returns HTML strain names for display.

getPlainTextStrain

public java.lang.String getPlainTextStrain()

Returns plain text of strain ids for archive.

getPlasmidConcats

public java.lang.String[] getPlasmidConcats(DBUtil bioRoot)

Returns an array of id: plasmidName, or empty String[]{""} if there are none.

savePlasmidIds

public boolean savePlasmidIds(DBUtil bioRoot,
                              boolean deleteOld)

Can delete old plasmidIds from AntibodyPlasmid table, and add new entries if any are present in the plasmidConcats.

getHotLinkedPlasmids

public java.lang.String getHotLinkedPlasmids(DBUtil bioRoot)

Returns HTML plasmid names for display.

getPlainTextPlasmid

public java.lang.String getPlainTextPlasmid()

Returns plain text of plasmid ids for archive.

submitNew

public boolean submitNew(DBUtil bioRoot)

Makes a new Antibody table entry, don't forget to save associated strains and plasmids after updating this bean with its new id number.

saveNewAntibodyPreps

public boolean saveNewAntibodyPreps(DBUtil bioRoot)

updateOld

public boolean updateOld(DBUtil bioRoot,
                         UserBean submitter)

Updates a Antibody entry, don't forget to update geneId

isAntibodyNameUnique

public boolean isAntibodyNameUnique(DBUtil bioRoot)

checks to see if antibody name is unique within labgroup, assumes a connection has been made

getGeneId

public java.lang.String getGeneId(DBUtil bioRoot)

getFileName

public java.lang.String getFileName()

setFileName

public void setFileName(java.lang.String fileName)

setPlasmidConcats

public void setPlasmidConcats(java.lang.String[] plasmidConcats)

getType

public java.lang.String getType()

setGeneId

public void setGeneId(int i)

setType

public void setType(java.lang.String type)

getAntigen

public java.lang.String getAntigen()

setAntigen

public void setAntigen(java.lang.String antigen)

getSource

public java.lang.String getSource()

setSource

public void setSource(java.lang.String source)

setAntibodyPreps

public void setAntibodyPreps(AntibodyPrep[] antibodyPrepBeans)

setGeneName

public void setGeneName(java.lang.String geneName)

setStrainConcats

public void setStrainConcats(java.lang.String[] strainConcats)

getOldFileName

public java.lang.String getOldFileName()

setOldFileName

public void setOldFileName(java.lang.String oldFileName)

isNameChanged

public boolean isNameChanged()

setNameChanged

public void setNameChanged(boolean nameChanged)

getNumberPrepUseLines

public int getNumberPrepUseLines()

setNumberPrepUseLines

public void setNumberPrepUseLines(int numberPrepsUses)