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

C

calendarIcon() - Method in interface edu.mayo.bsi.ngsportal.client.NGSPortalResources

canAdministerProjects() - Method in class edu.mayo.bsi.ngsportal.server.PortalConnection

canAdministerProjects() - Method in class edu.mayo.bsi.ngsportal.shared.ConnectionResponse

CancelableNodeClickHandler - Interface in edu.mayo.bsi.ngsportal.client

@author Gregory Dougherty

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

Routine called when the user has Canceled the AddSample dialog box

canEdit() - Method in class edu.mayo.bsi.ngsportal.shared.ConnectionResponse

canEditAll() - Method in class edu.mayo.bsi.ngsportal.server.PortalConnection

canSeeAll() - Method in class edu.mayo.bsi.ngsportal.server.PortalConnection

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

Extended functionality to allow for having arbitrary Canvas objects in a ListGrid [e.g.

CanvasListGrid() - Constructor for class edu.mayo.bsi.ngsportal.client.CanvasListGrid

CaseInsensitiveMap<V> - Class in edu.mayo.bsi.ngsportal.shared

A map class for Mapping SQL Strings (as keys) to values, since SQL Strings are case insensitive, and normal Maps are not

CaseInsensitiveMap(Map<String, V>) - Constructor for class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveMap

Create a Case-insensitive Map, that uses the sorting, etc.

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

A set class for holding SQL Strings, since SQL Strings are case insensitive

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

Create a Case-insensitive Set based upon a HashSet

CaseInsensitiveSet(Set<String>) - Constructor for class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveSet

Create a Case-insensitive Set, that uses the sorting, etc.

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

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

Create and show a dialog box that lets the user add a new Sample to the DB, or just change its name

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

Checks the user access

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

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

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

Checks if the Project Name entered by Admin already exists

cleanupH2() - Static method in class edu.mayo.bsi.ngsportal.server.BaseNGSPortalServiceTest

clear() - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveMap

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

close() - Static method in class edu.mayo.bsi.ngsportal.GetRunSamples

Close the connection to the servlet / db

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

@author Gregory Dougherty

CommandClickHandler(Command, Window) - Constructor for class edu.mayo.bsi.ngsportal.client.CommandClickHandler

CommandClickHandler(Command, Window, Validate) - Constructor for class edu.mayo.bsi.ngsportal.client.CommandClickHandler

compareTo(ContactSorter) - Method in class edu.mayo.bsi.ngsportal.server.ContactSorter

compareTo(InstrumentInfo) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfo

compareTo(ReportData) - Method in class edu.mayo.bsi.ngsportal.shared.ReportData

compareTo(VersionedString) - Method in class edu.mayo.bsi.ngsportal.shared.VersionedString

CompareToRLIMS - Class in edu.mayo.bsi.ngsportal

@author Gregory Dougherty

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

compareToRLIMS(String) - Static method in class edu.mayo.bsi.ngsportal.CompareToRLIMS

Run NGSPortalServiceImpl.compareToRLIMS

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

Parses the entire RLIMS system, checking to find those runs where we don't have as many samples for a run as RLIMS does

compressionUsed(File) - Static method in class edu.mayo.bsi.ngsportal.server.Compressor

Static function to tell the caller if the file is / will be compressed

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

Class that seamlessly handles reading and writing Zipped, Gzipped, and Bzipped files, using Java's built in code for dealing with Zipped files, and Apache's code for dealing with BZipped and Gzipped files.

Compressor(File, File) - Constructor for class edu.mayo.bsi.ngsportal.server.Compressor

Compressor(File, File, boolean) - Constructor for class edu.mayo.bsi.ngsportal.server.Compressor

ConnectionException - Exception in edu.mayo.bsi.ngsportal.shared

@author Gregory Dougherty

ConnectionException() - Constructor for exception edu.mayo.bsi.ngsportal.shared.ConnectionException

IsSerializable Constructor

ConnectionException(String) - Constructor for exception edu.mayo.bsi.ngsportal.shared.ConnectionException

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

Class to inform the client about the nature of the connection

ConnectionResponse(byte[], int, int, String, String[], int[], String, String, boolean, boolean) - Constructor for class edu.mayo.bsi.ngsportal.shared.ConnectionResponse

Normal constructor

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

Javabean that encapsulates data about a Contact.

ContactInfo(int, String, String, String, String, boolean, Map<Integer, Integer>) - Constructor for class edu.mayo.bsi.ngsportal.shared.ContactInfo

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

@author Gregory Dougherty

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

contains(Object) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveSet

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

containsKey(Object) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveMap

containsValue(Object) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveMap

convertByteStringToPassword(String) - Method in class edu.mayo.bsi.ngsportal.shared.Encryptor

Javascript apparently can't handle the non-utf8 strings that encoding creates, so on the client side we return a string of bytes (as integers) separated by "\t", and on the server side we decode that format

convertPassword(String, boolean) - Method in class edu.mayo.bsi.ngsportal.shared.Encryptor

Passing passwords as plain text is exceedingly poor security.

convertPassword(byte[], boolean) - Method in class edu.mayo.bsi.ngsportal.shared.Encryptor

Convert password call to make when you have a byte string

convertPasswordToByteString(String) - Method in class edu.mayo.bsi.ngsportal.shared.Encryptor

Javascript apparently can't handle the non-utf8 strings that this creates, so on the client side we return a string of bytes (as integers) separated by "\t"

CopyUserPermissions - Class in edu.mayo.bsi.ngsportal

Class for app that copies user permissions (i.e.

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

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

Copies user permissions (i.e.

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

Add an Analysis Group to the DB, setting up all the relevant information

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

Add an Analysis Group to the DB, setting up all the relevant information

createBarChart() - Method in class edu.mayo.bsi.ngsportal.client.SGEBarGraph

Sets options and creates the bar chart with an empty data table (call SGEBarGraph.UpdateTable to fill with real data).

createBarChart() - Method in class edu.mayo.bsi.ngsportal.client.SGEBarGraphImpl

createListGrid() - Method in class edu.mayo.bsi.ngsportal.client.SGEBarGraph

Returns an empty ListGrid for holding Chart data

createListGrid() - Method in class edu.mayo.bsi.ngsportal.client.SGEBarGraphImpl

CreateSecondaryProject - Class in edu.mayo.bsi.ngsportal

Class for app that creates a secondary analysis project via an HTTP call to the servlet

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