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

P

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

@author Gregory Dougherty

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

parseArgs(String[], Usage) - Static method in class edu.mayo.bsi.ngsportal.server.GetOpts

Parse a command line, given the already added GetOpts descriptions

parseDate(TextBox, boolean) - Static method in class edu.mayo.bsi.ngsportal.client.DatePickerButton

Date parser, made public so get the same answer no matter who needs it.

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

@author Gregory Dougherty

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

ParseFolders - Class in edu.mayo.bsi.ngsportal

Class for app that adds secondary analysis directly to the database

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

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

Parse a string representing a PI or non-PI, and turn it into a first name and last name

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

Parses the passed in directory, parses all the fastqc_data.txt files in that directory, or in any of its sub-directories.

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

Parses the passed in file.

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

Parses the entire RLIMS system.

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

Gets the data about a list of runs from RLIMS, and adds any new runs or samples to the DB

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

Parses the passed in file.

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

Parses the passed in file.

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

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

A combo box that does substring text matching

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

Default constructor

populate(QCResult) - Method in class edu.mayo.bsi.ngsportal.client.FastQCForm

populateDetails(String) - Method in class edu.mayo.bsi.ngsportal.client.InstrumentDashboardPage

populateProjectTreeByPI(List<ResultInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage

populateProjectTreeByPI(List<ResultInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage

populateSecondaryAnalysisDetails(int) - Method in class edu.mayo.bsi.ngsportal.client.InstrumentDashboardPage

populateTreeByProj(List<ResultInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage

Populates the tree widget with samples organized by project.

populateTreeByProj(List<ResultInfo>) - Method in class edu.mayo.bsi.ngsportal.client.ReportsPage

Populates the tree widget with samples organized by project.

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

Class that tracks information about a person who is using the NGS Portal

PortalConnection(Encryptor, int, boolean, boolean, boolean, int[], String, String, String) - Constructor for class edu.mayo.bsi.ngsportal.server.PortalConnection

Constructor

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

Class that extends HtmlEmail, and lets us block sending email messages during unit testing

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

Constructor that simply calls the HtmlEmail constructor

PortalTester - Class in edu.mayo.bsi.ngsportal

Class used to test features as they get added to NGSPortalService.

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

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

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

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

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

PrimaryStatusPanel(PrimaryAnalysisBean, InstrumentDashboardPage) - Constructor for class edu.mayo.bsi.ngsportal.client.PrimaryStatusPanel

printCollection(Collection<ReportData>, PrintStream) - Static method in class edu.mayo.bsi.ngsportal.shared.ReportData

Print out a Collection of ReportData to a PrintStream

printResults(List<SampleData>, boolean, boolean, boolean) - Static method in class edu.mayo.bsi.ngsportal.GetRunSamples

Print out the results

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

ProgressBar(int, int, String) - Constructor for class edu.mayo.bsi.ngsportal.client.ProgressBar

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

ProjectExplorerPage(NGSPortal, LinkedHashMap<String, String>, LinkedHashMap<String, String>, List<SampleInfo>) - Constructor for class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage

The Sample Explorer

ProjectExplorerPage.RunTreeNode - Class in edu.mayo.bsi.ngsportal.client

ProjectExplorerPage.RunTreeNode(String, String, String) - Constructor for class edu.mayo.bsi.ngsportal.client.ProjectExplorerPage.RunTreeNode

ProjectExplorerPage.SampleTreeNode - Class in edu.mayo.bsi.ngsportal.client

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

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

JavaBean passed between GWT RPC calls.

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

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

Class for adding, viewing, editing, and deleting Secondary Analysis Projects

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

Create the page for creating, viewing, and deleting Projects

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

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

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

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

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

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

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

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

Data Source that allows filtering in the ProjectSummaryPage.

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

Constructor that specifies the fields that will be filtered on in the ProjectSummaryPage

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

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

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

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

put(String, V) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveMap

putAll(Map<? extends String, ? extends V>) - Method in class edu.mayo.bsi.ngsportal.shared.CaseInsensitiveMap