A B C D E F G H I J K L M N O P Q R S T U V W X Z

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UCSCGeneLine - class util.bio.parsers.UCSCGeneLine.

UCSCGeneLine(String[], int) - Constructor for class util.bio.parsers.UCSCGeneLine

UCSCGeneLineComparator - class util.bio.parsers.UCSCGeneLineComparator.

UCSCGeneLineComparator() - Constructor for class util.bio.parsers.UCSCGeneLineComparator

UCSCGeneModelTableReader - class util.bio.parsers.UCSCGeneModelTableReader.

Parses a UCSC gene model table file, use table options for #hg17.refGene.name hg17.refLink.product hg17.geneName.name hg17.refSeqSummary.summary...

UCSCGeneModelTableReader(File, int) - Constructor for class util.bio.parsers.UCSCGeneModelTableReader

UseDilution - class bioroot.antibody.UseDilution.

UseDilution(ResultSet, int) - Constructor for class bioroot.antibody.UseDilution

UseDilution() - Constructor for class bioroot.antibody.UseDilution

UserBean - class bioroot.UserBean.

User information.

UserBean() - Constructor for class bioroot.UserBean

UserBean(DBUtil, LoginBean) - Constructor for class bioroot.UserBean

UserRegistration - class bioroot.UserRegistration.

UserRegistration() - Constructor for class bioroot.UserRegistration

UserRegistrationBean - class bioroot.UserRegistrationBean.

UserRegistrationBean() - Constructor for class bioroot.UserRegistrationBean

UserRegistrationBean(UserBean) - Constructor for class bioroot.UserRegistrationBean

Util - class bioroot.Util.

Utility class for BioRoot

Util() - Constructor for class bioroot.Util

Util - class trans.misc.Util.

Static helper methods for all things Affy

Util() - Constructor for class trans.misc.Util

UtilMeme - class meme.UtilMeme.

A catch all class to hold static methods and parameters set by different classes associated by MemeR.

UtilMeme() - Constructor for class meme.UtilMeme

UtilSelex - class selex.UtilSelex.

Utilites for the Selex package.

UtilSelex() - Constructor for class selex.UtilSelex

Utils - class com.amazon.s3.Utils.

Utils() - Constructor for class com.amazon.s3.Utils

updateAntibody(AntibodyBean, UserBean, DBUtil) - Static method in class bioroot.antibody.AntibodyModify

Attempts to update a AntibodyBean in the database, only checks that the name is unique if it has changed.

updateAntibodyPreps(AntibodyBean, DBUtil) - Static method in class bioroot.antibody.AntibodyModify

Attempts to update the AntibodyPreps and UseDilutions in the database.

updateCommonAccessFields(ReagentBean, String) - Method in class bioroot.DBUtil

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

updateCommonAccessFields(ReagentBean, UserBean, HttpServletRequest) - Method in class bioroot.DBUtil

Just update the commonly accessible fields: lastUser, comments

updateCommonAccessFields(DBUtil, String) - Method in class bioroot.ReagentBean

Just updates fields that are accessible by all lab group memebers, lastUser, comments given a reagent type: Oligo or Plasmid.

updateCommonAccessFields(AntibodyPrep[], DBUtil) - Static method in class bioroot.antibody.AntibodyModify

Just update the commonly accessible fields in each antibodyPrep as well as the useDilutions.

updateCommonAccessFields(DBUtil) - Method in class bioroot.antibody.AntibodyPrep

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

updateConsole() - Method in class gata.plotter.Console

updateLoginFailure(String) - Method in class bioroot.DBUtil

Increments the numberFailures for an ip in the Login table if it exists or creates a new record.

updateOld(DBUtil, UserBean) - Method in class bioroot.CellTypeBean

updateOld(DBUtil, UserBean) - Method in class bioroot.GeneBean

updateOld(DBUtil, UserBean) - Method in class bioroot.MarkerBean

updateOld(DBUtil, UserBean) - Method in class bioroot.OrganismBean

updateOld(DBUtil, UserBean) - Method in class bioroot.antibody.AntibodyBean

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

updateOld(DBUtil) - Method in class bioroot.antibody.AntibodyPrep

Updates a Antibody prep entry

updateOld(DBUtil) - Method in class bioroot.antibody.UseDilution

updateOld(DBUtil, UserBean) - Method in class bioroot.oligo.OligoBean

updateOld(DBUtil, UserBean) - Method in class bioroot.plasmid.PlasmidBean

updateOld(DBUtil, UserBean) - Method in class bioroot.strain.StrainBean

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

updateOligo(OligoBean, UserBean, HttpServletRequest, DBUtil) - Static method in class bioroot.oligo.OligoModify

Attempts to update an OligoBean in the database, only checks that the name is unique if it has changed.

updatePlasmid(PlasmidBean, UserBean, HashMap, HttpServletRequest, DBUtil) - Static method in class bioroot.plasmid.PlasmidModify

Attempts to update a PlasmidBean in the database, only checks that the name is unique if it has changed.

updateStrain(StrainBean, UserBean, HashMap, HttpServletRequest, DBUtil) - Static method in class bioroot.strain.StrainModify

Attempts to update a StrainBean in the database, only checks that the name is unique if it has changed.

updateStrainCommonAccessFields(DBUtil) - Method in class bioroot.strain.StrainBean

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

updateStrainCommonAccessFields(StrainBean, UserBean, HashMap, DBUtil) - Static method in class bioroot.strain.StrainModify

Just update the commonly accessible fields: restock, lastUser, remainingAliquots, comments

updateUser() - Method in class bioroot.UserRegistrationBean

updateUserLabGroupTable(int, int, String) - Method in class bioroot.UserRegistrationBean

upload(File[], String[]) - Method in class cgar.CommitFiles

upload(File[]) - Method in class util.amazon.S3Manager

Upload files to S3.

upload(String, File[]) - Method in class util.amazon.S3Manager

Uploads files to S3 using a different thread.

upload(String, File) - Method in class util.amazon.S3Manager

See threaded upload (String uniqueProcessName, File[] files).

upload(File) - Method in class util.amazon.S3Manager

See upload (File[] files).

useDilutionFeatureNames - Static variable in class bioroot.antibody.AntibodyBase

Used to see if any use dilutions are called for spreadsheet.

util.amazon - package util.amazon

util.apps - package util.apps

Scripts for printing arrays, manipulating files, scatter plots...

util.bio.annotation - package util.bio.annotation

For representing gene annotation.

util.bio.calc - package util.bio.calc

Calculators for aligments and nucleic acids.

util.bio.cluster - package util.bio.cluster

Clustering apps and methods.

util.bio.converters - package util.bio.converters

Bio format converters.

util.bio.digest - package util.bio.digest

Restriction enzyme digestion of DNA sequences.

util.bio.parsers - package util.bio.parsers

Parsers and extractors, fasta, quality, text, gff....

util.bio.parsers.gff - package util.bio.parsers.gff

GFF2 and GFF3 parsers.

util.bio.seq - package util.bio.seq

Nucleic acid sequence manipulation.

util.bio.wrappers - package util.bio.wrappers

Wrappers for other bio applications.

util.bio.xamer - package util.bio.xamer

Generation and manipulation of random sequence words of various lengths.

util.gen - package util.gen

Variety of helper methods for Email, IO, Encryption, HTML, Swing...

util.xml - package util.xml