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

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main(String[]) - Static method in class edu.mayo.bsi.ngsportal.AddNGSPortalMetadata

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.AddSecondaryAnalysis

Parse the arguments in order to add secondary analysis status information to the database

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.CompareToRLIMS

Get all the metadata from RLIMS, and load primary analysis information from the files in any Primary Analysis trees passed in

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.CopyUserPermissions

Parse the arguments in order to add secondary analysis status information to the database

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.CreateSecondaryProject

Parse the arguments in order to add secondary analysis status information to the database

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.DateUtilTester

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.DBAddSecondaryAnalysis

Parse the arguments in order to add secondary analysis status information to the database

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.EmailTester

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.GetRunSamples

Parse the arguments in order to get all the samples for a run from the database and print the results in the following order:
Run Name Flow Cell Instrument RLIMS BatchID Start Date Primary Analysis Status
Instrument Complete Date Primary Complete Date Primary QC Complete Date Primary Delivery Date
Sample Name Sample RLIMS ID Sequencing RLIMS Project ID Lane App Type Read Type
Num Cycles Is Control Is Vendor Index Index Sequence

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.GetRunSequences

Parse the arguments in order to get all the samples for a run from the database and print the results in the following order Run Name Flow Cell Instrument RLIMS BatchID Start Date Primary Analysis Status Instrument Complete Date Primary Complete Date Primary QC Complete Date Primary Delivery Date

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.GetSecondaryAnalysisDates

Get all the samples (possibly of a given application type) for all the runs from the database that had primary analysis finish within a specified time, and print the results in the following order:
Run Name Application Investigator CIM BIC Primary Delivered Secondary Complete Secondary Delivered

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.GetTableValues

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.LoadRLIMS

Get all the metadata from RLIMS, and load primary analysis information from the files in any Primary Analysis trees passed in

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.LoadRLIMSBatchIDs

Get all the metadata from RLIMS, and load primary analysis information from the files in any Primary Analysis trees passed in

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.LoadRLIMSRun

Get all the metadata from RLIMS, and load primary analysis information from the files in any Primary Analysis trees passed in

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.ParseFolders

Parse the arguments in order to add secondary analysis status information to the database

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.PortalTester

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.server.AnalysisDriver

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.server.BatchRun

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.server.BrainSurgery

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.server.ParseDriver

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.server.WeeklyProjectReports

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.SetFileLocations

main(String[]) - Static method in class edu.mayo.bsi.ngsportal.UpdateRunDates

Get all the metadata from RLIMS, and load primary analysis information from the files in any Primary Analysis trees passed in

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

Create a ConnectionResponse that describes the contents of this PortalConnection

makePI(String, String) - Static method in class edu.mayo.bsi.ngsportal.shared.SampleInfo

Make a string representing a PI or non-PI

makeSQLSafe(String) - Static method in class edu.mayo.bsi.ngsportal.server.NGSPortalServiceImpl

Utility routine for the common String test

makeString(String) - Method in class edu.mayo.bsi.ngsportal.shared.StringPair

Return a string that consists of first + separator + second

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

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

Class that displays the metadata associated with a run and its sequenced samples

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

Default constructor

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

Iterate over the SecondaryAnalysisLinker table, adding all the secondary analyses there to the AnalysisGroup table

mySplit(String, String, int) - Static method in class edu.mayo.bsi.ngsportal.shared.SplitFile

Return an array of strings split on the string split.