Uses of Class
bioroot.plasmid.PlasmidBean

Packages that use PlasmidBean

bioroot
bioroot.plasmid

Uses of PlasmidBean in bioroot

Methods in bioroot that return PlasmidBean

static PlasmidBean[]

Archive.makePlasmidBeans(DBUtil bioRoot, UserBean userBean) Makes an array of all visibile PlasmidBeans

Methods in bioroot with parameters of type PlasmidBean

static java.util.ArrayList

Archive.fetchFiles(PlasmidBean[] plasmids, StrainBean[] strains, AntibodyBean[] antibodies, java.lang.String filePath, DBUtil bioRoot) Fetches any plasmid or strain files.

Uses of PlasmidBean in bioroot.plasmid

Methods in bioroot.plasmid that return PlasmidBean

PlasmidBean[]	PlasmidUploadBean.getPlasmidBeans()
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 PlasmidBean[]	PlasmidBase.reversePlasmidBeans(PlasmidBean[] beans) Reverses the order of an array of PlasmidBeans.

Methods in bioroot.plasmid with parameters of type PlasmidBean

void	PlasmidUploadBean.setPlasmidBeans(PlasmidBean[] beans)
static void	PlasmidUpload.appendPlasmidBeans(javax.servlet.http.HttpSession session, PlasmidBean[] newBeans) Sets plasmidBeans attribute by appending any new beans to the beginning.
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.
static boolean	PlasmidModify.subtractAndSetPlasmidBeans(PlasmidBean[] plasmidBeans, javax.servlet.http.HttpSession session) Subtracts a bean from the PlasmidBean[] and resets it in plasmidBeansToEdit
static PlasmidBean[]	PlasmidBase.reversePlasmidBeans(PlasmidBean[] beans) Reverses the order of an array of PlasmidBeans.
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)