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

B

Background - Static variable in class edu.iastate.metnet.birdseyeview.TextPanel

background - Variable in class edu.iastate.metnet.metaomgraph.AboutFrame

BackgroundTask - Class in edu.iastate.metnet.hibernate

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

BareBonesBrowserLaunch - Class in edu.iastate.metnet.hivemindService

BareBonesBrowserLaunch() - Constructor for class edu.iastate.metnet.hivemindService.BareBonesBrowserLaunch

BASEGZ - Static variable in class fcmodeler.pathbinder.MedLeaseClient

BASEZIP - Static variable in class fcmodeler.pathbinder.MedLeaseClient

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

batch delete

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

batch delete

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

batch insert

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

batch insert

batchScan(String[]) - Method in class fcmodeler.pathbinder.MedCrawler

batchScan(File[]) - Method in class fcmodeler.pathbinder.MedCrawler

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

batch update

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

batch update

benchmark(String, int) - Static method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Benchmark the performance of the new RandomAccessFile class.

benchmark(String, int) - Static method in class edu.iastate.metnet.soft.RandomAccessFile

Benchmark the performance of the new RandomAccessFile class.

bevGetAllLocationInfo() - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetAllLocationInfo() - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetAllLocationInfo() - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetAllLocationInfo() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoBioProcesses(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoBioProcesses(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoBioProcesses(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoBioProcesses(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoChildren(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoChildren(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoChildren(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoChildren(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoFunctions(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoFunctions(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoFunctions(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoFunctions(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoGeneProductID(String) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoGeneProductID(String) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoGeneProductID(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoGeneProductID(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoNodeName(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoNodeName(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoNodeName(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoNodeName(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoNodesWithinDistance(Integer, int) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoNodesWithinDistance(Integer, int) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoNodesWithinDistance(Integer, int) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoNodesWithinDistance(Integer, int) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetGoTermAncestors(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetGoTermAncestors(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetGoTermAncestors(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetGoTermAncestors(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetLocations(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetLocations(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetLocations(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetLocations(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetLocusIDs(String) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetLocusIDs(String) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetLocusIDs(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetLocusIDs(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetMetnetEntityID(String) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetMetnetEntityID(String) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetMetnetEntityID(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetMetnetEntityID(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetPathways(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetPathways(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetPathways(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetPathways(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetPolypeptides(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetPolypeptides(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetPolypeptides(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetPolypeptides(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

bevGetProteinComplexes(Integer) - Method in class edu.iastate.metnet.export.GraphExporterImpl

bevGetProteinComplexes(Integer) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

BirdsEyeView code

bevGetProteinComplexes(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

BirdsEyeView code

bevGetProteinComplexes(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

BirdsEyeView code

BiblioPanel - Class in edu.iastate.jtm.assistant

BiblioPanel() - Constructor for class edu.iastate.jtm.assistant.BiblioPanel

biblioPanel - Static variable in class edu.iastate.jtm.assistant.Controller

BibTex - Class in edu.iastate.jtm.assistant

BibTex() - Constructor for class edu.iastate.jtm.assistant.BibTex

BIBTEX - Static variable in class edu.iastate.jtm.assistant.Exporter

BidiMultiHashMap - Class in edu.iastate.metnet.dao

bidirectional multi-singlekey <->multi-singlevalue mapping

BidiMultiHashMap() - Constructor for class edu.iastate.metnet.dao.BidiMultiHashMap

bind(AddPathwayForm, AddPathwayModel) - Method in class edu.iastate.metnet.controller.AddPathwayController

BiocycClass - Class in edu.iastate.biocyc.dao.txt

specialized class

BiocycClass(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycClass

default constructor

BiocycCompound - Class in edu.iastate.biocyc.dao.txt

biocyc compound

BiocycCompound(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycCompound

default constructor

BiocycElement - Interface in edu.iastate.biocyc.dao.txt

common properties of each file.

BiocycEnzrxn - Class in edu.iastate.biocyc.dao.txt

hold data for enzymatic reactions

BiocycEnzrxn(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycEnzrxn

default constrcutor

BiocycForm - Class in edu.iastate.biocyc.ui

BiocycForm(String) - Constructor for class edu.iastate.biocyc.ui.BiocycForm

Creates new form BiocycForm

BiocycGene - Class in edu.iastate.biocyc.dao.txt

gene object

BiocycGene(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycGene

default constructor

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

biocyc id

BiocycImporter - Class in edu.iastate.biocyc.io

read the Biocyc flat files

BiocycImporter() - Constructor for class edu.iastate.biocyc.io.BiocycImporter

initialize the class data

BiocycPathway - Class in edu.iastate.biocyc.dao.txt

pathway object

BiocycPathway(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycPathway

default constrcutor

BiocycProtein - Class in edu.iastate.biocyc.dao.txt

BiocycProtein(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycProtein

default constructor

BiocycReaction - Class in edu.iastate.biocyc.dao.txt

BiocycReaction(Map) - Constructor for class edu.iastate.biocyc.dao.txt.BiocycReaction

default constructor

BiocycUtils - Class in edu.iastate.biocyc.utils

Utilitiy class

biologicalType - Variable in class edu.iastate.metnet.dao.AbstractPathwayElementNode

the biological type

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

live entity, interaction or pathway

birdsEyeView - Variable in class edu.iastate.metnet.birdseyeview.AbstractView

BirdsEyeView - Class in edu.iastate.metnet.birdseyeview

The BirdsEyeView Class is the main class for the Bird's Eye View API in the Metnet Project.

BirdsEyeView(JFrame) - Constructor for class edu.iastate.metnet.birdseyeview.BirdsEyeView

Constructor.

BirdsEyeView(JFrame, int, String) - Constructor for class edu.iastate.metnet.birdseyeview.BirdsEyeView

Constructor.

birdsEyeView - Variable in class edu.iastate.metnet.hivemindService.ExportToBirdsEyeView

BirdsEyeView.LoadAnnotation - Class in edu.iastate.metnet.birdseyeview

This class uses thread to load annotation independently

BirdsEyeView.LoadAnnotation(int, ArrayList, ArrayList) - Constructor for class edu.iastate.metnet.birdseyeview.BirdsEyeView.LoadAnnotation

BirdsEyeView.Task - Class in edu.iastate.metnet.birdseyeview

BirdsEyeView.Task() - Constructor for class edu.iastate.metnet.birdseyeview.BirdsEyeView.Task

BirdsEyeViewException - Exception in edu.iastate.metnet.birdseyeview

The BirdsEyeViewException Class TODO

BirdsEyeViewException(String) - Constructor for exception edu.iastate.metnet.birdseyeview.BirdsEyeViewException

Constructor.

BirdsEyeViewWindow - Class in edu.iastate.metnet.birdseyeview

The BirdsEyeViewWindow Class enables clients to use the Bird's Eye View API as a stand alone application.

BirdsEyeViewWindow() - Constructor for class edu.iastate.metnet.birdseyeview.BirdsEyeViewWindow

Constructor.

BirdsEyeViewWindow(int, String) - Constructor for class edu.iastate.metnet.birdseyeview.BirdsEyeViewWindow

Constructor.

BLACK - Static variable in class edu.iastate.reload.skin.OceanThemeX

The OceanTheme value for black.

BLACK - Static variable in class javax.swing.plaf.metal.OceanTheme

The OceanTheme value for black.

Blip - Class in edu.iastate.metnet.ui

Simple animation in the style of a radar screen.

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

Creates a blip.

blip - Variable in class edu.iastate.metnet.ui.WaitingDialog

waiting animation

blockId - Variable in class edu.iastate.metnet.dao.AbstractPathwayElementNode

the blockid of the blockunit

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

blockid of the blockunit

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

blockid of the data

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

the id of the interaction

blockid - Variable in class edu.iastate.metnet.dao.ZVertex

blockid of the node

blockID - Variable in class edu.iastate.metnet.model.EntityConfidenceObservable

blockIdList - Variable in class edu.iastate.metnet.ui.BlockunitWorker

blockid list to be found

blockIdSet - Variable in class edu.iastate.metnet.graphmodel.PathwayElementMetaphor

blockid need to be highlighted

blockunit - Variable in class edu.iastate.metnet.dao.MetnetBlockUnit

always the latest version for user interface

Blockunit - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Blockunit instances.

Blockunit(Integer) - Constructor for class edu.iastate.metnet.hibernate.Blockunit

Constructor of Blockunit instances given a simple primary key.

blockunit - Variable in class edu.iastate.metnet.model.AbstractBlockunitDecorator

the internal blockunit

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

delegated blockunit

Blockunitabbreviation - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Blockunitabbreviation instances.

Blockunitabbreviation(Integer) - Constructor for class edu.iastate.metnet.hibernate.Blockunitabbreviation

Constructor of Blockunitabbreviation instances given a simple primary key.

BlockunitChoice - Class in edu.iastate.biocyc.dao.rdb

BlockunitChoice(Blockunit) - Constructor for class edu.iastate.biocyc.dao.rdb.BlockunitChoice

Blockunitcomment - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Blockunitcomment instances.

Blockunitcomment(BlockunitcommentKey) - Constructor for class edu.iastate.metnet.hibernate.Blockunitcomment

Constructor of Blockunitcomment instances given a composite primary key.

BlockunitcommentKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the blockunitcomment table.

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

Simple constructor of BlockunitcommentKey instances.

Blockunitconfidence - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Blockunitconfidence instances.

Blockunitconfidence(Integer) - Constructor for class edu.iastate.metnet.hibernate.Blockunitconfidence

Constructor of Blockunitconfidence instances given a simple primary key.

BlockunitFinder - Class in edu.iastate.metnet.ui

blockunitFinder - Static variable in class edu.iastate.metnet.ui.BlockunitFinder

BlockunitFinderTest - Class in edu.iastate.metnet.test

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

Constructor for BlockunitFinderTest.

BlockunitObject - Interface in edu.iastate.metnet.hiveface

BlockunitObjectImpl - Class in edu.iastate.metnet.export

BlockunitObjectImpl(Blockunit) - Constructor for class edu.iastate.metnet.export.BlockunitObjectImpl

Blockunitref - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Blockunitref instances.

Blockunitref(BlockunitrefKey) - Constructor for class edu.iastate.metnet.hibernate.Blockunitref

Constructor of Blockunitref instances given a composite primary key.

BlockunitrefKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the blockunitref table.

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

Simple constructor of BlockunitrefKey instances.

blockunitSink - Variable in class edu.iastate.metnet.ui.BlockunitWorker

blockunit sink

Blockunitsynonym - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Blockunitsynonym instances.

Blockunitsynonym(BlockunitsynonymKey) - Constructor for class edu.iastate.metnet.hibernate.Blockunitsynonym

Constructor of Blockunitsynonym instances given a composite primary key.

BlockunitSynonymCandidate - Class in edu.iastate.metnet.hibernate

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

BlockunitsynonymKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the blockunitsynonym table.

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

Simple constructor of BlockunitsynonymKey instances.

BlockunitTest - Class in edu.iastate.biocyc.test

BlockunitTest(String) - Constructor for class edu.iastate.biocyc.test.BlockunitTest

default constructor

BlockunitWorker - Class in edu.iastate.metnet.ui

blockunit find thread

BlockunitWorker(Collection, Vector) - Constructor for class edu.iastate.metnet.ui.BlockunitWorker

default constructor

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

both - Variable in class edu.iastate.metnet.ui.AddPathwayForm

dummy swing

both - Variable in class edu.iastate.metnet.ui.HelpWindow

both - Variable in class edu.iastate.metnet.ui.Splash

bottomLevel - Variable in class edu.iastate.metnet.birdseyeview.goview.GoView

BPathwaySelectionFrame - Class in edu.iastate.metnet.birdseyeview

Brendaactivatingcompound - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendaactivatingcompound instances.

Brendaactivatingcompound(BrendaactivatingcompoundKey) - Constructor for class edu.iastate.metnet.hibernate.Brendaactivatingcompound

Constructor of Brendaactivatingcompound instances given a composite primary key.

BrendaactivatingcompoundKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendaactivatingcompound table.

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

Simple constructor of BrendaactivatingcompoundKey instances.

Brendacofactor - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendacofactor instances.

Brendacofactor(BrendacofactorKey) - Constructor for class edu.iastate.metnet.hibernate.Brendacofactor

Constructor of Brendacofactor instances given a composite primary key.

BrendacofactorKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendacofactor table.

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

Simple constructor of BrendacofactorKey instances.

Brendainhibitor - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendainhibitor instances.

Brendainhibitor(BrendainhibitorKey) - Constructor for class edu.iastate.metnet.hibernate.Brendainhibitor

Constructor of Brendainhibitor instances given a composite primary key.

BrendainhibitorKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendainhibitor table.

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

Simple constructor of BrendainhibitorKey instances.

Brendametalion - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendametalion instances.

Brendametalion(BrendametalionKey) - Constructor for class edu.iastate.metnet.hibernate.Brendametalion

Constructor of Brendametalion instances given a composite primary key.

BrendametalionKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendametalion table.

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

Simple constructor of BrendametalionKey instances.

Brendaproduct - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendaproduct instances.

Brendaproduct(BrendaproductKey) - Constructor for class edu.iastate.metnet.hibernate.Brendaproduct

Constructor of Brendaproduct instances given a composite primary key.

BrendaproductKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendaproduct table.

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

Simple constructor of BrendaproductKey instances.

Brendarecommendname - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendarecommendname instances.

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

Constructor of Brendarecommendname instances given a simple primary key.

Brendaref - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendaref instances.

Brendasubstrate - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendasubstrate instances.

Brendasubstrate(BrendasubstrateKey) - Constructor for class edu.iastate.metnet.hibernate.Brendasubstrate

Constructor of Brendasubstrate instances given a composite primary key.

BrendasubstrateKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendasubstrate table.

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

Simple constructor of BrendasubstrateKey instances.

Brendasynonyms - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Brendasynonyms instances.

Brendasynonyms(BrendasynonymsKey) - Constructor for class edu.iastate.metnet.hibernate.Brendasynonyms

Constructor of Brendasynonyms instances given a composite primary key.

BrendasynonymsKey - Class in edu.iastate.metnet.hibernate

A class representing a composite primary key id for the _brendasynonyms table.

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

Simple constructor of BrendasynonymsKey instances.

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

Browser - Class in edu.iastate.metnet.hivemindService

HiveMind service opens AtGeneSearch/AtMetaboliteSearch webpage to search for a gene/metabolite

Browser() - Constructor for class edu.iastate.metnet.hivemindService.Browser

btnAppply - Variable in class edu.iastate.metnet.ui.SearchDialog

btnAppply_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SearchDialog

btnApprove - Variable in class edu.iastate.metnet.ui.SynonymCandidate

btnApprove_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate

btnCheckAll - Variable in class edu.iastate.metnet.ui.SynonymCandidate

btnCheckAll_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate

btnClose - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnClose - Variable in class edu.iastate.metnet.ui.InteractionSelector

close current window

btnClose - Variable in class edu.iastate.metnet.ui.SearchDialog

btnClose_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

btnClose_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SearchDialog

btnDelete - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnDelete_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

notice that the deletion is based on the string in the text field, not based on the volatile ID.

btnExtractLimit - Variable in class edu.iastate.metnet.ui.SynonymCandidate

btnExtractLimit_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate

btnGenerate - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnGenerate_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

btnInsert - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnInsert_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

insert new, call table directly

btnModify - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnModify_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

btnQuery - Variable in class edu.iastate.metnet.ui.InteractionSelector

query action

btnSortLongTerm - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnSortLongTerm_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

btnSortShortTerm - Variable in class edu.iastate.metnet.ui.AbbreviationRules

btnSortShortTerm_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules

btnUncheckAll - Variable in class edu.iastate.metnet.ui.SynonymCandidate

btnUncheckAll_actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate

buffer - Variable in class edu.iastate.metnet.dao.MetnetBlockUnit

store the original copy for reloaded user interface

buffer - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

The buffer used to load the data.

buffer - Variable in class edu.iastate.metnet.soft.RandomAccessFile

The buffer used to load the data.

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

bufferModified - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

True if the data in the buffer has been modified.

bufferModified - Variable in class edu.iastate.metnet.soft.RandomAccessFile

True if the data in the buffer has been modified.

bufferStart - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

The offset in bytes of the start of the buffer, from the start of the file.

bufferStart - Variable in class edu.iastate.metnet.soft.RandomAccessFile

The offset in bytes of the start of the buffer, from the start of the file.

bufferToHex(byte[]) - Static method in class edu.iastate.metnet.utils.HexUtil

Returns a string containing the hexadecimal representation of the input byte array.

bufferToHex(byte[], int, int) - Static method in class edu.iastate.metnet.utils.HexUtil

Returns a string containing the hexadecimal representation of the input byte array.

buildFiles(ArrayList, ArrayList, JProgressBar, boolean, boolean, boolean, File) - Static method in class edu.iastate.metnet.mapbuilder.XMLBuilder

Compiles graph files for the given list of pathways, using the given build options.

buildPanel - Variable in class edu.iastate.metnet.mapbuilder.MapBuilderPanel

buildTree(CellView) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

build the tree for one cell view recursively

buildTrees(List) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

build tree for each root

button - Variable in class edu.iastate.metnet.StripedTable.ColorEditor

buttonGroup1 - Variable in class edu.iastate.metnet.ui.SearchDialog

ButtonPanel - Class in edu.iastate.metnet.birdseyeview

The ButtonPanel Class holds the view combo box, the 'main' experiment combo box, the 'load new data' button, and the GO view buttons.

ButtonPanel(BirdsEyeView, Dimension, ArrayList) - Constructor for class edu.iastate.metnet.birdseyeview.ButtonPanel

Constructor.

bytesTransferred(long) - Method in class fcmodeler.pathbinder.MedLeaseClient