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

A

aaQuery(Collection, Collection, Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade

run approximately amorphous graph query and visualize it

aaQuery(Collection, Collection, Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

run approximately amorphous graph query and visualize it

aaQuery(Collection, Collection, Collection) - Method in class edu.iastate.metnet.ui.PathwayEditor

run approximately amorphous graph query and visualize it

abbreviation() - Method in class edu.iastate.jtm.jmed.Query.Field

abbreviation - Variable in class edu.iastate.metnet.dao.AbbreviationObject

AbbreviationChecker - Class in edu.iastate.jtm

AbbreviationChecker() - Constructor for class edu.iastate.jtm.AbbreviationChecker

AbbreviationObject - Class in edu.iastate.metnet.dao

AbbreviationObject(Integer, String, boolean) - Constructor for class edu.iastate.metnet.dao.AbbreviationObject

AbbreviationObject(String) - Constructor for class edu.iastate.metnet.dao.AbbreviationObject

Abbreviationrules - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Abbreviationrules instances.

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

Constructor of Abbreviationrules instances given a simple primary key.

AbbreviationRules - Class in edu.iastate.metnet.ui

Edit the abbreviation rules, and then apply to the name and synonym in the current database

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

AbbreviationRules_btnClose_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnClose_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnClose_actionAdapter

AbbreviationRules_btnDelete_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnDelete_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnDelete_actionAdapter

AbbreviationRules_btnGenerate_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnGenerate_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnGenerate_actionAdapter

AbbreviationRules_btnInsert_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnInsert_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnInsert_actionAdapter

AbbreviationRules_btnModify_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnModify_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnModify_actionAdapter

AbbreviationRules_btnSortLongTerm_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnSortLongTerm_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnSortLongTerm_actionAdapter

AbbreviationRules_btnSortShortTerm_actionAdapter - Class in edu.iastate.metnet.ui

AbbreviationRules_btnSortShortTerm_actionAdapter(AbbreviationRules) - Constructor for class edu.iastate.metnet.ui.AbbreviationRules_btnSortShortTerm_actionAdapter

AbbreviationRulesModel - Class in edu.iastate.metnet.model

Table model for the entitywithcontext list table

AbbreviationRulesModel() - Constructor for class edu.iastate.metnet.model.AbbreviationRulesModel

AbbreviationTableModel - Class in edu.iastate.metnet.model

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

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

AboutFrame - Class in edu.iastate.metnet.metaomgraph

Frame that displays when user chooses Help->About.

AboutFrame() - Constructor for class edu.iastate.metnet.metaomgraph.AboutFrame

AboutWindow - Class in edu.iastate.metnet.dataManager

class represents "about" window

AboutWindow() - Constructor for class edu.iastate.metnet.dataManager.AboutWindow

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

abstract_ - Variable in class edu.iastate.metnet.dao.TairReferenceObject

AbstractAbbreviationrules - Class in edu.iastate.metnet.hibernate

A class that represents a row in the abbreviationrules table.

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

Simple constructor of AbstractAbbreviationrules instances.

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

Constructor of AbstractAbbreviationrules instances given a simple primary key.

AbstractAracycEntity - Class in edu.iastate.metnet.aracyc

AbstractAracycEntity() - Constructor for class edu.iastate.metnet.aracyc.AbstractAracycEntity

AbstractAracycEntity(Map) - Constructor for class edu.iastate.metnet.aracyc.AbstractAracycEntity

AbstractAracycEntityWithLocation - Class in edu.iastate.metnet.aracyc

AbstractAracycEntityWithLocation() - Constructor for class edu.iastate.metnet.aracyc.AbstractAracycEntityWithLocation

AbstractAracycFileReader - Class in edu.iastate.metnet.aracyc

abstract reader which implements read line stuff

AbstractAracycFileReader() - Constructor for class edu.iastate.metnet.aracyc.AbstractAracycFileReader

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

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

default constructor

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

default constructor

AbstractBlockunit - Class in edu.iastate.metnet.hibernate

A class that represents a row in the blockunit table.

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

Simple constructor of AbstractBlockunit instances.

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

Constructor of AbstractBlockunit instances given a simple primary key.

AbstractBlockunitabbreviation - Class in edu.iastate.metnet.hibernate

A class that represents a row in the blockunitabbreviation table.

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

Simple constructor of AbstractBlockunitabbreviation instances.

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

Constructor of AbstractBlockunitabbreviation instances given a simple primary key.

AbstractBlockunitcomment - Class in edu.iastate.metnet.hibernate

A class that represents a row in the blockunitcomment table.

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

Simple constructor of AbstractBlockunitcomment instances.

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

Constructor of AbstractBlockunitcomment instances given a composite primary key.

AbstractBlockunitconfidence - Class in edu.iastate.metnet.hibernate

A class that represents a row in the blockunitconfidence table.

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

Simple constructor of AbstractBlockunitconfidence instances.

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

Constructor of AbstractBlockunitconfidence instances given a simple primary key.

AbstractBlockunitDecorator - Class in edu.iastate.metnet.model

AbstractBlockunitDecorator() - Constructor for class edu.iastate.metnet.model.AbstractBlockunitDecorator

AbstractBlockunitref - Class in edu.iastate.metnet.hibernate

A class that represents a row in the blockunitref table.

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

Simple constructor of AbstractBlockunitref instances.

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

Constructor of AbstractBlockunitref instances given a composite primary key.

AbstractBlockunitsynonym - Class in edu.iastate.metnet.hibernate

A class that represents a row in the blockunitsynonym table.

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

Simple constructor of AbstractBlockunitsynonym instances.

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

Constructor of AbstractBlockunitsynonym instances given a composite primary key.

AbstractBrendaactivatingcompound - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendaactivatingcompound table.

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

Simple constructor of AbstractBrendaactivatingcompound instances.

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

Constructor of AbstractBrendaactivatingcompound instances given a composite primary key.

AbstractBrendacofactor - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendacofactor table.

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

Simple constructor of AbstractBrendacofactor instances.

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

Constructor of AbstractBrendacofactor instances given a composite primary key.

AbstractBrendainhibitor - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendainhibitor table.

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

Simple constructor of AbstractBrendainhibitor instances.

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

Constructor of AbstractBrendainhibitor instances given a composite primary key.

AbstractBrendametalion - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendametalion table.

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

Simple constructor of AbstractBrendametalion instances.

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

Constructor of AbstractBrendametalion instances given a composite primary key.

AbstractBrendaproduct - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendaproduct table.

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

Simple constructor of AbstractBrendaproduct instances.

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

Constructor of AbstractBrendaproduct instances given a composite primary key.

AbstractBrendarecommendname - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendarecommendname table.

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

Simple constructor of AbstractBrendarecommendname instances.

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

Constructor of AbstractBrendarecommendname instances given a simple primary key.

AbstractBrendaref - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendaref table.

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

Simple constructor of AbstractBrendaref instances.

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

Constructor of AbstractBrendaref instances given a simple primary key.

AbstractBrendasubstrate - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendasubstrate table.

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

Simple constructor of AbstractBrendasubstrate instances.

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

Constructor of AbstractBrendasubstrate instances given a composite primary key.

AbstractBrendasynonyms - Class in edu.iastate.metnet.hibernate

A class that represents a row in the _brendasynonyms table.

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

Simple constructor of AbstractBrendasynonyms instances.

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

Constructor of AbstractBrendasynonyms instances given a composite primary key.

AbstractChebiChemicalData - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_chemical_data table.

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

Simple constructor of AbstractChebiChemicalData instances.

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

Constructor of AbstractChebiChemicalData instances given a simple primary key.

AbstractChebiComments - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_comments table.

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

Simple constructor of AbstractChebiComments instances.

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

Constructor of AbstractChebiComments instances given a simple primary key.

AbstractChebiCompounds - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_compounds table.

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

Simple constructor of AbstractChebiCompounds instances.

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

Constructor of AbstractChebiCompounds instances given a simple primary key.

AbstractChebiDatabaseAccession - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_database_accession table.

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

Simple constructor of AbstractChebiDatabaseAccession instances.

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

Constructor of AbstractChebiDatabaseAccession instances given a simple primary key.

AbstractChebiNames - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_names table.

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

Simple constructor of AbstractChebiNames instances.

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

Constructor of AbstractChebiNames instances given a simple primary key.

AbstractChebiOntology - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_ontology table.

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

Simple constructor of AbstractChebiOntology instances.

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

Constructor of AbstractChebiOntology instances given a simple primary key.

AbstractChebiReference - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_reference table.

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

Simple constructor of AbstractChebiReference instances.

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

Constructor of AbstractChebiReference instances given a simple primary key.

AbstractChebiRelation - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_relation table.

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

Simple constructor of AbstractChebiRelation instances.

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

Constructor of AbstractChebiRelation instances given a simple primary key.

AbstractChebiVertices - Class in edu.iastate.metnet.hibernate

A class that represents a row in the chebi_vertices table.

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

Simple constructor of AbstractChebiVertices instances.

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

Constructor of AbstractChebiVertices instances given a simple primary key.

AbstractClassName - Class in edu.iastate.metnet.hibernate

hibernate class

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

Simple constructor of AbstractBlockunit instances.

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

Simple constructor of AbstractBlockunit instances.

AbstractCodeconfidence - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codeconfidence table.

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

Simple constructor of AbstractCodeconfidence instances.

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

Constructor of AbstractCodeconfidence instances given a simple primary key.

AbstractCodedatasource - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codedatasource table.

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

Simple constructor of AbstractCodedatasource instances.

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

Constructor of AbstractCodedatasource instances given a simple primary key.

AbstractCodeentitytype - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codeentitytype table.

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

Simple constructor of AbstractCodeentitytype instances.

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

Constructor of AbstractCodeentitytype instances given a simple primary key.

AbstractCodeinteractiontype - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codeinteractiontype table.

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

Simple constructor of AbstractCodeinteractiontype instances.

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

Constructor of AbstractCodeinteractiontype instances given a simple primary key.

AbstractCodelocation - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codelocation table.

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

Simple constructor of AbstractCodelocation instances.

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

Constructor of AbstractCodelocation instances given a simple primary key.

AbstractCodeorganism - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codeorganism table.

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

Simple constructor of AbstractCodeorganism instances.

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

Constructor of AbstractCodeorganism instances given a simple primary key.

AbstractCodePresentation - Class in edu.iastate.metnet.model

AbstractCodePresentation() - Constructor for class edu.iastate.metnet.model.AbstractCodePresentation

AbstractCodereferencetype - Class in edu.iastate.metnet.hibernate

A class that represents a row in the codereferencetype table.

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

Simple constructor of AbstractCodereferencetype instances.

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

Constructor of AbstractCodereferencetype instances given a simple primary key.

AbstractCoderule - Class in edu.iastate.metnet.hibernate

A class that represents a row in the coderule table.

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

Simple constructor of AbstractCoderule instances.

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

Constructor of AbstractCoderule instances given a simple primary key.

AbstractDictionary - Class in edu.iastate.jtm.dic

AbstractDictionary() - Constructor for class edu.iastate.jtm.dic.AbstractDictionary

AbstractDictionary(boolean) - Constructor for class edu.iastate.jtm.dic.AbstractDictionary

AbstractDictionary(SlidingWindow, boolean, boolean) - Constructor for class edu.iastate.jtm.dic.AbstractDictionary

AbstractEntity - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entity table.

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

Simple constructor of AbstractEntity instances.

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

Constructor of AbstractEntity instances given a simple primary key.

AbstractEntityabbreviation - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entityabbreviation table.

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

Simple constructor of AbstractEntityabbreviation instances.

AbstractEntityabbreviation(EntityabbreviationKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractEntityabbreviation

Constructor of AbstractEntityabbreviation instances given a composite primary key.

AbstractEntitycomment - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entitycomment table.

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

Simple constructor of AbstractEntitycomment instances.

AbstractEntitycomment(EntitycommentKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractEntitycomment

Constructor of AbstractEntitycomment instances given a composite primary key.

AbstractEntityOntology - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entity_ontology table.

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

Simple constructor of AbstractEntityOntology instances.

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

Constructor of AbstractEntityOntology instances given a simple primary key.

AbstractEntityPubchem - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entity_pubchem table.

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

Simple constructor of AbstractEntityPubchem instances.

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

Constructor of AbstractEntityPubchem instances given a simple primary key.

AbstractEntityPubchemName - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entity_pubchem_name table.

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

Simple constructor of AbstractEntityPubchemName instances.

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

Constructor of AbstractEntityPubchemName instances given a simple primary key.

AbstractEntityref - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entityref table.

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

Simple constructor of AbstractEntityref instances.

AbstractEntityref(EntityrefKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractEntityref

Constructor of AbstractEntityref instances given a composite primary key.

AbstractEntitysynonym - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entitysynonym table.

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

Simple constructor of AbstractEntitysynonym instances.

AbstractEntitysynonym(EntitysynonymKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractEntitysynonym

Constructor of AbstractEntitysynonym instances given a composite primary key.

AbstractEntitywithcontext - Class in edu.iastate.metnet.hibernate

A class that represents a row in the entitywithcontext table.

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

Simple constructor of AbstractEntitywithcontext instances.

AbstractEntitywithcontext(EntitywithcontextKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractEntitywithcontext

Constructor of AbstractEntitywithcontext instances given a composite primary key.

AbstractExcelSheet - Class in edu.iastate.metnet.analysis

AbstractExcelSheet() - Constructor for class edu.iastate.metnet.analysis.AbstractExcelSheet

AbstractExternaldb - Class in edu.iastate.metnet.hibernate

A class that represents a row in the externaldb table.

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

Simple constructor of AbstractExternaldb instances.

AbstractExternaldb(ExternaldbKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractExternaldb

Constructor of AbstractExternaldb instances given a composite primary key.

AbstractGraphMetaphor - Class in edu.iastate.metnet.graphmodel

abstract graph metaphor containing common utility functions and default behaviors.

AbstractGraphMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

defualt constrcutor

AbstractGraphProcessor - Class in edu.iastate.metnet.graphmodel

AbstractGraphProcessor() - Constructor for class edu.iastate.metnet.graphmodel.AbstractGraphProcessor

default constructor

AbstractGroupList - Class in edu.iastate.metnet.hibernate

A class that represents a row in the group_list table.

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

Simple constructor of AbstractGroupList instances.

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

Constructor of AbstractGroupList instances given a simple primary key.

AbstractGroupMember - Class in edu.iastate.metnet.hibernate

A class that represents a row in the group_member table.

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

Simple constructor of AbstractGroupMember instances.

AbstractGroupMember(GroupMemberKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractGroupMember

Constructor of AbstractGroupMember instances given a composite primary key.

AbstractGroupShare - Class in edu.iastate.metnet.hibernate

A class that represents a row in the group_share table.

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

Simple constructor of AbstractGroupShare instances.

AbstractGroupShare(GroupShareKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractGroupShare

Constructor of AbstractGroupShare instances given a composite primary key.

AbstractGtairProperty - Class in edu.iastate.metnet.hibernate

A class that represents a row in the gtair_property table.

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

Simple constructor of AbstractGtairProperty instances.

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

Constructor of AbstractGtairProperty instances given a simple primary key.

AbstractHistoryFlatInteraction - Class in edu.iastate.metnet.hibernate

hibernate class

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

Simple constructor of AbstractBlockunit instances.

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

Simple constructor of AbstractBlockunit instances.

AbstractHistoryFlatLiveEntity - Class in edu.iastate.metnet.hibernate

A class that represents a row in the history_flat_live_entity table.

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

Simple constructor of AbstractBlockunit instances.

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

Simple constructor of AbstractBlockunit instances.

AbstractHistoryFlatPathway - Class in edu.iastate.metnet.hibernate

hibernate class

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

Simple constructor of AbstractBlockunit instances.

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

Simple constructor of AbstractBlockunit instances.

AbstractInteraction - Class in edu.iastate.metnet.hibernate

A class that represents a row in the interaction table.

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

Simple constructor of AbstractInteraction instances.

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

Constructor of AbstractInteraction instances given a simple primary key.

AbstractInteractionparts - Class in edu.iastate.metnet.hibernate

A class that represents a row in the interactionparts table.

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

Simple constructor of AbstractInteractionparts instances.

AbstractInteractionparts(InteractionpartsKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractInteractionparts

Constructor of AbstractInteractionparts instances given a composite primary key.

AbstractInteractionproperties - Class in edu.iastate.metnet.hibernate

A class that represents a row in the interactionproperties table.

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

Simple constructor of AbstractInteractionproperties instances.

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

Constructor of AbstractInteractionproperties instances given a simple primary key.

AbstractJExcelClient - Class in edu.iastate.metnet.analysis

AbstractJExcelClient() - Constructor for class edu.iastate.metnet.analysis.AbstractJExcelClient

AbstractMetNetTable - Class in edu.iastate.metnet.db

AbstractMetNetTable() - Constructor for class edu.iastate.metnet.db.AbstractMetNetTable

AbstractMetnetWindow - Class in edu.iastate.metnet.ui

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

AbstractMultiBlockunitDecorator - Class in edu.iastate.metnet.model

AbstractMultiBlockunitDecorator() - Constructor for class edu.iastate.metnet.model.AbstractMultiBlockunitDecorator

default constructor

AbstractMultiBlockunitDecorator(Blockunit, Blockunit) - Constructor for class edu.iastate.metnet.model.AbstractMultiBlockunitDecorator

default constructor

AbstractMultiPathwayElementNode - Class in edu.iastate.metnet.dao

pathway element nodes which holds multiple element nodes from different pathway graphs.

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

default constructor

AbstractMultiPathwayElementNode(PathwayElementNode, PathwayElementNode) - Constructor for class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

create a multi-node containing two nodes

AbstractPathwayElementNode - Class in edu.iastate.metnet.dao

pathway element node.

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

AbstractPathwayparts - Class in edu.iastate.metnet.hibernate

A class that represents a row in the pathwayparts table.

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

Simple constructor of AbstractPathwayparts instances.

AbstractPathwayparts(PathwaypartsKey) - Constructor for class edu.iastate.metnet.hibernate.AbstractPathwayparts

Constructor of AbstractPathwayparts instances given a composite primary key.

AbstractPlotData - Class in edu.iastate.metnet.model

AbstractPlotData() - Constructor for class edu.iastate.metnet.model.AbstractPlotData

AbstractPlotData(DefaultExcelSheet) - Constructor for class edu.iastate.metnet.model.AbstractPlotData

AbstractRClient - Class in edu.iastate.metnet.analysis

AbstractRClient() - Constructor for class edu.iastate.metnet.analysis.AbstractRClient

AbstractTairAffy25kArrayElements - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_affy25k_array_elements table.

AbstractTairAffy25kArrayElements() - Constructor for class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements

Simple constructor of AbstractTairAffy25kArrayElements instances.

AbstractTairAffy25kArrayElements(Integer) - Constructor for class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements

Constructor of AbstractTairAffy25kArrayElements instances given a simple primary key.

AbstractTairAffy8kArrayElements - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_affy8k_array_elements table.

AbstractTairAffy8kArrayElements() - Constructor for class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements

Simple constructor of AbstractTairAffy8kArrayElements instances.

AbstractTairAffy8kArrayElements(Integer) - Constructor for class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements

Constructor of AbstractTairAffy8kArrayElements instances given a simple primary key.

AbstractTairAfgcArrayElements - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_afgc_array_elements table.

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

Simple constructor of AbstractTairAfgcArrayElements instances.

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

Constructor of AbstractTairAfgcArrayElements instances given a simple primary key.

AbstractTairAgiToUniprot - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_agi_to_uniprot table.

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

Simple constructor of AbstractTairAgiToUniprot instances.

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

Constructor of AbstractTairAgiToUniprot instances given a simple primary key.

AbstractTairAracycDump - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_aracyc_dump table.

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

Simple constructor of AbstractTairAracycDump instances.

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

Constructor of AbstractTairAracycDump instances given a simple primary key.

AbstractTairAthGoGoslim - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_ath_go_goslim table.

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

Simple constructor of AbstractTairAthGoGoslim instances.

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

Constructor of AbstractTairAthGoGoslim instances given a simple primary key.

AbstractTairSequencedGenes - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_sequenced_genes table.

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

Simple constructor of AbstractTairSequencedGenes instances.

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

Constructor of AbstractTairSequencedGenes instances given a simple primary key.

AbstractTairTargetpAnalysis - Class in edu.iastate.metnet.hibernate

A class that represents a row in the tair_targetp_analysis table.

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

Simple constructor of AbstractTairTargetpAnalysis instances.

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

Constructor of AbstractTairTargetpAnalysis instances given a simple primary key.

AbstractTreeModel - Class in edu.iastate.metnet.model

copy from http://java.sun.com/products/jfc/tsc/articles/jtree/ This class takes care of the event listener lists required by TreeModel.

AbstractTreeModel() - Constructor for class edu.iastate.metnet.model.AbstractTreeModel

AbstractTrieNode - Class in edu.iastate.jtm.dic

Provide methods for all TrieNode.

AbstractTrieNode() - Constructor for class edu.iastate.jtm.dic.AbstractTrieNode

AbstractUser - Class in edu.iastate.metnet.hibernate

A class that represents a row in the user table.

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

Simple constructor of AbstractUser instances.

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

Constructor of AbstractUser instances given a simple primary key.

AbstractVersionGraphMetaphor - Class in edu.iastate.metnet.graphmodel

special metaphor for version graph

AbstractVersionGraphMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.AbstractVersionGraphMetaphor

default costructor

AbstractView - Class in edu.iastate.metnet.birdseyeview

The AbstractView Class is a template for subclasses to implement specific Bird's Eye Views.

AbstractView(ViewInfo, BirdsEyeView, ArrayList, Dimension, String) - Constructor for class edu.iastate.metnet.birdseyeview.AbstractView

Constructor.

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

accept(File) - Method in class edu.iastate.metnet.dataManager.FileFilterImpl

accept(File) - Method in class edu.iastate.metnet.metaomgraph.GraphFileFilter

Determines whether or not to display a given file in the file chooser.

ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.RangeSelector

actionList - Variable in class edu.iastate.metnet.birdseyeview.ActionListComboBoxListener

ActionListComboBoxListener - Class in edu.iastate.metnet.birdseyeview

ActionListComboBoxListener(JComboBox) - Constructor for class edu.iastate.metnet.birdseyeview.ActionListComboBoxListener

actionPerformed(ActionEvent) - Method in class edu.iastate.jtm.gui.StatusBar

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.actions.HelpButtonAction

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.actions.LaunchApplicationListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.ActionListComboBoxListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.ExploRaseSubmitListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.GoDownListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.GoUpListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.LabelsButtonListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.LoadButtonListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.LoadCancelButtonListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.LoadFileButtonListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.LoadOkButtonListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.PathwaySubmitListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.birdseyeview.SaveButtonListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.dataManager.DescriptionFrame

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.dataManager.MenuActionListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.dataManager.PathwaySubmitListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.launch.MainMenuListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.mapbuilder.MapBuilderPanel.BuildListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.mapbuilder.ResetButton

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.mapbuilder.SelectAllButton

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.mapbuilder.SelectPathwayPanel.UpdateListingListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartDataExporter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartToolBar

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.CreateListFrame

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.DualListPanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.ExploRaseSubmitListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.ImportListDialog

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.ListPanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.MetaOmGraph

ActionListener for the MetaOmGraph window's menu items.

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.MetaOmHelpListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.NewProjectDialog

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.PathwaySubmitListener

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.test.AffyChipAnimationPanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.StripedTable.ColorEditor

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnClose_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnDelete_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnGenerate_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnInsert_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnModify_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnSortLongTerm_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.AbbreviationRules_btnSortShortTerm_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.Blip

Advances animation to next frame.

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SearchDialog_btnAppply_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SearchDialog_btnClose_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate_btnApprove_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate_btnCheckAll_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate_btnExtractLimit_actionAdapter

actionPerformed(ActionEvent) - Method in class edu.iastate.metnet.ui.SynonymCandidate_btnUncheckAll_actionAdapter

actionPerformed(ActionEvent) - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel

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

when it is done

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

insert, delete or modify

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

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnClose_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnDelete_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnGenerate_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnInsert_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnModify_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnSortLongTerm_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.AbbreviationRules_btnSortShortTerm_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.SearchDialog_btnAppply_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.SearchDialog_btnClose_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.SelectionListener

adaptee - Variable in class edu.iastate.metnet.ui.SynonymCandidate_btnApprove_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.SynonymCandidate_btnCheckAll_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.SynonymCandidate_btnExtractLimit_actionAdapter

adaptee - Variable in class edu.iastate.metnet.ui.SynonymCandidate_btnUncheckAll_actionAdapter

adaptee - Variable in class edu.iastate.reload.ui.ModelListerner

actual listener implementation

adaptee - Variable in class edu.iastate.reload.ui.SelectionListener

actual listener implementation

add(Object) - Method in class edu.iastate.metnet.model.DomainObjectListModel

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

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

addAffy25kID(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new affy25k id

addAffy25kID(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAffy8kID(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new affy8k id

addAffy8kID(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAfgcID(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new afgc id

addAfgcID(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAffy25kID(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllAffy25kID(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAffy8kID(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllAffy8kID(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAfgcID(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllAfgcID(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisActivatedBy(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all activated by loci

addAllAgrisActivatedBy(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisActivates(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all activates loci

addAllAgrisActivates(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisAffectedBy(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all affected by loci

addAllAgrisAffectedBy(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisAffects(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all affects loci

addAllAgrisAffects(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisCisBinindSite(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all binding site information

addAllAgrisCisBinindSite(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisReference(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all references

addAllAgrisReference(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisRepressedBy(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all repressed by loci

addAllAgrisRepressedBy(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAgrisRepresses(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all represses loci

addAllAgrisRepresses(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllAracycPathway(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add all pathways

addAllAracycPathway(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllComment(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new comment

addAllComment(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllGeneName(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add locus synonym and abbreviation

addAllGeneName(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllIncomingInteractionIDs(Collection) - Method in class edu.iastate.metnet.model.IntermediumEntityInformation

add all incoming interaction ids

addAllMapmanBinId(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add mapman bin id

addAllMapmanBinId(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllMapmanCategory(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add mapman category

addAllMapmanCategory(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllMapmanDescription(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add mapman description

addAllMapmanDescription(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllMetnetLocation(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllMetnetLocation(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllMetnetPathway(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new metnet pathway

addAllMetnetPathway(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllOutgoingInteractionIDs(Collection) - Method in class edu.iastate.metnet.model.IntermediumEntityInformation

add all outgoing interaction ids

addAllPredGuid(Collection) - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

add all pred node

addAllPredGuid(Collection) - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode

add all pred node

addAllReference(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllReference(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllSuccGuid(Collection) - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

add all succ node

addAllSuccGuid(Collection) - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode

add all succ node

addAllTairAnnotation(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllTairAnnotation(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAllUniprotID(Collection) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

addAllUniprotID(Collection) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAndRelation(IMetnetBlockUnit, IMetnetBlockUnit, Integer) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

addAndRelation(IMetnetBlockUnit, IMetnetBlockUnit) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

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

This method adds the given annotation to the bottom of the annotation panel list.

addAnotation(Annotation) - Method in class edu.iastate.metnet.birdseyeview.cellview.CellularLocation

add a annotation into the list

addAracycPathway(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new aracyc pathway

addAracycPathway(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addAttribute(String) - Method in class edu.iastate.metnet.soft.Entity

addAttribute(String, String) - Method in class edu.iastate.metnet.soft.Entity

addAttribute(String, String) - Method in class edu.iastate.metnet.soft.Sample

addBatch(String) - Method in class edu.iastate.jtm.util.MySqlConnector

addChangeListener(ChangeListener) - Method in class edu.iastate.metnet.ColorChooseButton

Adds a ChangeListener to be notified when the user changes the button's color.

addChangeListener(ChangeListener) - Method in class edu.iastate.metnet.metaomgraph.DualListPanel

Adds a ChangeListener to this DualListPanel.

addChangeListener(ChangeListener) - Method in class edu.iastate.metnet.metaomgraph.DualTablePanel

Adds a ChangeListener to this DualListPanel.

addChangeListener(ChangeListener) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Registers a ChangeListener to this project.

addChildren(DefaultMutableTreeNode, Element) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

Adds the given Element and its children to the given parent.

addCitationListener(CitationListener) - Method in class edu.iastate.jtm.assistant.CitationPool

addCitations(String) - Method in class edu.iastate.metnet.aracyc.AracycEntity

add citations

addCitations(ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity

add citations

addComment(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new comment

addComment(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addComment(String) - Method in class edu.iastate.metnet.mapbuilder.NodeInfo

Adds a comment for this node.

addComments(String) - Method in class edu.iastate.metnet.aracyc.AracycEntity

add comments

addComments(ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity

add comments

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

addCustomEntriesToTable(UIDefaults) - Method in class edu.iastate.reload.skin.OceanThemeX

Adds customized entries to the UIDefaults table.

addCustomEntriesToTable(UIDefaults) - Method in class javax.swing.plaf.metal.OceanTheme

Adds customized entries to the UIDefaults table.

addDownstreamGuid(String) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode

add a downstream node

addDownstreamGuid(String) - Method in interface edu.iastate.metnet.dao.PathwayElementNode

add a downstream node

addDownstreamNodeId(Integer) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode

add a downstream node

addDownstreamNodeId(Integer) - Method in class edu.iastate.metnet.dao.MyVersionNode

add a downstream node

addDownstreamNodeId(Integer) - Method in interface edu.iastate.metnet.dao.PathwayElementNode

add a donwstream node id

addEdge(Integer, Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph

add an edge

addEdge(Integer, Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

addEdge(Integer, Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph

addEdge(String) - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo

addEdge(Point2D, Point2D, PortView, PortView) - Method in class edu.iastate.reload.ui.MyMarqueeHandler

addEditorForColumn(int, TableCellEditor) - Method in class edu.iastate.metnet.model.ColumnEditorModel

addEditorForRow(int, TableCellEditor) - Method in class edu.iastate.metnet.model.RowEditorModel

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

addEntity(Entity) - Method in class edu.iastate.metnet.soft.Series

addEntity(String, String, boolean) - Method in class fcmodeler.pathbinder.gui.EntityPanel

Interface for other programs specifying entities.

addEntity(String, String, boolean) - Method in class fcmodeler.pathbinder.gui.PbFrame

Interface for other programs specifying entities.

AddEntityForm - Class in edu.iastate.metnet.ui

AddEntity user interface to edit entity with location

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

Constructor, initial the user interface and data binding paramters

addEntityForm - Static variable in class edu.iastate.metnet.ui.MainWindow2

entitywithlocation editor window instance

addEntry(String, Object) - Method in class edu.iastate.jtm.dic.AbstractDictionary

addExtInfoTab() - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel

addFileToList(SOFTFile) - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel

addFilterListener(ActionListener) - Method in class fcmodeler.pathbinder.gui.LocationPanel

addFolder(String) - Method in class edu.iastate.metnet.metaomgraph.ListTree

addFolderToRoot(String) - Method in class edu.iastate.metnet.metaomgraph.ListTree

addGene(Annotation) - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode

This method adds the given gene to the gene list.

addGene(Annotation) - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway

This method adds a gene panel to represent the given gene product annotation to the gene panel list.

addGeneList(String, int[]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Adds a gene list to the project.

addGeneList(int[]) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Adds a gene list to the project.

addGeneList(Vector) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Adds a gene list to the project.

addGenesToNodes(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoBioProcessView

addGenesToNodes(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoFunctionView

addGenesToNodes(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoView

Subclasses must provide a way to match nodes and annotations (genes).

addGoBiologicalProcess(GoTermID) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new biological process

addGoBiologicalProcess(GoTermID) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addGoCellularComponent(GoTermID) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new cellular component

addGoCellularComponent(GoTermID) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addGoMolecularFunction(GoTermID) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new molecular function

addGoMolecularFunction(GoTermID) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addHeaderDescriptor(String, String) - Method in class edu.iastate.metnet.soft.Entity

addIncomingInteractionID(Integer) - Method in class edu.iastate.metnet.model.IntermediumEntityInformation

add incoming interaction id

AddInteractionForm - Class in edu.iastate.metnet.ui

Main window for edit interaction

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

constrcutor, initialize the layout of the main window and data model of the controls

addInteractionForm - Static variable in class edu.iastate.metnet.ui.MainWindow2

interaction editor window instance

addJGraphEdge(Edge) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Adds an edge corresponding to the specified JGraph edge to the underlying JGraphT graph.

addJGraphTEdge(Edge) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Adds the specified JGraphT edge to be reflected by this graph model.

addJGraphTVertex(Object) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Adds the specified JGraphT vertex to be reflected by this graph model.

addJGraphVertex(GraphCell) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Add a vertex corresponding to this JGraph vertex to the JGraphT graph.

addJob(String, EUtility.Processor, boolean) - Method in class edu.iastate.jtm.jmed.EUtility

Entry point for subclasses.

addLayoutComponent(String, Component) - Method in class edu.iastate.metnet.birdseyeview.GenePanelLayout

addLeaf(String) - Method in class edu.iastate.metnet.birdseyeview.TreePanel

addLeftAndRight(Object, Object) - Method in class edu.iastate.metnet.dao.BidiMultiHashMap

addListAtSelection(GeneList) - Method in class edu.iastate.metnet.metaomgraph.ListTree

addListDataListener(ListDataListener) - Method in class com.jgoodies.binding.extras.ListModelHolder

Adds a listener to the list that's notified each time a change to the data model occurs.

addLocations(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.Annotation

Add the locations and set the location string.

addMarkListener(MarkListener) - Method in class edu.iastate.jtm.assistant.CitationPool

addMarkListener(MarkListener) - Method in interface edu.iastate.jtm.gui.Markable

addMetnetLocation(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new metnet location

addMetnetLocation(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addMetnetPathway(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new metnet pathway

addMetnetPathway(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addMouseListenerToHeaderInTable(JTable) - Method in class edu.iastate.metnet.model.TableSorter

There is no-where else to put this.

addName(String) - Method in class edu.iastate.metnet.dao.Candidate

addNameSource(NameSource) - Method in class edu.iastate.metnet.dao.ChebiOntologyName

addNode(GoNode) - Method in class edu.iastate.metnet.birdseyeview.goview.GoLevel

This method adds a node to this level.

addNode(PathwayElementNode) - Method in interface edu.iastate.metnet.dao.PathwayGraph

add an element

addNode(PathwayElementNode) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

addNode(PathwayElementNode) - Method in class edu.iastate.metnet.export.MyPathwayGraph

add an element

addOldNewLink(Integer, Integer) - Method in class edu.iastate.metnet.dao.MyVersionGraph

add a version relation

addOrRelation(IMetnetBlockUnit, IMetnetBlockUnit, Integer) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

addOrRelation(IMetnetBlockUnit, IMetnetBlockUnit) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

addOutgoingInteractionID(Integer) - Method in class edu.iastate.metnet.model.IntermediumEntityInformation

add outgoing interaction id

addParentAndChild(Object, Object) - Method in class edu.iastate.metnet.dao.RelationMap

add one relation

addPart() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo

Increases the number of parts in the reaction.

AddPathwayController - Class in edu.iastate.metnet.controller

AddPathwayController() - Constructor for class edu.iastate.metnet.controller.AddPathwayController

AddPathwayController(AddPathwayForm) - Constructor for class edu.iastate.metnet.controller.AddPathwayController

AddPathwayForm - Class in edu.iastate.metnet.ui

create and edit the pathway information like name, source

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

new window for editing pathway information

AddPathwayModel - Class in edu.iastate.metnet.model

AddPathwayModel() - Constructor for class edu.iastate.metnet.model.AddPathwayModel

addPathways(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.Annotation

Adds the pathways and sets the pathway string.

addPmid(String, boolean, int) - Method in class edu.iastate.jtm.assistant.CitationPool

addPredGuid(String) - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

add one pred node

addPredGuid(String) - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode

add one pred node

addProcessListener(ProcessListener) - Method in class edu.iastate.jtm.util.ProcessWrapper

addProtein(Protein) - Method in class edu.iastate.metnet.birdseyeview.Annotation

This method adds the given protein to the protein list.

addQueryConsumer(QueryConsumer) - Method in class edu.iastate.jtm.assistant.QueryBuilder

addQueueListener(QueueListener) - Method in class edu.iastate.jtm.assistant.CitationPool

addRecentProject(File) - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph

addRef(String, String) - Method in class edu.iastate.metnet.mapbuilder.NodeInfo

Adds a reference/citation for this node.

addRemoteReceiver(RemoteReceiver) - Method in class edu.iastate.jtm.util.RemoteControl

addSearchResult(PubMedQuerier, int) - Method in class edu.iastate.jtm.assistant.CitationPool

addSuccGuid(String) - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

add one succ node

addSuccGuid(String) - Method in interface edu.iastate.metnet.dao.MultiPathwayElementNode

add one succ node

addSynonym(String) - Method in class edu.iastate.metnet.mapbuilder.NodeInfo

Adds a synonym for this node.

addSynonyms(String) - Method in class edu.iastate.metnet.aracyc.AracycEntity

add new synonym

addSynonyms(ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity

add new synonym

addSynonymSources(Collection) - Method in class edu.iastate.metnet.dao.ChebiOntologyName

addTairAnnotation(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add new tait annotation

addTairAnnotation(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addTaxEntry(FilterEntry) - Method in class fcmodeler.pathbinder.PmidFilter

Add a tax_id to the filter.

addTerm(Query.CompositeTerm, Query.Term) - Method in class edu.iastate.jtm.jmed.Query

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

addTip(String, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTips

addTip(String, JTextPane) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTips

addTreeModelListener(TreeModelListener) - Method in class edu.iastate.metnet.model.TreeModelSupport

addUniprotID(String) - Method in class edu.iastate.metnet.dao.AtGeneSearchLocusObject

add another uniprot id

addUniprotID(String) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

addUpstreamGuid(String) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode

add an upstream node

addUpstreamGuid(String) - Method in interface edu.iastate.metnet.dao.PathwayElementNode

add an upstream node

addUpstreamNodeId(Integer) - Method in class edu.iastate.metnet.dao.AbstractPathwayElementNode

add an upstream node

addUpstreamNodeId(Integer) - Method in class edu.iastate.metnet.dao.MyVersionNode

add an upstream node

addUpstreamNodeId(Integer) - Method in interface edu.iastate.metnet.dao.PathwayElementNode

add an upstream node id

addValueChangeListener(PropertyChangeListener) - Method in class com.jgoodies.binding.extras.ListModelHolder

Adds the given PropertyChangeListener that will be notified if the value has been changed.

addVersion(Integer) - Method in class edu.iastate.metnet.dao.MyVersionGraph

add a new version

addVertexnPorts(Rectangle2D) - Method in class edu.iastate.reload.ui.MyMarqueeHandler

This is a convenient hook to automatically add a cell, its ports and a custom user object.

AdjacencyGraphWalker - Class in edu.iastate.metnet.graphmodel

specialized graph walker which walk throigh all adjacecy interaction nodes in the graph model in each pass

AdjacencyGraphWalker() - Constructor for class edu.iastate.metnet.graphmodel.AdjacencyGraphWalker

initialize something i do not know yet

adjacentIbidList(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

things are complicated if we support multiple catalysis for one enzymatic reaction.

adjacentIbidList(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

things are complicated if we support multiple catalysis for one enzymatic reaction.

adjustmentValueChanged(AdjustmentEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.ChartScrollBar

adjustName(Map) - Static method in class edu.iastate.biocyc.dao.txt.AbstractBiocycElement

adjust the name so it is unique in the whole name space.

adjustWindow() - Method in class fcmodeler.pathbinder.gui.HiddenLinkFrame

advancedUrl(String, String) - Static method in class edu.iastate.jtm.assistant.GoogleScholar

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

AFFY25K - Static variable in class edu.iastate.metnet.metaomgraph.utils.Utils

Affy25kID - Interface in edu.iastate.metnet.datamodel.attributes

interface representing Affy25KID

AFFY8K - Static variable in class edu.iastate.metnet.metaomgraph.utils.Utils

Affy8kID - Interface in edu.iastate.metnet.datamodel.attributes

Interface representing Affy8kID

AffyChipAnimationPanel - Class in edu.iastate.metnet.metaomgraph.test

AffyChipAnimationPanel() - Constructor for class edu.iastate.metnet.metaomgraph.test.AffyChipAnimationPanel

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

Interface representing AfgcID

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

algorithm - Static variable in class edu.iastate.metnet.birdseyeview.AbstractView

align(InteractionStructure) - Method in class edu.iastate.metnet.dao.InteractionStructure

generate alignment based on the entity id, i guess this should be changed to other condition for new release

alignMap - Variable in class edu.iastate.metnet.dao.AlignmentObject

alignment

alignment - Variable in class edu.iastate.metnet.graphmodel.AlignmentMetaphor

alignment used to metaphor

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

default alignment

AlignmentAlgorithm - Interface in edu.iastate.metnet.dao

define the interface of pathway alignment, following the way like metaphor and process

alignmentIndex - Variable in class edu.iastate.metnet.ui.PathwayEditor

indicate current index of alignment result

alignmentMbidMap - Variable in class edu.iastate.metnet.dao.PathwayAlignmentImpl

member element blockid mapping

AlignmentMetaphor - Class in edu.iastate.metnet.graphmodel

given the alignment, metaphor the current graph view

AlignmentMetaphor() - Constructor for class edu.iastate.metnet.graphmodel.AlignmentMetaphor

default constructor

AlignmentObject - Class in edu.iastate.metnet.dao

used to store the information of alignment over the network

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

alignmentSink - Variable in class edu.iastate.metnet.ui.CompileWorker

alignment result sinker, should from the parent window

alignPathwayGraph(PathwayAlignment) - Method in interface edu.iastate.metnet.dao.MultiPathwayGraph

standard interface to align two patway graph to generate a single graph model

alignPathwayGraph(PathwayAlignment) - Method in class edu.iastate.metnet.dao.MultiPathwayGraphImpl

standard interface to align two patway graph to generate a single graph model

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

ALL_MARKED - Static variable in interface edu.iastate.jtm.gui.Markable

ALL_WORDS - Static variable in class edu.iastate.jtm.assistant.GoogleScholar

ALLCAP - Static variable in interface edu.iastate.jtm.Stemmer

allCapPattern - Static variable in interface edu.iastate.jtm.Stemmer

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

allIcon - Variable in class edu.iastate.jtm.gui.MarkableHeaderRenderer

alternateRowColor - Static variable in class edu.iastate.metnet.MetNetLAF

alternateRowColor - Static variable in class edu.iastate.metnet.StripedTable

alternateRowColor - Static variable in class edu.iastate.reload.skin.MetNetLAF

AmorphousQueryForm - Class in edu.iastate.metnet.ui

EntitySelector

AmorphousQueryForm(Object) - Constructor for class edu.iastate.metnet.ui.AmorphousQueryForm

default constructor

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

andRelation - Variable in class edu.iastate.metnet.graphmodel.RelationObject

ANGLE - Static variable in class edu.iastate.metnet.ui.Blip

Sweep increment per frame, in degrees.

AnimatedSwingWorker - Class in edu.iastate.metnet.metaomgraph

This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread.

AnimatedSwingWorker(String, boolean) - Constructor for class edu.iastate.metnet.metaomgraph.AnimatedSwingWorker

Start a thread that will call the construct method and then exit.

AnimatedSwingWorker(String) - Constructor for class edu.iastate.metnet.metaomgraph.AnimatedSwingWorker

Annotation - Class in edu.iastate.metnet.birdseyeview

The Annotation Class encapsulates the annotation data for one gene product.

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

Constructor.

Annotation(String, String, ArrayList, ArrayList, double, ArrayList, ArrayList) - Constructor for class edu.iastate.metnet.birdseyeview.Annotation

Constructor.

AnnotationRenderer - Class in edu.iastate.metnet.birdseyeview

The AnnotationRenderer Class renders an Annotation Text Panel for display in a JList.

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

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

AnnotationService - Class in edu.iastate.metnet.hivemindService

HiveMind service provides annotation and ontology data (mostly used by BirdsEyeView)

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

AnnotationTextPanel - Class in edu.iastate.metnet.birdseyeview

The AnnotationTextPanel Class holds the text areas that display the annotation data for one gene product.

AnnotationTextPanel(Annotation, Color, Color, Font, Dimension) - Constructor for class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

Constructor for setting non-blank annotation.

AnnotationTextPanel(Color, Color, Font, Dimension) - Constructor for class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

Constructor for setting blank annotation.

AnnotationThread - Class in edu.iastate.metnet.threads

Thread to get annotation of all genes in batch mode

AnnotationThread() - Constructor for class edu.iastate.metnet.threads.AnnotationThread

ANYWORD - Static variable in interface edu.iastate.jtm.Stemmer

anyWordPattern - Static variable in interface edu.iastate.jtm.Stemmer

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

appendColumn(Object[], String) - Method in class edu.iastate.metnet.NoneditableTableModel

appendQuery(String) - Method in class edu.iastate.jtm.assistant.QueryPanel

appendResultSet(ResultSet, int) - Method in class edu.iastate.metnet.model.JDBCComboModel

append another row data from another result set

appendResultSet(ResultSet, String) - Method in class edu.iastate.metnet.model.JDBCComboModel

append another row data from another result set

appendResultSet(ResultSet) - Method in class edu.iastate.metnet.model.JDBCComboModel

appendRow(Object[]) - Method in class edu.iastate.metnet.NoneditableTableModel

appendRows(Object[][]) - Method in class edu.iastate.metnet.NoneditableTableModel

appendTerm(String, String, String, boolean) - Method in class edu.iastate.jtm.jmed.ESearch

appendTerm(String, String, String, boolean) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

application - Variable in class edu.iastate.metnet.actions.LaunchApplicationListener

applyFilter(String, boolean) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

applyFilter(String[], boolean) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

applyFilter(String[], boolean) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel

applyFilter(String, boolean) - Method in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel

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

applyMetaphore(IGraphMetaphor) - Method in class edu.iastate.metnet.graphmodel.JCategoryGraph

apply the metaphor instance, similar to the layout

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

apply the metaphor instance, similar to the layout

applyMetaphore(IGraphMetaphor) - Method in class edu.iastate.metnet.graphmodel.VersionGraph

apply the metaphor instance, similar to the layout

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

applyProcessor(IGraphProcessor) - Method in class edu.iastate.metnet.graphmodel.MultiPathwayModel

general method for post-modification on the graph data model

applyProcessor(IGraphProcessor) - Method in class edu.iastate.metnet.graphmodel.PathwayModel

general method for post-modification on the graph data model

applyQuery(Query) - Method in interface edu.iastate.jtm.assistant.QueryConsumer

applyQuery(Query) - Method in class edu.iastate.jtm.assistant.QueryPanel

applyTheme(String) - Method in class edu.iastate.metnet.utils.Utils

regardless the user options, always use the Eve's look and feel for MetNet tools.

applyTheme2(String) - Method in class edu.iastate.metnet.utils.Utils

apply the theme from the theme file based on metal theme

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

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

approve the candidate maybe we need lock the table to prevent any concurrent approve procedure???

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

approve the candidate maybe we need lock the table to prevent any concurrent approve procedure???

approved - Variable in class edu.iastate.metnet.model.CheckCandidate

ArabReaderTest - Class in edu.iastate.biocyc.test

import some data of Aracyc

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

AracycClass - Class in edu.iastate.metnet.aracyc

specialized class

AracycClass(Map) - Constructor for class edu.iastate.metnet.aracyc.AracycClass

AracycCompound - Class in edu.iastate.metnet.aracyc

AracycCompound() - Constructor for class edu.iastate.metnet.aracyc.AracycCompound

AracycCompound(Map) - Constructor for class edu.iastate.metnet.aracyc.AracycCompound

AracycEntity - Class in edu.iastate.metnet.aracyc

data object to match Blockunit/Entity

AracycEntity() - Constructor for class edu.iastate.metnet.aracyc.AracycEntity

AraCycForm - Class in edu.iastate.biocyc.ui

AraCycForm() - Constructor for class edu.iastate.biocyc.ui.AraCycForm

Creates new form AraCycForm

aracycid - Variable in class edu.iastate.metnet.aracyc.AracycEntity

UNIQUE-ID

aracycid - Variable in class edu.iastate.metnet.aracyc.AracycInteraction

UNIQUE-ID

AracycImporter - Class in edu.iastate.metnet.aracyc

dispatcher to other file reader and importer
the zip file format

AracycImporter() - Constructor for class edu.iastate.metnet.aracyc.AracycImporter

AracycInteraction - Class in edu.iastate.metnet.aracyc

data object for aracyc interaction

AracycInteraction() - Constructor for class edu.iastate.metnet.aracyc.AracycInteraction

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

Interface representing AracycPathway

AraCycPathwayModel - Class in edu.iastate.biocyc.ui

AraCycPathwayModel(ListModel) - Constructor for class edu.iastate.biocyc.ui.AraCycPathwayModel

aracycUpdate - Variable in class edu.iastate.metnet.graphmodel.JMetaphorGraph

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

arrayToVector(Object[]) - Method in class edu.iastate.metnet.utils.Utils

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

ASCENDING - Static variable in class edu.iastate.metnet.metaomgraph.TableSorter

ascending - Variable in class edu.iastate.metnet.model.TableSorter

ascIcon - Variable in class edu.iastate.jtm.gui.SortableHeaderRenderer

AsciiTrieNode - Class in edu.iastate.jtm.dic

AscII character TrieNode (95 characters: 32 ~ 126).

AsciiTrieNode() - Constructor for class edu.iastate.jtm.dic.AsciiTrieNode

asFilter() - Method in class fcmodeler.pathbinder.gui.LocationPanel

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

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

AT_LEAST_ONE - Static variable in class edu.iastate.jtm.assistant.GoogleScholar

AtGeneSearch - Class in edu.iastate.metnet.metaomgraph

AtGeneSearch() - Constructor for class edu.iastate.metnet.metaomgraph.AtGeneSearch

ATGENESEARCH_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel

AtGeneSearchLocusObject - Class in edu.iastate.metnet.dao

get all information for locus id

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

default constructor

AtGeneSearchObject - Interface in edu.iastate.metnet.hiveface

store the Arabidopsis annnotation

AtGeneSearchObjectImpl - Class in edu.iastate.metnet.export

delegate the data access object AtGeneSearch and implement some interfaces

AtGeneSearchObjectImpl(AtGeneSearchLocusObject) - Constructor for class edu.iastate.metnet.export.AtGeneSearchObjectImpl

default constructor

athLocus - Variable in class edu.iastate.metnet.dao.SoybeanHomology

ath locus

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

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

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

attach the interaciton to the pathway

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

attach the interaciton to the pathway

attachPathwayToClass(Integer, Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

add pathway to selected category

attachPathwayToClass(Integer, Collection) - Method in interface edu.iastate.metnet.interfaces.MyPaper

add pathway to selected category

attachProcess(Monitorable) - Method in class edu.iastate.jtm.gui.StatusBar

Attach a monitorable process to the statusbar.

attachProcess(Monitorable, boolean) - Method in class edu.iastate.jtm.gui.StatusBar

Attribute<V> - Interface in edu.iastate.metnet.datamodel

Attribute - Class in edu.iastate.metnet.soft

Attribute(String, String) - Constructor for class edu.iastate.metnet.soft.Attribute

AttributeFileReader - Class in edu.iastate.metnet.aracyc

read in the attribute like file from aracyc

AttributeFileReader() - Constructor for class edu.iastate.metnet.aracyc.AttributeFileReader

AttributeFileReaderEx - Class in edu.iastate.biocyc.io

same as AttributeFileReader except implementing the data structure by Map of MultiMap

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

AttributeFileReaderEx - Class in edu.iastate.metnet.aracyc

same as AttributeFileReader except implementing the data structure by Map of MultiMap

AttributeFileReaderEx() - Constructor for class edu.iastate.metnet.aracyc.AttributeFileReaderEx

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

AUTHOR - Static variable in class edu.iastate.jtm.assistant.GoogleScholar

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

autoscroll(Point) - Method in class edu.iastate.metnet.metaomgraph.ListTree

autoSizeBox(JGraph, Object, CellView) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

change the vertex size according to the content