bioroot.strain
Class StrainBean

java.lang.Object
  bioroot.ReagentBean
      bioroot.strain.StrainBean

All Implemented Interfaces:

java.lang.Comparable

public class StrainBean

extends ReagentBean

Author:

nix Container for holding Strain information

Field Summary

Fields inherited from class bioroot.ReagentBean

log

Constructor Summary

StrainBean()

StrainBean(int id, DBUtil bioRoot)

StrainBean(java.sql.ResultSet results)

StrainBean(java.lang.String[] cells, IdNameMatch[] cellTypes, IdNameMatch[] organisms, IdNameMatch[] markerIDMatch, UserBean userBean, DBUtil bioRoot)
For bulk file upload should be 23 cells 0 Name 1 Alias 2 Source 4 Reference 5 Type Bacteria, Yeast, Worm, Insect, Plant, Fish, Cell Line, Bird, Mammal or Other 6 Recipients 7 Organism name 8 Markers names, comma seperated 9 Plasmid Ids 10 Parent Strain Ids 11 Storage Location 12 Mutagen EMS, ENU, MMS, MNU, X-ray, UV, Transposon, T-DNA, Spontaneous or Other 13 Genotype/ Background 14 Phenotype 15 Growth Conditions 16 Restock 17 Remaining Aliquots 18 Array Type Extra Chromosomal or Integration 19 Seed Type Individual Line, Individual Pool, Set of Lines, or Set of Pools 20 Cell Type (Cell Lines) 21 Passage Number ( Cell Lines) 22 Mating Type ( Yeast) diploid, a, alpha, h+, or h-) 23 Availability 24 Visibility 25 Notes

Method Summary

int	compareTo(java.lang.Object obj)
java.lang.String	getArrayType()
int	getCellTypeId()
java.lang.String	getCellTypeName(DBUtil bioRoot) Will look one time for a name, all other times will just return "".
java.lang.String	getFileName()
java.lang.String	getGenotype()
java.lang.String	getGrowthConditions()
java.lang.String	getHotLinkedParents(DBUtil bioRoot) Returns HTML parent/ strain names for display.
java.lang.String	getHotLinkedPlasmids(DBUtil bioRoot) Returns HTML plasmid names for display.
java.lang.String[]	getMarkers(DBUtil bioRoot)
java.lang.String	getMatingType()
java.lang.String	getMutagen()
java.lang.String[]	getParentConcats(DBUtil bioRoot) Returns an array of id: strainName, or empty String[]{""} if there are none.
java.lang.String	getPassageNumber()
java.lang.String	getPhenotype()
java.lang.String	getPlainTextParent() Returns plain text of parent ids for archive.
java.lang.String	getPlainTextPlasmid() Returns plain text of plasmid 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	getRecipients()
java.lang.String	getRemainingAliquots()
java.lang.String	getRestock()
java.lang.String	getSeedType()
java.lang.String	getSource()
java.lang.String	getType()
boolean	isStrainNameUnique(DBUtil bioRoot) checks to see if strain name is unique within labgroup, assumes a connection has been made
void	loadStrainBean(java.sql.ResultSet results)
boolean	saveMarkers(DBUtil bioRoot, boolean deleteOld)
boolean	saveParentIds(DBUtil bioRoot, boolean deleteOld) Can delete old strainIds from StrainParent table, and add new entries if any are present in the parentConcats.
boolean	savePlasmidIds(DBUtil bioRoot, boolean deleteOld) Can delete old plasmidIds from StrainPlasmid table, and add new entries if any are present in the plasmidConcats.
void	setArrayType(java.lang.String arrayType)
void	setCellTypeId(int tissueId)
void	setCellTypeName(java.lang.String tissueName)
void	setFileName(java.lang.String fileName)
void	setGenotype(java.lang.String genotype)
void	setGrowthConditions(java.lang.String growthConditions)
void	setMarkers(java.lang.String[] markers)
void	setMatingType(java.lang.String matingType)
void	setMutagen(java.lang.String mutagen)
void	setParentConcats(java.lang.String[] parentConcats)
void	setPassageNumber(java.lang.String passageNumber)
void	setPhenotype(java.lang.String phenotype)
void	setPlasmidConcats(java.lang.String[] plasmidConcats)
void	setRecipients(java.lang.String recipients)
void	setRemainingAliquots(java.lang.String remainingAliquots)
void	setRestock(java.lang.String restock)
void	setSeedType(java.lang.String seedType)
void	setSource(java.lang.String source)
void	setType(java.lang.String type)
boolean	submitNew(DBUtil bioRoot) Makes a new Strain table entry, don't forget to save associated markers and plasmids after updating this bean with its new id number.
boolean	updateOld(DBUtil bioRoot, UserBean submitter) Updates a Strain entry, don't forget to update markers and plasmids.
boolean	updateStrainCommonAccessFields(DBUtil bioRoot) Just updates fields that are accessible by all lab group memebers.

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

StrainBean

public StrainBean()

StrainBean

public StrainBean(int id,
                  DBUtil bioRoot)

StrainBean

public StrainBean(java.sql.ResultSet results)

StrainBean

public StrainBean(java.lang.String[] cells,
                  IdNameMatch[] cellTypes,
                  IdNameMatch[] organisms,
                  IdNameMatch[] markerIDMatch,
                  UserBean userBean,
                  DBUtil bioRoot)

For bulk file upload should be 23 cells 0 Name 1 Alias 2 Source 4 Reference 5 Type Bacteria, Yeast, Worm, Insect, Plant, Fish, Cell Line, Bird, Mammal or Other 6 Recipients 7 Organism name 8 Markers names, comma seperated 9 Plasmid Ids 10 Parent Strain Ids 11 Storage Location 12 Mutagen EMS, ENU, MMS, MNU, X-ray, UV, Transposon, T-DNA, Spontaneous or Other 13 Genotype/ Background 14 Phenotype 15 Growth Conditions 16 Restock 17 Remaining Aliquots 18 Array Type Extra Chromosomal or Integration 19 Seed Type Individual Line, Individual Pool, Set of Lines, or Set of Pools 20 Cell Type (Cell Lines) 21 Passage Number ( Cell Lines) 22 Mating Type ( Yeast) diploid, a, alpha, h+, or h-) 23 Availability 24 Visibility 25 Notes

Method Detail

compareTo

public int compareTo(java.lang.Object obj)

Specified by:

compareTo in interface java.lang.Comparable

Overrides:

compareTo in class ReagentBean

getCellTypeName

public java.lang.String getCellTypeName(DBUtil bioRoot)

Will look one time for a name, all other times will just return "".

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 StrainPlasmid 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.

getMarkers

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

setMarkers

public void setMarkers(java.lang.String[] markers)

saveMarkers

public boolean saveMarkers(DBUtil bioRoot,
                           boolean deleteOld)

getParentConcats

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

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

saveParentIds

public boolean saveParentIds(DBUtil bioRoot,
                             boolean deleteOld)

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

getHotLinkedParents

public java.lang.String getHotLinkedParents(DBUtil bioRoot)

Returns HTML parent/ strain names for display.

getPlainTextParent

public java.lang.String getPlainTextParent()

Returns plain text of parent ids for archive.

loadStrainBean

public void loadStrainBean(java.sql.ResultSet results)

submitNew

public boolean submitNew(DBUtil bioRoot)

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

updateOld

public boolean updateOld(DBUtil bioRoot,
                         UserBean submitter)

Updates a Strain entry, don't forget to update markers and plasmids.

updateStrainCommonAccessFields

public boolean updateStrainCommonAccessFields(DBUtil bioRoot)

Just updates fields that are accessible by all lab group memebers.

isStrainNameUnique

public boolean isStrainNameUnique(DBUtil bioRoot)

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

getFileName

public java.lang.String getFileName()

setFileName

public void setFileName(java.lang.String fileName)

getSource

public java.lang.String getSource()

setSource

public void setSource(java.lang.String source)

getGenotype

public java.lang.String getGenotype()

setGenotype

public void setGenotype(java.lang.String genotype)

getGrowthConditions

public java.lang.String getGrowthConditions()

setGrowthConditions

public void setGrowthConditions(java.lang.String growthConditions)

getRemainingAliquots

public java.lang.String getRemainingAliquots()

setRemainingAliquots

public void setRemainingAliquots(java.lang.String remainingAliquots)

getPassageNumber

public java.lang.String getPassageNumber()

setPassageNumber

public void setPassageNumber(java.lang.String passageNumber)

getPhenotype

public java.lang.String getPhenotype()

setPhenotype

public void setPhenotype(java.lang.String phenotype)

setPlasmidConcats

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

getRestock

public java.lang.String getRestock()

setRestock

public void setRestock(java.lang.String restock)

setCellTypeName

public void setCellTypeName(java.lang.String tissueName)

getType

public java.lang.String getType()

setType

public void setType(java.lang.String type)

getCellTypeId

public int getCellTypeId()

setCellTypeId

public void setCellTypeId(int tissueId)

getArrayType

public java.lang.String getArrayType()

setArrayType

public void setArrayType(java.lang.String arrayType)

getMatingType

public java.lang.String getMatingType()

setMatingType

public void setMatingType(java.lang.String matingType)

getMutagen

public java.lang.String getMutagen()

setMutagen

public void setMutagen(java.lang.String mutagen)

getSeedType

public java.lang.String getSeedType()

setSeedType

public void setSeedType(java.lang.String seedType)

setParentConcats

public void setParentConcats(java.lang.String[] parentConcats)

getRecipients

public java.lang.String getRecipients()

setRecipients

public void setRecipients(java.lang.String recipients)