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

A

accept(File, String) - Method in class edu.mayo.bsi.ngsportal.server.FileNamePlusFilter

actionPerformed(SampleInfo) - Method in interface edu.mayo.bsi.ngsportal.client.sample.SampleActionCallback

add(String) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveSet

addAll(Collection<? extends String>) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveSet

addCommand(Command) - Method in class edu.mayo.bsi.ngsportal.client.EnterButtonItem

Add a command to be executed when the button is fired

addCommand(Command) - Method in class edu.mayo.bsi.ngsportal.client.SmartEnterButton

Add a command to be executed when the button is fired

addEditListener(RunEditPanel.RunEditListener) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

Adds a client that needs to be notified of run edits.

addExternalUser(String, String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add an external user to the database

addExternalUser(String, String, String) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Add an external user to the database

addExternalUser(String, String, String, AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addGroup(int, String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Adds a new group

addGroup(int, String, String) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Adds a new group

addGroup(int, String, String, AsyncCallback<Integer>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addKeyValuePair(int, int, String, String, String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add a Key : Value pair about a specified item to the DB

addKeyValuePair(int, int, String, String, String, String) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Add a Key : Value pair about a specified item to the DB

addKeyValuePair(int, int, String, String, String, String, AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addLocationInformation(String[], String[], String[], int[], String[], String[], String[], String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add location information to the Sequenced Sample table

addMetadata(String[], String[], String[], String[], String[], String[], String[], int[], String[], String[], String[], int[], String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add metadata to the DB.

addNewNote(Note) - Method in class edu.mayo.bsi.ngsportal.client.NoteWidget

Adds a new note to the widget that is not currently stored on the DB backend.

addNewRerun(int, int, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

addNewRerun(int, int, String) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

addNewRerun(int, int, String, AsyncCallback<String>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

AddNGSPortalMetadata - Class in edu.mayo.bsi.ngsportal

This class creates a command line tool that takes a file whose comma delimited lines are of the form:

AddNGSPortalMetadata() - Constructor for class edu.mayo.bsi.ngsportal.AddNGSPortalMetadata

addNonPI(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

Add a non-PI to the list of non-PIs for this sample

addNote(int, String, String, int) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Adds a note to the database

addNote(int, String, String, int) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Adds a note to the database

addNote(int, String, String, int, AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addOption(char, String, GetOpts.ArgType, GetOpts.OptType) - Static method in class edu.mayo.bsi.ngsportal.server.GetOpts

addPI(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

Add a PI to the list of PIs for this sample

addProject(int, String, boolean, int[], Integer, Integer, Integer) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

addProject(int, String, boolean, int[], Integer, Integer, Integer) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Adds a new project.

addProject(int, String, boolean, int[], Integer, Integer, Integer, AsyncCallback<String>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addRLIMSBatchIDs(String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Gets the runs that don't have RLIMS Batch IDs, and looks for the IDs, adding them if they exist

addSample(String, String, String, String, String, String, Record, Command) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

Routine called when the user has added a new sample via the AddSample dialog box

addSampleAnalysis(String, String, double, String, Date, String, String, boolean, boolean) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add a Secondary analysis to the DB, setting up all the relevant information

addSampleAnalysis(int, int, String, double, String, Date, boolean, boolean) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add a Secondary analysis to the DB, setting up all the relevant information

AddSampleDialog - Class in edu.mayo.bsi.ngsportal.client

Class to put up and handle a dialog box that lets the user add a new Sample

AddSampleDialog(String, String, String, String, RunEditPanel, Record, Command) - Constructor for class edu.mayo.bsi.ngsportal.client.AddSampleDialog

Create and show a dialog box that lets the user add a new Sample to the DB

addSecAnLinks(int[][]) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add these sequenced samples and Secondary Analysis to the Secondary Analysis linker table

AddSecondaryAnalysis - Class in edu.mayo.bsi.ngsportal

Class for app that adds secondary analysis via an HTTP call to the servlet

AddSecondaryAnalysis() - Constructor for class edu.mayo.bsi.ngsportal.AddSecondaryAnalysis

addToFamily(int, String, String, String, String, String, Boolean) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add a sample to a family, creating the family if necessary.

addToFamily(int, String, String, String, String, String, Boolean) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Add a sample to a family, creating the family if necessary.

addToFamily(int, String, String, String, String, String, Boolean, AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addUser(String, int) - Method in class edu.mayo.bsi.ngsportal.shared.GroupInfo

Add a user and role to the Map of users and roles

addUsersToGroup(int, int, Map<String, Integer>) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Add users to an existing group

addUsersToGroup(int, int, Map<String, Integer>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Add users to an existing group

addUsersToGroup(int, int, Map<String, Integer>, AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

addUsersToProject(int, Map<String, Boolean>, int, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Give one or more users' access to a project

addUsersToProject(int, Map<String, Boolean>, int, String) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Give one or more users' access to a project

addUsersToProject(int, Map<String, Boolean>, int, String, AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

Analysis2 - Class in edu.mayo.bsi.ngsportal.shared

@author Gregory Dougherty

Analysis2(String, String, double, boolean, Date, Date, String) - Constructor for class edu.mayo.bsi.ngsportal.shared.Analysis2

AnalysisDriver - Class in edu.mayo.bsi.ngsportal.server

AnalysisDriver() - Constructor for class edu.mayo.bsi.ngsportal.server.AnalysisDriver

AnalysisInfo - Class in edu.mayo.bsi.ngsportal.shared

@author Gregory Dougherty

AnalysisInfo() - Constructor for class edu.mayo.bsi.ngsportal.shared.AnalysisInfo

Empty constructor to make Serialization happy

AnalysisInfo(String, String, String, String) - Constructor for class edu.mayo.bsi.ngsportal.shared.AnalysisInfo

Default Constructor

ArrayRoutines - Class in edu.mayo.bsi.ngsportal.server

Routines for manipulating arrays of Objects, since Java's class does a poor job of it.

ArrayRoutines() - Constructor for class edu.mayo.bsi.ngsportal.server.ArrayRoutines

assignAnalysisGroups(String, String) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Iterate over the AnalysisGroup table, looking for AnalysisGroups that are not assigned to a Secondary Project, but have the same sequenced samples as an existing Secondary Project, and assign the AnalysisGroup to the SecondaryProject

authenticate(String, String) - Method in interface edu.mayo.bsi.ngsportal.server.Authenticator

Determines whether the specified LAN ID & password are valid.

authenticate(String, String) - Method in class edu.mayo.bsi.ngsportal.server.AuthenticatorLdapImpl

Authenticator - Interface in edu.mayo.bsi.ngsportal.server

Interface for determining whether a specified LAN ID & password are valid.

AuthenticatorLdapImpl - Class in edu.mayo.bsi.ngsportal.server

Adapter between interface Authenticator and the mayo-commons-directory LdapWrapper implementation.

AuthenticatorLdapImpl() - Constructor for class edu.mayo.bsi.ngsportal.server.AuthenticatorLdapImpl