Uses of Class
bioroot.UserBean

Packages that use UserBean

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

Uses of UserBean in bioroot

Methods in bioroot that return UserBean

static UserBean	Util.fetchUserBean(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Sets a guest user bean if there is none.
UserBean	UserRegistrationBean.getSubmitterUserBean()
UserBean	LoginBean.createUserBean(DBUtil bioRoot, java.lang.String host, java.lang.String IP)
UserBean	LoginBean.getUserBean()

Methods in bioroot with parameters of type UserBean

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.setSubmitterUserBean(UserBean bean)
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.makeHashSelectStatement(java.lang.String table, java.util.HashMap rowScore, UserBean userBean) Makes an SQL SELECT statement using a HashMap.
boolean	ReagentBean.canView(UserBean user, DBUtil bioRoot)
boolean	ReagentBean.canModifyAll(UserBean user)
boolean	ReagentBean.canModifyCommon(UserBean user)
java.lang.String[]	Preference.getVisibilities(DBUtil bioRoot, UserBean userBean)
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	GeneBean.submitNew(DBUtil bioRoot, UserBean user)
boolean	GeneBean.updateOld(DBUtil bioRoot, UserBean user)
boolean	DBUtil.canAlter(UserBean userBean, java.lang.String tableName, int id) Checks whether the user can modify or delete an item.
boolean	DBUtil.canView(UserBean user, java.lang.String tableName, int id) Checks whether the user can view an item without creating a bean, just an id
java.lang.String[]	DBUtil.canView(UserBean user, java.lang.String tableName, java.lang.String[] ids) Checks whether the user can view multiple items based on id.
boolean	DBUtil.updateCommonAccessFields(ReagentBean bean, UserBean userBean, javax.servlet.http.HttpServletRequest request) Just update the commonly accessible fields: lastUser, comments
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.
int[]	DBUtil.fetchReagentCounts(UserBean user, java.lang.String tableName) Fetches the number of reagents in the users labgroup, and the number owned by the user.
java.lang.String[]	DBUtil.fetchCellTypeConcats(int id, UserBean user) Fetches concatinate of name and notes from CellType
java.lang.String[]	DBUtil.fetchGeneConcat(int id, UserBean user) Fetches concatinate of name and notes from Gene
static java.io.File	CronArchive.makeArchive(DBUtil bioRoot, UserBean superUser) Returns null or a zip file containing a labGroup's full archive.
boolean	CellTypeBean.submitNew(DBUtil bioRoot, UserBean user)
boolean	CellTypeBean.updateOld(DBUtil bioRoot, UserBean user)
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	Archive.buildSqlStatement(UserBean user, java.lang.String tableName) Creates a sql statement for super users and standard users returns null for everyone else, lab specific.

Constructors in bioroot with parameters of type UserBean

UserRegistrationBean(UserBean user)

Uses of UserBean in bioroot.antibody

Methods in bioroot.antibody with parameters of type UserBean

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 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.
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 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.
boolean	AntibodyBean.updateOld(DBUtil bioRoot, UserBean submitter) Updates a Antibody entry, don't forget to update geneId
static void	AntibodyBase.addStrain(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static void	AntibodyBase.addPlasmid(AntibodyBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static java.lang.String	AntibodyBase.getAntibodyForm(AntibodyBean ab, DBUtil bioRoot, UserBean userBean) Returns an antibody form filled with the values in the bean.
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.

Uses of UserBean in bioroot.oligo

Methods in bioroot.oligo with parameters of type UserBean

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	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.
boolean	OligoBean.updateOld(DBUtil bioRoot, UserBean submitter)
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 UserBean

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 UserBean in bioroot.plasmid

Methods in bioroot.plasmid with parameters of type UserBean

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.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.
boolean	PlasmidBean.updateOld(DBUtil bioRoot, UserBean submitter)
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.

Constructors in bioroot.plasmid with parameters of type UserBean

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 UserBean in bioroot.strain

Methods in bioroot.strain with parameters of type UserBean

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.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.
boolean	StrainBean.updateOld(DBUtil bioRoot, UserBean submitter) Updates a Strain entry, don't forget to update markers and plasmids.
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.addPlasmid(StrainBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)
static void	NewStrain.addParent(StrainBean bean, java.util.HashMap nameValue, DBUtil bioRoot, UserBean userBean)

Constructors in bioroot.strain with parameters of type UserBean

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