Uses of Class
bioroot.DBUtil

Packages that use DBUtil

bioroot
bioroot.antibody
bioroot.oligo
bioroot.plasmid
bioroot.strain

Uses of DBUtil in bioroot

Methods in bioroot that return DBUtil

DBUtil

UserRegistrationBean.getBioroot()

Methods in bioroot with parameters of type DBUtil

static java.lang.String[]	Util.getVisibilities(UserBean userBean, DBUtil bioRoot) If user is part of an organization, it returns WWW, orgName, Lab Mates, Private.
void	UserRegistrationBean.setBioroot(DBUtil util)
int	UserBean.getLabGroupSchedule(DBUtil bioRoot)
SearchHit[]	SearchBean.searchForSimilarMatches(java.lang.String[] columns, java.lang.String[] words, DBUtil util, boolean searchForWordBoundaryMatches, UserBean userBean) Searches a list of columns for a set of words, case insensitive, %word% matches.
static java.lang.String	Search.checkPlasmidDBFile(DBUtil bioRoot) Looks for an upto date blast database file.
static java.lang.String	Search.makeMultiFASTA(java.lang.String tableName, DBUtil bioRoot)
boolean	ReagentBean.updateCommonAccessFields(DBUtil bioRoot, java.lang.String reagentType) Just updates fields that are accessible by all lab group memebers, lastUser, comments given a reagent type: Oligo or Plasmid.
boolean	ReagentBean.isReagentNameUnique(DBUtil bioRoot, java.lang.String tableName) checks to see if oligo name is unique within labgroup, assumes a connection has been made
boolean	ReagentBean.canView(UserBean user, DBUtil bioRoot)
java.lang.String	ReagentBean.getVisibility(DBUtil bioRoot)
java.lang.String	ReagentBean.getLabGroupName(DBUtil bioRoot)
java.lang.String	ReagentBean.getOwnerName(DBUtil bioRoot)
java.lang.String	ReagentBean.getOrganismName(DBUtil bioRoot)
Organization	ReagentBean.getOrganization(DBUtil bioRoot)
java.lang.String[]	Preference.getVisibilities(DBUtil bioRoot, UserBean userBean)
void	Organization.loadOrganizationInfo(DBUtil bioRoot, int labGroupId)
boolean	OrganismBean.submitNew(DBUtil bioRoot, UserBean user)
boolean	OrganismBean.updateOld(DBUtil bioRoot, UserBean user)
boolean	MarkerBean.submitNew(DBUtil bioRoot, UserBean user)
boolean	MarkerBean.updateOld(DBUtil bioRoot, UserBean user)
boolean	LoginBean.checkParams(DBUtil bioRoot)
UserBean	LoginBean.createUserBean(DBUtil bioRoot, java.lang.String host, java.lang.String IP)
boolean	GeneBean.submitNew(DBUtil bioRoot, UserBean user)
boolean	GeneBean.updateOld(DBUtil bioRoot, UserBean user)
static java.lang.String	DBUtil.buildSqlStatement(java.lang.String reagentType, UserBean user, DBUtil bioRoot, boolean descending) Creates a sql statement given a UserBean and a boolean as to whether to add a DESC to the order by where appropriate.
static boolean	CronArchive.setLastArchiveDate(LabGroup[] labGroups, DBUtil bioRoot) If archived will set that labgroups lastArchive to today
static java.io.File	CronArchive.makeArchive(DBUtil bioRoot, UserBean superUser) Returns null or a zip file containing a labGroup's full archive.
static void	CronArchive.loadSuperUserEmailAddresses(DBUtil bioRoot, LabGroup[] labGroups) Loads an array of LabGroup[] with superuser email addresses.
static LabGroup[]	CronArchive.getLabGroupsToArchive(DBUtil bioRoot) Identifies lab groups that should be archived based on their last archive date and schedule.
void	ContactBean.loadContactInfo(DBUtil bioRoot)
boolean	CellTypeBean.submitNew(DBUtil bioRoot, UserBean user)
boolean	CellTypeBean.updateOld(DBUtil bioRoot, UserBean user)
static java.util.ArrayList	Archive.fetchFiles(PlasmidBean[] plasmids, StrainBean[] strains, AntibodyBean[] antibodies, java.lang.String filePath, DBUtil bioRoot) Fetches any plasmid or strain files.
static OligoBean[]	Archive.makeOligoBeans(DBUtil bioRoot, UserBean userBean) Makes an array of all visibile OligoBeans
static PlasmidBean[]	Archive.makePlasmidBeans(DBUtil bioRoot, UserBean userBean) Makes an array of all visibile PlasmidBeans
static AntibodyBean[]	Archive.makeAntibodyBeans(DBUtil bioRoot, UserBean userBean) Makes an array of all visibile AntibodyBeans
static StrainBean[]	Archive.makeStrainBeans(DBUtil bioRoot, UserBean userBean) Makes an array of all visibile StrainBeans
static java.lang.String[]	AccountManagement.getUsers(DBUtil bioroot, int labGroupId) Returns a String[] of Users belonging to a particular labgroup.
static java.sql.ResultSet	AccountManagement.getUser(DBUtil mysql, java.lang.String login) fetch all items from a specific user

Constructors in bioroot with parameters of type DBUtil

UserBean(DBUtil db, LoginBean loginBean)

Organization(DBUtil bioRoot, int labGroupId)

OrganismBean(int id, DBUtil bioRoot)

MarkerBean(int id, DBUtil bioRoot)

GeneBean(int id, DBUtil bioRoot)

CellTypeBean(int id, DBUtil bioRoot)

Uses of DBUtil in bioroot.antibody

Methods in bioroot.antibody with parameters of type DBUtil

boolean	UseDilution.updateOld(DBUtil bioRoot)
boolean	UseDilution.submitNew(DBUtil bioRoot, int antibodyPrepId)
static void	NewAntibody.addAnAntibodyPrep(AntibodyBean bean, DBUtil bioRoot) Adds a new antibodyPrep to the AntibodyBean
static void	NewAntibody.addUseDilution(AntibodyBean bean, DBUtil bioRoot, int idAntibodyPrep) Adds a new UseDilution to the indicated AntibodyPrep
static void	NewAntibody.loadAntibodyBean(java.util.HashMap nameValue, DBUtil bioRoot, AntibodyBean ab, javax.servlet.http.HttpServletRequest request)
static void	NewAntibody.loadAntibodyPrepBeans(java.util.HashMap nameValue, DBUtil bioRoot, AntibodyBean ab, javax.servlet.http.HttpServletRequest request)
static void	AntibodySpreadSheet.makeAndSetAntibodyBeans(javax.servlet.http.HttpSession session, DBUtil bioRoot, UserBean userBean) Makes an array of AntibodyBeans based on Users AntibodyPreferences and sets them in the session.
static java.lang.String	AntibodySpreadSheet.fetchAntibodyTableRows(UserBean userBean, AntibodyBean[] beans, int[] startStop, DBUtil bioRoot, boolean checked, boolean allTabs) Returns table rows for every oligo according to a Preference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.
static int	AntibodySpreadSheet.addUseDilutionBlankLines(boolean useDilutionsPresent, java.lang.String[] items, AntibodyPrep prep, int k, DBUtil bioRoot) Adds "" to items based on the number of use dilutions present in the Antibody Prep bean.
static AntibodyBean[]	AntibodySpreadSheet.fetchAntibodyBeans(java.lang.String sql, DBUtil bioRoot) Build AntibodyBean[] from Antibody table in database.
static AntibodyBean[]	AntibodySpreadSheet.orderAntibodies(java.lang.String featureName, UserBean userBean, AntibodyBean[] beans, DBUtil bioRoot) Orders antibodys, sort of nasty, can't figure another way, reflection is way too slow.
boolean	AntibodyPrep.submitNew(DBUtil bioRoot) Makes a new AntibodyPrep table entry.
boolean	AntibodyPrep.updateOld(DBUtil bioRoot) Updates a Antibody prep entry
boolean	AntibodyPrep.saveNewUseDilutions(DBUtil bioRoot)
java.lang.String	AntibodyPrep.getOrganismName(DBUtil bioRoot)
UseDilution[]	AntibodyPrep.getUseDilutions(DBUtil bioRoot)
boolean	AntibodyPrep.updateCommonAccessFields(DBUtil bioRoot) Just updates fields that are accessible by all lab group memebers.
static java.lang.String	AntibodyModify.deleteAntibody(AntibodyBean ab, UserBean userBean, DBUtil bioRoot) Attempts to delete an antibody, if sucessful, returns a "" String, otherwise an error message.
static boolean	AntibodyModify.updateCommonAccessFields(AntibodyPrep[] preps, DBUtil bioRoot) Just update the commonly accessible fields in each antibodyPrep as well as the useDilutions.
static java.lang.String	AntibodyModify.updateAntibodyPreps(AntibodyBean bean, DBUtil bioRoot) Attempts to update the AntibodyPreps and UseDilutions in the database.
static java.lang.String	AntibodyModify.updateAntibody(AntibodyBean bean, UserBean userBean, DBUtil bioRoot) Attempts to update a AntibodyBean in the database, only checks that the name is unique if it has changed.
AntibodyPrep[]	AntibodyBean.getAntibodyPreps(DBUtil bioRoot)
java.lang.String	AntibodyBean.getGeneName(DBUtil bioRoot)
java.lang.String[]	AntibodyBean.getStrainConcats(DBUtil bioRoot) Returns an array of id: strainName, or empty String[]{""} if there are none.
boolean	AntibodyBean.saveStrainIds(DBUtil bioRoot, boolean deleteOld) Can delete old strainIds from AntibodyStrain table, and add new entries if any are present in the strainConcats.
java.lang.String	AntibodyBean.getHotLinkedStrains(DBUtil bioRoot) Returns HTML strain names for display.
java.lang.String[]	AntibodyBean.getPlasmidConcats(DBUtil bioRoot) Returns an array of id: plasmidName, or empty String[]{""} if there are none.
boolean	AntibodyBean.savePlasmidIds(DBUtil bioRoot, boolean deleteOld) Can delete old plasmidIds from AntibodyPlasmid table, and add new entries if any are present in the plasmidConcats.
java.lang.String	AntibodyBean.getHotLinkedPlasmids(DBUtil bioRoot) Returns HTML plasmid names for display.
boolean	AntibodyBean.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	AntibodyBean.saveNewAntibodyPreps(DBUtil bioRoot)
boolean	AntibodyBean.updateOld(DBUtil bioRoot, UserBean submitter) Updates a Antibody entry, don't forget to update geneId
boolean	AntibodyBean.isAntibodyNameUnique(DBUtil bioRoot) checks to see if antibody name is unique within labgroup, assumes a connection has been made
java.lang.String	AntibodyBean.getGeneId(DBUtil bioRoot)
static void	AntibodyBase.addStrain(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static void	AntibodyBase.removeStrain(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot)
static void	AntibodyBase.addPlasmid(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static void	AntibodyBase.removePlasmid(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot)
static java.lang.String	AntibodyBase.deleteUseDilutionIndex(AntibodyBean a, DBUtil bioRoot, java.util.HashMap m) Scans a hashmap for a use dilution to delete returns the index string or null.
static int	AntibodyBase.deleteAntibodyPrepIndex(AntibodyBean a, DBUtil bioRoot, java.util.HashMap m) Scans a hashmap for an antibody prep to delete returns the index number
static int	AntibodyBase.newUseDilutionIndex(AntibodyBean a, DBUtil bioRoot, java.util.HashMap m) Scans a hashmap for a newUseDilution selection, returns the index number
static java.lang.String	AntibodyBase.getAntibodyForm(AntibodyBean ab, DBUtil bioRoot, UserBean userBean) Returns an antibody form filled with the values in the bean.
static void	AntibodyBase.getAntibodyPrepForms(AntibodyBean ab, DBUtil bioRoot, java.lang.StringBuffer b)
static void	AntibodyBase.getAntibodyPrepForm(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int index)
static void	AntibodyBase.getUseDilutionForms(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int apbIndex) Pumps out useDilution forms, should always have one with each Prep
static java.lang.String	AntibodyBase.getAntibodyReport(AntibodyBean ab, DBUtil bioRoot, UserBean user, boolean commonForm) Returns an antibody report filled with the values in the bean.
static void	AntibodyBase.getAntibodyPrepReports(AntibodyBean ab, DBUtil bioRoot, java.lang.StringBuffer b, boolean commonForm)
static void	AntibodyBase.getAntibodyPrepReport(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int index, boolean commonForm)
static void	AntibodyBase.getUseDilutionReports(AntibodyPrep a, DBUtil bioRoot, java.lang.StringBuffer b, int apbIndex, boolean commonForm) Pumps out useDilution reports

Constructors in bioroot.antibody with parameters of type DBUtil

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

Uses of DBUtil in bioroot.oligo

Methods in bioroot.oligo with parameters of type DBUtil

static void	OligoSpreadSheet.makeAndSetOligoBeans(javax.servlet.http.HttpSession session, DBUtil bioRoot, UserBean userBean) Makes an array of OligoBeans based on Users OligoPreferences and sets them in the session.
static java.lang.String	OligoSpreadSheet.fetchOligoTableRows(Preference pref, OligoBean[] beans, int[] startStop, DBUtil bioRoot, boolean checked, boolean allTabs) Returns table rows for every oligo according to an OligoPreference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.
static OligoBean[]	OligoSpreadSheet.fetchOligoBeans(java.lang.String sql, DBUtil bioRoot) Build OligoBean[] from Oligo table in database.
static OligoBean[]	OligoSpreadSheet.orderOligos(java.lang.String featureName, Preference pref, OligoBean[] beans, DBUtil bioRoot) Orders oligos, sort of nasty, can't figure another way, reflection is way too slow.
static java.lang.String	OligoModify.deleteOligo(OligoBean oligoBean, UserBean userBean, DBUtil bioRoot) Attempts to delete an oligo, if sucessful, returns a "" String, otherwise an error message.
static java.lang.String	OligoModify.updateOligo(OligoBean oligoBean, UserBean userBean, javax.servlet.http.HttpServletRequest request, DBUtil bioRoot) Attempts to update an OligoBean in the database, only checks that the name is unique if it has changed.
java.lang.String	OligoBean.getGeneName(DBUtil bioRoot)
boolean	OligoBean.submitNew(DBUtil bioRoot)
boolean	OligoBean.updateOld(DBUtil bioRoot, UserBean submitter)
boolean	OligoBean.isOligoNameUnique(DBUtil bioRoot) checks to see if oligo name is unique within labgroup, assumes a connection has been made
static java.lang.String	OligoBase.getOligoReport(OligoBean ob, DBUtil bioRoot, UserBean userBean, boolean commonForm) Returns an oligo report.
static java.lang.String	OligoBase.getOligoForm(OligoBean ob, DBUtil bioRoot, UserBean userBean) Returns an oligo form filled it with the values in the oligo bean.

Constructors in bioroot.oligo with parameters of type DBUtil

OligoBean(int id, DBUtil bioRoot)

OligoBean(java.lang.String[] cells, IdNameMatch[] genes, IdNameMatch[] organisms, UserBean userBean, DBUtil bioRoot)
For bulk file upload should be 17? cells Name, Alias Oligo Sequence, Matching Gene Sequence, uM Stock Concentration, ng/uL Stock Concentration, Volume(uL), Purification, 0 1 2 3 4 5 6 7 Modifications, Orientation, Type, Storage Location, Availibility, Visibility, Handling Instructions, Target Gene Name, Organism, Notes 8 9 10 11 12 13 14 15 16 17

Uses of DBUtil in bioroot.plasmid

Methods in bioroot.plasmid with parameters of type DBUtil

static void	PlasmidSpreadSheet.makeAndSetPlasmidBeans(javax.servlet.http.HttpSession session, DBUtil bioRoot, UserBean userBean) Makes an array of PlasmidBeans based on Users PlasmidPreferences and sets them in the session.
static java.lang.String	PlasmidSpreadSheet.fetchPlasmidTableRows(UserBean userBean, PlasmidBean[] beans, int[] startStop, DBUtil bioRoot, boolean checked, boolean allTabs) Returns table rows for every oligo according to a Preference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.
static PlasmidBean[]	PlasmidSpreadSheet.fetchPlasmidBeans(java.lang.String sql, DBUtil bioRoot) Build PlasmidBean[] from Plasmid table in database.
static PlasmidBean[]	PlasmidSpreadSheet.orderPlasmids(java.lang.String featureName, UserBean userBean, PlasmidBean[] beans, DBUtil bioRoot) Orders plasmids, sort of nasty, can't figure another way, reflection is way too slow.
static java.lang.String	PlasmidModify.deletePlasmid(PlasmidBean plasmidBean, UserBean userBean, DBUtil bioRoot) Attempts to delete an plasmid, if sucessful, returns a "" String, otherwise an error message.
static java.lang.String	PlasmidModify.updatePlasmid(PlasmidBean bean, UserBean userBean, java.util.HashMap nameValue, javax.servlet.http.HttpServletRequest request, DBUtil bioRoot) Attempts to update a PlasmidBean in the database, only checks that the name is unique if it has changed.
java.lang.String	PlasmidBean.getGeneName(DBUtil bioRoot)
java.lang.String[]	PlasmidBean.getMarkers(DBUtil bioRoot)
boolean	PlasmidBean.saveMarkers(DBUtil bioRoot, boolean deleteOld)
java.lang.String[]	PlasmidBean.getStrainConcats(DBUtil bioRoot) Returns an array of id: strainName, or empty String[]{""} if there are none.
boolean	PlasmidBean.saveStrainIds(DBUtil bioRoot, boolean deleteOld) Can delete old strainIds from PlasmidStrain table, and add new entries if any are present in the strainConcats.
java.lang.String	PlasmidBean.getHotLinkedStrains(DBUtil bioRoot) Returns HTML strain names for display.
boolean	PlasmidBean.submitNew(DBUtil bioRoot)
boolean	PlasmidBean.updateOld(DBUtil bioRoot, UserBean submitter)
boolean	PlasmidBean.isPlasmidNameUnique(DBUtil bioRoot) checks to see if plasmid name is unique within labgroup, assumes a connection has been made
static java.lang.String	PlasmidBase.getPlasmidReport(PlasmidBean pb, DBUtil bioRoot, UserBean userBean, boolean commonForm) Returns an plasmid report.
static java.lang.String	PlasmidBase.getPlasmidForm(PlasmidBean ob, DBUtil bioRoot, UserBean userBean) Returns a plasmid form filled with the values in the bean.
static void	PlasmidBase.findOligos(UserBean user, PlasmidBean plasmid, DBUtil bioRoot) Uses Blast to find oligo matches to a plasmid from all the oligos in a labgroup visible to the user.
static void	PlasmidBase.findOligos(UserBean user, PlasmidBean[] plasmids, DBUtil bioRoot) Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user.
static void	PlasmidBase.findOligoMatches(UserBean user, PlasmidBean[] plasmids, DBUtil bioRoot) Uses Blast to find oligo matches to a given array of plasmid from all the oligos in a labgroup visible to the user.
static void	NewPlasmid.addStrain(PlasmidBean bean, java.util.HashMap nameValue, int labGroupId, DBUtil bioRoot)
static void	NewPlasmid.removeStrain(java.util.HashMap nameValue, PlasmidBean bean, DBUtil bioRoot)

Constructors in bioroot.plasmid with parameters of type DBUtil

PlasmidBean(int id, DBUtil bioRoot)

PlasmidBean(java.lang.String[] cells, IdNameMatch[] genes, IdNameMatch[] organisms, IdNameMatch[] markerIDMatch, UserBean userBean, DBUtil bioRoot)
For bulk file upload should be 16 cells 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Name Alias Source Recipients Reference Gene Organism Markers StrainIds Location Concentration Volume Purification Availability Visibility Notes Sequence

Uses of DBUtil in bioroot.strain

Methods in bioroot.strain with parameters of type DBUtil

static void	StrainSpreadSheet.makeAndSetStrainBeans(javax.servlet.http.HttpSession session, DBUtil bioRoot, UserBean userBean) Makes an array of StrainBeans based on Users StrainPreferences and sets them in the session.
static java.lang.String	StrainSpreadSheet.fetchStrainTableRows(UserBean userBean, StrainBean[] beans, int[] startStop, DBUtil bioRoot, boolean checked, boolean allTabs) Returns table rows for every oligo according to a Preference, if allTabs==true, then all features are returned in a tab delimited format, otherwise its HTML.
static StrainBean[]	StrainSpreadSheet.fetchStrainBeans(java.lang.String sql, DBUtil bioRoot) Build StrainBean[] from Strain table in database.
static StrainBean[]	StrainSpreadSheet.orderStrains(java.lang.String featureName, UserBean userBean, StrainBean[] beans, DBUtil bioRoot) Orders strains, sort of nasty, can't figure another way, reflection is way too slow.
static java.lang.String	StrainModify.deleteStrain(StrainBean strainBean, UserBean userBean, DBUtil bioRoot) Attempts to delete an strain, if sucessful, returns a "" String, otherwise an error message.
static boolean	StrainModify.updateStrainCommonAccessFields(StrainBean bean, UserBean userBean, java.util.HashMap nameValue, DBUtil bioRoot) Just update the commonly accessible fields: restock, lastUser, remainingAliquots, comments
static java.lang.String	StrainModify.updateStrain(StrainBean bean, UserBean userBean, java.util.HashMap nameValue, javax.servlet.http.HttpServletRequest request, DBUtil bioRoot) Attempts to update a StrainBean in the database, only checks that the name is unique if it has changed.
java.lang.String	StrainBean.getCellTypeName(DBUtil bioRoot) Will look one time for a name, all other times will just return "".
java.lang.String[]	StrainBean.getPlasmidConcats(DBUtil bioRoot) Returns an array of id: plasmidName, or empty String[]{""} if there are none.
boolean	StrainBean.savePlasmidIds(DBUtil bioRoot, boolean deleteOld) Can delete old plasmidIds from StrainPlasmid table, and add new entries if any are present in the plasmidConcats.
java.lang.String	StrainBean.getHotLinkedPlasmids(DBUtil bioRoot) Returns HTML plasmid names for display.
java.lang.String[]	StrainBean.getMarkers(DBUtil bioRoot)
boolean	StrainBean.saveMarkers(DBUtil bioRoot, boolean deleteOld)
java.lang.String[]	StrainBean.getParentConcats(DBUtil bioRoot) Returns an array of id: strainName, or empty String[]{""} if there are none.
boolean	StrainBean.saveParentIds(DBUtil bioRoot, boolean deleteOld) Can delete old strainIds from StrainParent table, and add new entries if any are present in the parentConcats.
java.lang.String	StrainBean.getHotLinkedParents(DBUtil bioRoot) Returns HTML parent/ strain names for display.
boolean	StrainBean.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	StrainBean.updateOld(DBUtil bioRoot, UserBean submitter) Updates a Strain entry, don't forget to update markers and plasmids.
boolean	StrainBean.updateStrainCommonAccessFields(DBUtil bioRoot) Just updates fields that are accessible by all lab group memebers.
boolean	StrainBean.isStrainNameUnique(DBUtil bioRoot) checks to see if strain name is unique within labgroup, assumes a connection has been made
static java.lang.String	StrainBase.getStrainReport(StrainBean sb, DBUtil bioRoot, UserBean userBean, boolean commonForm) Returns an strain report.
static java.lang.String	StrainBase.getStrainForm(StrainBean sb, DBUtil bioRoot, UserBean userBean) Returns a strain form filled with the values in the bean.
static void	NewStrain.removePlasmid(StrainBean bean, java.util.HashMap nameValue, DBUtil bioRoot)
static void	NewStrain.addPlasmid(StrainBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static void	NewStrain.removeParent(StrainBean bean, java.util.HashMap nameValue, DBUtil bioRoot)
static void	NewStrain.addParent(StrainBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)

Constructors in bioroot.strain with parameters of type DBUtil

StrainBean(int id, DBUtil bioRoot)

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