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

O

Oasis - Class in edu.iastate.metnet.ui

also can extends com.jgoodies.plaf.plastic.PlasticTheme

Oasis() - Constructor for class edu.iastate.metnet.ui.Oasis

observe(Object, String) - Method in class com.jgoodies.binding.extras.ChangeTracker

Observes the specified readable bound bean property in the given bean.

observe(ValueModel) - Method in class com.jgoodies.binding.extras.ChangeTracker

Observes value changes in the given ValueModel.

obtainWriteLock() - Static method in class edu.iastate.metnet.ui.MainWindow2

obtain the write lock

OceanTheme - Class in javax.swing.plaf.metal

A modern theme for the Metal Look & Feel.

OceanTheme() - Constructor for class javax.swing.plaf.metal.OceanTheme

OceanThemeX - Class in edu.iastate.reload.skin

A modern theme for the Metal Look & Feel.

OceanThemeX() - Constructor for class edu.iastate.reload.skin.OceanThemeX

off - Variable in class edu.iastate.metnet.metaomgraph.PolygonPanel

offscreen - Variable in class edu.iastate.metnet.metaomgraph.test.AffyChipAnimationPanel

OK_ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

OK_COMMAND - Static variable in class edu.iastate.metnet.soft.SOFTParserOptionPanel

oldBlockunit - Variable in class edu.iastate.metnet.model.SelectedBlockunit

true if included in the merge operation

oldcompareTo(Object) - Method in class edu.iastate.metnet.metaomgraph.CorrelationValue

oldDataOpener - Class in edu.iastate.metnet.newgui

Wizard for opening existing data.

oldDataOpener() - Constructor for class edu.iastate.metnet.newgui.oldDataOpener

oldName - Variable in class edu.iastate.metnet.ui.CategoryRenameForm

old name

oldPearsonCorrelation(double[]) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc

Calculates the Pearson Correlation of this calculator's base data with another set of data.

oldWizardPanel - Class in edu.iastate.metnet.newgui

Abstract class for Wizard Panels.

oldWizardPanel() - Constructor for class edu.iastate.metnet.newgui.oldWizardPanel

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

onChoose(int, CategoryNode) - Method in class edu.iastate.metnet.ui.CategoryEditForm

callback function for category choice

onParen(Element, int) - Method in class edu.iastate.jtm.util.ParenParser

onParen(int) - Method in class edu.iastate.jtm.util.ParenParser

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

open(File, int) - Method in class edu.iastate.jtm.assistant.CitationPool

open(boolean) - Method in class edu.iastate.jtm.jmed.MedlineParser

open(String, boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

Open an XML file.

open(String) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

open(File, boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

Open an XML file.

open(File) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

open(InputStream, boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

Open an XML inputstream

open(InputStream) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

open(boolean) - Method in class edu.iastate.jtm.jmed.StreamXMLParser

open(String, boolean) - Static method in class edu.iastate.jtm.util.WriterOpener

open(File, boolean) - Static method in class edu.iastate.jtm.util.WriterOpener

OPEN_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmGraph

openProject(MetaOmProject) - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph

openSelectedTabs() - Method in class edu.iastate.metnet.ui.MainWindow2

the EXPERT USER request that when the program start up, all useful windows should be opened already

openURL(String) - Static method in class edu.iastate.metnet.hivemindService.BareBonesBrowserLaunch

operator(Query.Operator) - Method in class edu.iastate.jtm.jmed.Query.CompositeTerm

operator() - Method in class edu.iastate.jtm.jmed.Query.CompositeTerm

OPT - Static variable in class edu.iastate.jtm.util.TokenProcessor

OPT_LEFT - Static variable in class edu.iastate.jtm.util.TokenProcessor

OPT_RIGHT - Static variable in class edu.iastate.jtm.util.TokenProcessor

options - Variable in class edu.iastate.metnet.launch.RunCytoscape

OR - Static variable in class edu.iastate.jtm.jmed.Query.Operator

OrderableTable - Class in edu.iastate.metnet.metaomgraph.chart

A JTable in which you can use drag and drop to re-order the rows.

OrderableTable(NoneditableTableModel) - Constructor for class edu.iastate.metnet.metaomgraph.chart.OrderableTable

orderByLongTerm(String) - Method in class edu.iastate.metnet.db.TableAbbreviationRules

orderByShortTerm(String) - Method in class edu.iastate.metnet.db.TableAbbreviationRules

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

organism

organism - Variable in class edu.iastate.metnet.dao.PathwayObject

organism

oricolorRange - Variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView

orientation - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

default orientation, this decide the position of the root in the whole screen

originalGraph - Variable in class edu.iastate.metnet.ui.OverviewPanel

originalGraph - Variable in class edu.iastate.reload.ui.OverviewPanel

originalNodeSet - Variable in class edu.iastate.metnet.graphmodel.FCMetaphor

original system node need to be red colored

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

OTHER - Static variable in class edu.iastate.jtm.util.CharType

outputData(File) - Method in class edu.iastate.metnet.soft.SOFTParser

outputHits() - Method in class edu.iastate.jtm.EntityFinder

outputMetadata(File) - Method in class edu.iastate.metnet.soft.SOFTParser

outputStream(InputStream, Writer) - Static method in class edu.iastate.jtm.jmed.EFetch

outputStream(InputStream, Writer) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

outputTree(OutputStream) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

Outputs this ExtendedInfoTree to the given OutputStream.

overlay(JGraph, Graphics, boolean) - Method in class edu.iastate.reload.ui.MyMarqueeHandler

OverviewPanel - Class in edu.iastate.metnet.ui

OverviewPanel(JGraph, JViewport) - Constructor for class edu.iastate.metnet.ui.OverviewPanel

GPOverviewPanel provides a 'birds-eye' view of the active document.

OverviewPanel - Class in edu.iastate.reload.ui

OverviewPanel(JGraph, JViewport) - Constructor for class edu.iastate.reload.ui.OverviewPanel

GPOverviewPanel provides a 'birds-eye' view of the active document.

OverviewPanel.PannerViewfinder - Class in edu.iastate.metnet.ui

OverviewPanel.PannerViewfinder(Container, JViewport) - Constructor for class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

OverviewPanel.PannerViewfinder - Class in edu.iastate.reload.ui

OverviewPanel.PannerViewfinder(Container, JViewport) - Constructor for class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

OverviewPanel.ViewRedirector - Class in edu.iastate.metnet.ui

OverviewPanel.ViewRedirector(GraphLayoutCache) - Constructor for class edu.iastate.metnet.ui.OverviewPanel.ViewRedirector

OverviewPanel.ViewRedirector - Class in edu.iastate.reload.ui

OverviewPanel.ViewRedirector(GraphLayoutCache) - Constructor for class edu.iastate.reload.ui.OverviewPanel.ViewRedirector

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