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

S

SampleAction - Class in edu.mayo.bsi.ngsportal.client.sample

SampleAction(String, String, SampleActionCallback) - Constructor for class edu.mayo.bsi.ngsportal.client.sample.SampleAction

SampleActionCallback - Interface in edu.mayo.bsi.ngsportal.client.sample

SampleActionListGrid - Class in edu.mayo.bsi.ngsportal.client.sample

Decorates a SampleListGrid with additional columns that perform an action via Button widgets.

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

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

Class holding the sample data from a Sequenced Sample, so it can be printed out

SampleData(RunData, String, String, String, int, int, boolean, boolean, String, String, String, String, String) - Constructor for class edu.mayo.bsi.ngsportal.server.SampleData

Normal Constructor

SampleData(ContactInfo, RunData, String, String, String, int, int, int, boolean, boolean, String, String, String, String, String) - Constructor for class edu.mayo.bsi.ngsportal.server.SampleData

Constructor for PI and numReads

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

@author Gregory Dougherty

SampleHandler(NGSPortal, String) - Constructor for class edu.mayo.bsi.ngsportal.client.SampleHandler

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

@author Gregory Dougherty

SampleInfo(int, int, String, String, String, String, int, int, boolean, boolean, String, String, String, String, String, String, String, String, String, String[], long, String, Date, String, boolean, Boolean) - Constructor for class edu.mayo.bsi.ngsportal.shared.SampleInfo

Normal Constructor

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

No Sequenced Sample Info Constructor

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

SampleInfoListGridRecord(String, String, String, String, int, int, boolean, boolean, String, String, String, String, String, String, String, String, String) - Constructor for class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

Normal Constructor

SampleListGrid - Class in edu.mayo.bsi.ngsportal.client.sample

Reusable ListGrid for displaying samples.

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

SampleTreeGrid - Class in edu.mayo.bsi.ngsportal.client.sample

Specialized TreeGrid widget that works with SampleInfo objects to display/select samples.

SampleTreeGrid(SampleTreeGrid.ViewMode, SampleTreeGrid.SampleField...) - Constructor for class edu.mayo.bsi.ngsportal.client.sample.SampleTreeGrid

Constructor

SampleTreeGrid.SampleField - Enum in edu.mayo.bsi.ngsportal.client.sample

SampleTreeGrid.ViewMode - Enum in edu.mayo.bsi.ngsportal.client.sample

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

Saves the batched value

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

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

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

Save the current changes back to the server, then execute the follow up command

SaveEnum - Enum in edu.mayo.bsi.ngsportal.client

@author Gregory Dougherty

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

Save Notes to the Database.

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

Save Notes to the Database.

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

Save Notes to the Database.

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

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

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

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

Replace the notes for a secondary analysis.

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

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

saveSecondaryAssignedDate(int, int, Date) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

saveSecondaryAssignedDate(int, int, Date) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

saveSecondaryAssignedDate(int, int, Date, AsyncCallback<Void>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

saveSecondaryCompleteDate(int, int, Date) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Saves the secondary Complete Date.

saveSecondaryCompleteDate(int, int, Date) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

saveSecondaryCompleteDate(int, int, Date, AsyncCallback<Void>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

saveSecondaryDeliveryDate(int, int, Date) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Saves the Secondary Delivery Date

saveSecondaryDeliveryDate(int, int, Date) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

saveSecondaryDeliveryDate(int, int, Date, AsyncCallback<Void>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

saveSecondaryStartDate(int, int, Date) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Saves the Secondary Start Date

saveSecondaryStartDate(int, int, Date) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

saveSecondaryStartDate(int, int, Date, AsyncCallback<Void>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

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

Class to present the search form users will start with

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

Build the Search Form

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

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

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

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

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

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

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

SecondaryDetails(int, int, int, String, String, String, Date, String) - Constructor for class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

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

SecondaryDetailsListGridRecord(int, int, int, String, String, String, Date, String) - Constructor for class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

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

Class that holds the information about a Secondary Project, its users, and its samples

SecondaryProjectInfo(String, String, String, Date, Integer, Integer, Integer, Integer, List<SampleInfo>) - Constructor for class edu.mayo.bsi.ngsportal.shared.SecondaryProjectInfo

Standard Constructor

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

SecondaryRunStatusPanel(String, List<SecondaryAnalysisBean>, InstrumentDashboardPage) - Constructor for class edu.mayo.bsi.ngsportal.client.SecondaryRunStatusPanel

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

SecondaryStatusPanel(SecondaryAnalysisBean, InstrumentDashboardPage) - Constructor for class edu.mayo.bsi.ngsportal.client.SecondaryStatusPanel

selectSamples(List<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleListGrid

selectSamples(List<SampleInfo>, boolean) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleTreeGrid

Programmatic way to select samples rendered in the tree.

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

Class that takes a List of Strings, puts up a Dialog Box with a ComboBox holding the strings, a Cancel button, and a Select button, and reports the user's choice

SelectStringDialog(String, String, List<String>, StringCommand, Command) - Constructor for class edu.mayo.bsi.ngsportal.client.SelectStringDialog

Create and show a dialog that has a ComboBox for choosing one of a list of Strings

send() - Method in class edu.mayo.bsi.ngsportal.server.PortalEmail

Does not send an email if we are unit testing

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

Saves the Assigned Date and Personnel to the DB

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

Send an email to the new person assigned to a project, and the old person no longer assigned to a project

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

Send an email to the new person assigned to a project, and the old person no longer assigned to a project

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

Generate an EMail Weekly Report

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

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

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

Checks to see if any of the passed in values are meaningful and different from the existing values

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

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

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

setActions(SampleAction...) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleActionListGrid

setAllprojects(List<ProjectsSummaryInfo>) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectSummaryBuilder

setAllprojects(List<ProjectsSummaryInfo>) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBuilder

setAnalysisFilter(String) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

setAnalysisID(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setAnalysisID(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setAppFilter(String) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

setApplication(String) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setApplication(String) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setApplicationTypes(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

private ComboBoxItem rlimsID; private ComboBoxItem rlimsProject; Set the application types users can chose from

setAppType(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setAppType(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setAppTypes(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

setBatched(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setBatched(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setBic(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setCanAdmin(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectSummaryPage

setCanEdit(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage

setCanEdit(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectMgmtPage

Routine to call to let the panel know if the user has permission to Add, Edit, and / or Delete Projects

setCanvasFieldNames(String...) - Method in class edu.mayo.bsi.ngsportal.client.CanvasListGrid

setCaptureKit(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setCim(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setContacts(Collection<ContactInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ProjectMgmtPage

Set the list of people known to the Portal

setControl(boolean) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setCycles(int) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setDateFilter(Date, Date) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

Set as a date filter

setDifference(long) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setDuplicationLevel(StaticTextItem) - Method in class edu.mayo.bsi.ngsportal.client.FastQCForm

setDuplicationLevel(double) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setEMail(String) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setErrorFilter() - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

Set as a filter for errors

setFamilyID(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setFileLocation(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setFileLocations(String, String) - Static method in class edu.mayo.bsi.ngsportal.AddNGSPortalMetadata

Parse the files and add the information to the database

setFileLocations(List<FileLocation>) - Static method in class edu.mayo.bsi.ngsportal.client.MetadataTab

Give MetaDataTab the list of FileLocations for teh sample file locations

SetFileLocations - Class in edu.mayo.bsi.ngsportal

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

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

setFileLocations(String, String) - Static method in class edu.mayo.bsi.ngsportal.SetFileLocations

Parse the files and add the information to the database

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

setFirstName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setFlowcell(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setFlowCell(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setFlowcell(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setGcContent(double) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setGcContentField(StaticTextItem) - Method in class edu.mayo.bsi.ngsportal.client.FastQCForm

setId(int) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setId(int) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

setId(int) - Method in class edu.mayo.bsi.ngsportal.shared.RunData

Set the run's DB ID

setID(int) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

setIndex(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setIndex(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setIndexSeq(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setIndexVendor(boolean) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setInputStream(InputStream, String) - Method in class edu.mayo.bsi.ngsportal.server.Compressor

setInstrumentName(String) - Method in class edu.mayo.bsi.ngsportal.client.InstrumentPanel

setInstrumentName(String) - Method in class edu.mayo.bsi.ngsportal.client.PrimaryStatusPanel

setInstrumentName(String) - Method in class edu.mayo.bsi.ngsportal.client.SecondaryRunStatusPanel

setInstrumentName(String) - Method in class edu.mayo.bsi.ngsportal.client.SecondaryStatusPanel

setInternal(boolean) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setInvestigator(String) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setInvestigator(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setIsAllowed(NoteWidget.Action, boolean) - Method in class edu.mayo.bsi.ngsportal.client.NoteWidget

Determines whether the user is allowed to perform the action or not.

setIsBIC(int, boolean, int) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Sets all the samples for a project to have their isBIC field either be true or false

setIsBIC(int, boolean, int) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Sets all the samples for a project to have their isBIC field either be true or false

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

Sets all the samples for a project to have their isBIC field either be true or false

setIsEnabled(NoteWidget.Action, boolean) - Method in class edu.mayo.bsi.ngsportal.client.NoteWidget

Direct control over whether the widget for the action is enabled or disabled.

setLabel(int, String) - Method in class edu.mayo.bsi.ngsportal.shared.SGEScriptSummary

Sets a label for the value at the position provided

setLane(int) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setLane(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setLane(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setLanID(String) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setLastModified(Date) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfoListGridRecord

Set the last modified Date

setLastModified(String) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setLastName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setLeadContactID(Integer) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

setMetadata(List<SampleInfo>, RunData, boolean) - Method in class edu.mayo.bsi.ngsportal.client.MetadataTab

Update the displayed data, getting rid of what was previously displayed

setName(String) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setName(String) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.SampleTreeNode

setName(String) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setName(String) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.SampleTreeNode

setName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

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

setName(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setNotePopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setNotes(Collection<Note>) - Method in class edu.mayo.bsi.ngsportal.client.NoteWidget

Sets the notes to be displayed by the widget.

setNotes(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

setNotes(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setNotes(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setNotes(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setNotes(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setNumBadBases(int) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setNumBases(int) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setOtherPicker(DatePickerButton) - Method in class edu.mayo.bsi.ngsportal.client.DatePickerButton

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

setParentID(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setPercentDone(int) - Method in class edu.mayo.bsi.ngsportal.client.ProgressBar

setPercentSeqHigh(double) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setPercentSeqLow(double) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setPersonnel(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setPersonnel(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setPersonnel(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setPi(String) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setPi(String) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setPI(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setPIContactID(Integer) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

setPIName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setPINames(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

Set the PI Names users can chose from

setPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.SampleTreeNode

setPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.SampleTreeNode

setPosition(int, int) - Method in class edu.mayo.bsi.ngsportal.client.DatePickerButton

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

setPosition(int) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfoListGridRecord

Set the position

setPosition(int) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setPosition(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setPrimaryDeliveryDate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setPrimaryDeliverydate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setProgressColor(String) - Method in class edu.mayo.bsi.ngsportal.client.ProgressBar

setProjectid(int) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setProjectid(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setProjectName(String) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setProjectName(String) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setProjectName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setProjectName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setProjectNames(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage

setProjectNames(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

Set the Project Names users can chose from

setProjectNames(List<String>) - Method in class edu.mayo.bsi.ngsportal.shared.ResultInfo

Set the list of project names to be the passed in list.

setQCPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setQCPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setQCPopulated(boolean) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

setQCResult(List<QCResult>) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

Update the QC Result List.

setQcResults(List<QCResult>) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.SampleTreeNode

setQcResults(List<QCResult>) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.SampleTreeNode

setQueueFilter(String) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

setReadType(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setReadType(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setReadTypes(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

setReanalysis(boolean) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

setResult(String) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setResultField(StaticTextItem) - Method in class edu.mayo.bsi.ngsportal.client.FastQCForm

setRlimsID(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setRLIMSIDs(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

Set the RLIMS IDs users can chose from

setRLIMSProjectID(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setRLIMSProjectName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setRLIMSProjectName() - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setRLIMSProjectName(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setRLIMSProjects(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

Set the RLIMS Project names users can chose from

setRoles(Map<Integer, Integer>) - Method in class edu.mayo.bsi.ngsportal.shared.ContactInfo

setRun(String, String, RunData, List<SampleInfo>, int[], Command) - Method in class edu.mayo.bsi.ngsportal.client.NGSPortal

Update all the metadata for a given run, owned by a given PI

setRun(String) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setRun(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setRun(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setRunData(RunData) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setRunData(RunData) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setRunData(int, String, String, RunData, List<SampleInfo>, int[]) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Update all the metadata for a given run, owned by a given PI

setRunData(int, String, String, RunData, List<SampleInfo>, int[]) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalService

Update all the metadata for a given run, owned by a given PI, and for its samples

setRunData(int, String, String, RunData, List<SampleInfo>, int[], AsyncCallback<Boolean>) - Method in interface edu.mayo.bsi.ngsportal.shared.NGSPortalServiceAsync

setRunFilter(String) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

setRunID(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setRunIDs(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

Set the run ids / names users can chose from

setRunInformation(RunData, String) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

Set the tab to display the latest run data

setRunName(String) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.SampleTreeNode

setRunName(String) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.SampleTreeNode

setRunName(String) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfoListGridRecord

Set the run name

setRunName(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setRunStartDate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setRunType(String) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setSampleID(int) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

setSampleID(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setSampleID(int) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setSampleInfo(SampleInfo) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.SampleTreeNode

setSampleInfo(SampleInfo) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.SampleTreeNode

setSampleName(String) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setSampleNames(List<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

Update the list of available Sample Names

setSampleNames(LinkedHashMap<String, String>) - Method in class edu.mayo.bsi.ngsportal.client.SearchForm

Set the sample names users can chose from

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

setSamples(List<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

setSamples(List<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage.RunTreeNode

setSamples(List<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.RunEditPanel

Update the samples ListGrid with the SampleInfo for the current run

setSamples(Collection<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleListGrid

Sets the sample data to be displayed in the grid.

setSamples(List<SampleInfo>) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleTreeGrid

Sets the sample data to be displayed in the tree.

setSamplesIsEnabled(List<SampleInfo>, boolean) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleListGrid

Marks the specified samples in the ListGrid as enabled/disabled.

setSamplesIsEnabled(List<SampleInfo>, boolean) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleTreeGrid

Marks the specified samples as enabled/disabled.

setSecAssigneddate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setSecCompletedate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setSecdashboard(Map<String, SecondaryAnalysisBean>) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBuilder

setSecDeliverydate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfoListGridRecord

setSecondaryAssignedDate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setSecondaryCompleteDate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setSecondaryDeliveryDate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setSecondaryStartDate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectsSummaryInfo

setSequenceCount(StaticTextItem) - Method in class edu.mayo.bsi.ngsportal.client.FastQCForm

setSequenceCount(int) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

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

Sets the type of data to display from the types contained in SGEBarGraph; See SGEBarGraph Type Constants for possible values.

setSGEData(SGEBarGraph.SGEGraphType) - Method in class edu.mayo.bsi.ngsportal.client.SGEBarGraphImpl

setSpecContactID(Integer) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectInfo

setSpecies(String) - Method in class edu.mayo.bsi.ngsportal.shared.SampleInfoListGridRecord

setStage(String) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfoListGridRecord

Set the Stage of the instrument

setStage(String) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setStage(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setStage(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setStageFilterPrimary() - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

Set as a filter for primary analysis

setStageFilterSecondary() - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

Set as a filter for secondary analysis

setStatus(String) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfoListGridRecord

Set the status of the instrument

setStatus(String) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setStatus(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setStatus(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setStatus(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setTask(String) - Method in class edu.mayo.bsi.ngsportal.shared.InstrumentInfoListGridRecord

Set the task of the instrument

setTask(String) - Method in class edu.mayo.bsi.ngsportal.shared.PrimaryAnalysisBean

setTask(String) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBean

setThedate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetails

setThedate(Date) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryDetailsListGridRecord

setType(SGEBarGraph.SGEGraphType) - Method in class edu.mayo.bsi.ngsportal.client.SGEBarGraphImpl

Set the type of bargraph to construct.

setUp() - Method in class edu.mayo.bsi.ngsportal.server.BaseNGSPortalServiceTest

setupH2() - Static method in class edu.mayo.bsi.ngsportal.server.BaseNGSPortalServiceTest

setupImage(NGSPortalResources) - Static method in class edu.mayo.bsi.ngsportal.client.DatePickerButton

Tells the class how to get to the resources bundle so it can get the image for its buttons.

setUrl(String) - Method in class edu.mayo.bsi.ngsportal.shared.QCResultListGridRecord

setUrlField(LinkItem) - Method in class edu.mayo.bsi.ngsportal.client.FastQCForm

setUser(int, boolean, boolean, boolean, int[], String, String, String) - Method in class edu.mayo.bsi.ngsportal.server.PortalConnection

Called when the user has logged in

setUserFilter(String) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

setUsername(String) - Method in class edu.mayo.bsi.ngsportal.client.NoteWidget

Sets the username to be used for newly added notes.

setValidRunIDs(List<String>) - Method in class edu.mayo.bsi.ngsportal.shared.SGEFilter

Accepts a list of RunIDs to filter against

setValue(String) - Method in class edu.mayo.bsi.ngsportal.server.GetOpts

Set the value.

setValue(Long) - Method in class edu.mayo.bsi.ngsportal.shared.SGEScriptSummary

setValue(int, Long) - Method in class edu.mayo.bsi.ngsportal.shared.SGEScriptSummary

Sets the value at a particular index for script summaries holding multiple values

setViewMode(SampleTreeGrid.ViewMode) - Method in class edu.mayo.bsi.ngsportal.client.sample.SampleTreeGrid

Changes how the samples are viewed in a tree structure.

setYourprojects(List<ProjectsSummaryInfo>) - Method in class edu.mayo.bsi.ngsportal.shared.ProjectSummaryBuilder

setYourprojects(List<ProjectsSummaryInfo>) - Method in class edu.mayo.bsi.ngsportal.shared.SecondaryAnalysisBuilder

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

SGEBarGraph is an abstract class definition defining methods needed to fill and update a bargraph with data from grid engine metrics.

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

SGEBarGraph.SGEGraphType - Enum in edu.mayo.bsi.ngsportal.client

List of types of graphs for the bar graph to display.

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

SGEBarGraphImpl provides a concrete implementation of SGEBarGraph and is responsible for filling the grid engine metrics graph with data obtained from the server at the direction of the SGETabController.

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

Construct a new SGEBarGraph of the specified type @see SGEBarGraph.SGEGraphType

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

The SGEFilter class holds a set of filter settings for generating metrics.

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

Constructs a new filter object.

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

SGEScriptSummary encapsulates information about script usage for RPC data transfer.

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

Creates a new SGEScriptSummary of the specified size and name.

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

Creates a new SGEScriptSummary holding only one value

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

SGETab lays out and draws the the controls and graphs comprising the Grid Engine Metrics Tab.

showAlert(String, String, Command) - Static method in class edu.mayo.bsi.ngsportal.client.NGSPortal

Show a Alert with a title and message, and possible a command to execute when the alert is dismissed

showAlert(String, String, Command) - Method in class edu.mayo.bsi.ngsportal.client.NGSPortalDashboard

Show a Alert with a title and message, and possible a command to execute when the alert is dismissed

showAnalysisResults(List<AnalysisInfo>) - Method in class edu.mayo.bsi.ngsportal.client.NGSPortal

Clear out the old analysis results and then display the new results from the server.

showAnalysisResults(List<AnalysisInfo>) - Method in class edu.mayo.bsi.ngsportal.client.NGSPortalDashboard

Clear out the old analysis results and then display the new results from the server.

showSaveAlert(String, String, Command[]) - Static method in class edu.mayo.bsi.ngsportal.client.NGSPortal

Show a Save Alert with a title, a message, and three different commands to execute depending upon how the user dismisses the alert

showWarning(String, String, String[], Command[]) - Static method in class edu.mayo.bsi.ngsportal.client.NGSPortal

Show a Alert with a title and message, and possible a set of commands to execute when the alert is dismissed.

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

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

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

@author Gregory Dougherty

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

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

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

SmartEnterButton(String, Command) - Constructor for class edu.mayo.bsi.ngsportal.client.SmartEnterButton

sortResultInfoListByPI(List<ResultInfo>) - Static method in class edu.mayo.bsi.ngsportal.shared.ResultInfo

Sort the result list in increasing alphabetical order of the PI name

sortResultInfoListByRun(List<ResultInfo>) - Static method in class edu.mayo.bsi.ngsportal.shared.ResultInfo

Sort the result list in decreasing alphabetical order of the run name

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

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

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

Class to handle all the SQL Parsing, to decrease the size of the NGSPortalServiceImpl class

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

sqlresultToSecondaryAnalysis(ResultSet) - Method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Converts Secondary Analysis Result set to SecondaryAnalysisBean

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

Sibling to {Command}, whose StringCommand.execute(java.lang.String, com.google.gwt.user.client.Command) routine takes a String argument and a Command to use

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

A class for holding two case insensitive strings (since equals uses equalsIgnoreCase)

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

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

Class that can handle receiving a non-null string