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

U

uid - Static variable in class edu.iastate.jtm.jmed.Limits

UID - Static variable in class edu.iastate.jtm.jmed.Query.Field

UILIST - Static variable in class edu.iastate.jtm.jmed.Limits

UISwitchListener - Class in edu.iastate.metnet.event

This class listens for UISwitches, and updates a given component.

UISwitchListener(JComponent) - Constructor for class edu.iastate.metnet.event.UISwitchListener

UmlsQueryClient - Class in edu.iastate.jtm.jmed

A client utilizing UMLS server's xml query facility.

UmlsQueryClient(String) - Constructor for class edu.iastate.jtm.jmed.UmlsQueryClient

Create a new UmlsQueryClient with a template query.

UmlsSocketClient - Class in edu.iastate.jtm.jmed

A client utilizing UMLS server's socket query facility.

UmlsSocketClient(File) - Constructor for class edu.iastate.jtm.jmed.UmlsSocketClient

Create a new UmlsSocketQuery object with a template query.

uncheckAll() - Method in class edu.iastate.metnet.model.CandidateModel

undeleteBlockunit(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

undelete one history

undeleteBlockunit(Integer, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

undelete one history

unHighlightAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

This method unhighlights the given annotation.

unHighlightAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.RootPanel

This method unhighlights the given annotation.

unHighlightAnnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.TextPanel

This method removes the highlighting from the given selected annotation.

UNIGENE - Static variable in class edu.iastate.jtm.jmed.Entrez

UniprotID - Interface in edu.iastate.metnet.datamodel.attributes

Interface represents UniprotID

UNISTS - Static variable in class edu.iastate.jtm.jmed.Entrez

unit - Variable in class edu.iastate.jtm.jmed.StreamXMLParser

A DOM representation of a unit element.

unmark() - Method in class edu.iastate.jtm.util.SlidingWindow

unread() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Unread the last byte read.

unread() - Method in class edu.iastate.metnet.soft.RandomAccessFile

Unread the last byte read.

unregisterComponent(JComponent) - Method in class edu.iastate.metnet.newgui.MetNetStatusbar

unselectedBorder1 - Variable in class edu.iastate.metnet.StripedTable.ColorRenderer

unselectedBorder2 - Variable in class edu.iastate.metnet.StripedTable.ColorRenderer

UNSORTABLE - Static variable in class edu.iastate.jtm.gui.TableSorter

update(Graphics) - Method in class edu.iastate.jtm.gui.SplashWindow

Updates the display area of the window.

update(Graphics) - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel

update(Observable, Object) - Method in class edu.iastate.metnet.ui.AddEntityForm

follow the MVC pattern, but the controller (listener) are inner in the GUI component

update(Graphics) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

update(Graphics) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

update() - Method in class fcmodeler.pathbinder.InteractUpdate

updateAbbreviationrules(Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

update the rules changed by users

updateAbbreviationrules(Vector) - Method in interface edu.iastate.metnet.interfaces.MyPaper

update the rules changed by users

updateBirdEye() - Method in class edu.iastate.metnet.ui.PathwayEditor

updateBirdEye() - Method in class edu.iastate.reload.ui.NetworkEditForm

refresh the overview graph

updateBlockunitConfidence(int, int, int) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

update existing confidence

updateBlockunitConfidence(int, int, int) - Method in interface edu.iastate.metnet.interfaces.MyPaper

update existing confidence

updateCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

this method update the gene dots' capacity value in legend panel

updateCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.LegendPanel

this method update the gene dots' capacity

updateCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.RootPanel

this method update the gene dots' capacity when new data loaded

updateCitation(MedCitation, Element) - Method in class edu.iastate.jtm.assistant.BiblioPanel

updateCitation(MedCitation, Element) - Method in interface edu.iastate.jtm.assistant.CitationListener

updateCitation(MedCitation, Element) - Method in class edu.iastate.jtm.assistant.CitationPanel

updateDatabase() - Method in class edu.iastate.metnet.aracyc.ChangeName

updateDatabase() - Method in class edu.iastate.metnet.model.AbbreviationRulesModel

updateDictionary() - Method in class edu.iastate.jtm.assistant.Highlighter

updateDuplicationChecker(int, int) - Method in class fcmodeler.pathbinder.MedCrawler

updateElement(Element) - Method in class edu.iastate.jtm.gui.XmlTreeModel

updateEntry(String, List, boolean, boolean, Limits) - Method in class fcmodeler.pathbinder.FilterUpdater

updateFile(File, boolean, boolean, Limits) - Method in class fcmodeler.pathbinder.FilterUpdater

updateFile(File) - Method in class fcmodeler.pathbinder.MetaCrawler

updateFilterTable(boolean, Set) - Method in class fcmodeler.pathbinder.PmidFilter

updateGraphEdges() - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

update the edge in the graph model and must call after any add/delete operation

updateHistory(Document) - Method in class edu.iastate.jtm.jmed.Limits

updateMembers(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

update the member list

updateMembers(Integer, Vector) - Method in interface edu.iastate.metnet.interfaces.MyPaper

update the member list

updateminiCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

this method update the gene dots' capacity minimum value in legend panel when new data loaded

updateminiCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.LegendPanel

this method update the gene dots' minimum capacity when new data loaded

updateminiCapacity(int) - Method in class edu.iastate.metnet.birdseyeview.RootPanel

this method update the gene dots' mininum capacity when new data loaded

updatePannerLocation(MouseEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

updatePannerLocation(MouseEvent) - Method in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

updateStroke() - Method in class edu.iastate.metnet.metaomgraph.chart.RangeSelector

updateUI() - Method in class edu.iastate.jtm.gui.RowHeaderRenderer

updateUI() - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph

Override parent method with custom GraphUI.

updateUnit() - Method in class fcmodeler.pathbinder.MetaCrawler

updateUser(User) - Method in interface edu.iastate.metnet.interfaces.MyFacade

create a new user and presume that the user does not exist

updateUser(User) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

create a new user and presume that the user does not exist

upLevel(Element) - Method in class edu.iastate.jtm.util.ParenParser

UPPER_HORIZONTAL - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

UPPER_HORIZONTAL - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

UPPERCASE - Static variable in class edu.iastate.jtm.util.NameCharType

useFilter(PmidFilter) - Method in class fcmodeler.pathbinder.HiddenLink

useFilter(PmidFilter) - Method in class fcmodeler.pathbinder.PathBinder

user - Variable in class edu.iastate.metnet.dao.InteractionInformation

user who submit the interaction

User - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'user' table.

User() - Constructor for class edu.iastate.metnet.hibernate.User

Simple constructor of User instances.

User(String) - Constructor for class edu.iastate.metnet.hibernate.User

Constructor of User instances given a simple primary key.

USER_KEY - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication

user name node in the configure file

USER_KEYWORD - Static variable in class edu.iastate.jtm.assistant.Highlighter

userDataFolder - Variable in class edu.iastate.metnet.dataManager.DataManager

UserListTableModel - Class in edu.iastate.metnet.model

UserListTableModel(ListModel) - Constructor for class edu.iastate.metnet.model.UserListTableModel

username - Variable in class edu.iastate.biocyc.dao.rdb.ClassName

username

username - Variable in class edu.iastate.metnet.dao.CommentObject

username - Variable in class edu.iastate.metnet.dao.HistoryBlockunitImpl

user name

username - Variable in class edu.iastate.metnet.dao.HistoryInformation

who do this

username - Variable in class edu.iastate.metnet.dao.MyVersionNode

who imput the data

username - Variable in class edu.iastate.metnet.dao.ReferenceObject

utils - Static variable in class edu.iastate.biocyc.utils.BiocycUtils

the database statement instance

Utils - Class in edu.iastate.metnet.metaomgraph.utils

Utils() - Constructor for class edu.iastate.metnet.metaomgraph.utils.Utils

Utils - Class in edu.iastate.metnet.utils

Utilitiy class

utils - Static variable in class edu.iastate.metnet.utils.Utils

the database statement instance

UtilsTest - Class in edu.iastate.metnet.test

UtilsTest(String) - Constructor for class edu.iastate.metnet.test.UtilsTest

Constructor for UtilsTest.