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

E

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

get the graph model from the node list

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

run exactly amorphous graph query and visualize it

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

run exactly amorphous graph query and visualize it

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

we use some default values and do NOT generate JUNG graph model since it is not serializable.

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

we use some default values and do NOT generate JUNG graph model since it is not serializable.

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

run exactly amorphous graph query and visualize it

ebid - Variable in class edu.iastate.metnet.ui.AddInteractionForm

ebid

echo - Class in fcmodeler.pathbinder

echo() - Constructor for class fcmodeler.pathbinder.echo

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

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

EDGE_CREATION - Static variable in class edu.iastate.reload.ui.NetworkEditForm

drag to create an edge

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

edgeSeparation - Variable in class edu.iastate.reload.ui.JGraphParallelEdgeRouter

The distance between the control point and the middle line.

edgeViewMap - Variable in class edu.iastate.metnet.graphmodel.CategoryLayoutAlgorithm

store the edge view by using the (source id, target id) as the key

edgeViewMap - Variable in class edu.iastate.metnet.graphmodel.EditingLayoutAlgorithm

store the edge view by using the (source id, target id) as the key

edgeViewMap - Variable in class edu.iastate.metnet.graphmodel.HierachyLayoutAlgorithm

store the edge view by using the (source id, target id) as the key

edgeViewMap - Variable in class edu.iastate.metnet.graphmodel.InputLayoutAlgorithm

store the edge view by using the (source id, target id) as the key

edgeViewMap - Variable in class edu.iastate.metnet.graphmodel.VersionyLayoutAlgorithm

store the edge view by using the (source id, target id) as the key

edit(Map) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Applies the specified attributes to the model, as in GraphModel.edit(java.util.Map, org.jgraph.graph.ConnectionSet, org.jgraph.graph.ParentMap, javax.swing.undo.UndoableEdit[]) method.

EDIT - Static variable in class edu.iastate.metnet.StripedTable.ColorEditor

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

editableColumns - Variable in class edu.iastate.metnet.NoneditableTableModel

A list of the editable columns

editDescription(JTextArea, String) - Method in class edu.iastate.metnet.dataManager.DataManager

editDialog - Variable in class edu.iastate.metnet.graphmodel.JMetaphorGraph.EditorGraphUI

EditingLayoutAlgorithm - Class in edu.iastate.metnet.graphmodel

support the general network layout based on the node id

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

EditingMetaphor - Class in edu.iastate.metnet.graphmodel

follow the FCMetaphor but never look at the database.

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

default constructor

edu.iastate.biocyc.dao.rdb - package edu.iastate.biocyc.dao.rdb

edu.iastate.biocyc.dao.txt - package edu.iastate.biocyc.dao.txt

edu.iastate.biocyc.io - package edu.iastate.biocyc.io

edu.iastate.biocyc.test - package edu.iastate.biocyc.test

edu.iastate.biocyc.ui - package edu.iastate.biocyc.ui

edu.iastate.biocyc.utils - package edu.iastate.biocyc.utils

edu.iastate.jtm - package edu.iastate.jtm

edu.iastate.jtm.assistant - package edu.iastate.jtm.assistant

edu.iastate.jtm.dic - package edu.iastate.jtm.dic

edu.iastate.jtm.gui - package edu.iastate.jtm.gui

edu.iastate.jtm.jmed - package edu.iastate.jtm.jmed

edu.iastate.jtm.util - package edu.iastate.jtm.util

edu.iastate.metnet - package edu.iastate.metnet

edu.iastate.metnet.actions - package edu.iastate.metnet.actions

edu.iastate.metnet.admin - package edu.iastate.metnet.admin

administrator utility used by curator features

edu.iastate.metnet.analysis - package edu.iastate.metnet.analysis

Data analysis.

edu.iastate.metnet.aracyc - package edu.iastate.metnet.aracyc

importing the Aracyc's Biocyc-format flatfiles

edu.iastate.metnet.birdseyeview - package edu.iastate.metnet.birdseyeview

edu.iastate.metnet.birdseyeview.cellview - package edu.iastate.metnet.birdseyeview.cellview

edu.iastate.metnet.birdseyeview.db - package edu.iastate.metnet.birdseyeview.db

edu.iastate.metnet.birdseyeview.goview - package edu.iastate.metnet.birdseyeview.goview

edu.iastate.metnet.birdseyeview.pathwayview - package edu.iastate.metnet.birdseyeview.pathwayview

edu.iastate.metnet.controller - package edu.iastate.metnet.controller

edu.iastate.metnet.dao - package edu.iastate.metnet.dao

edu.iastate.metnet.dataManager - package edu.iastate.metnet.dataManager

edu.iastate.metnet.datamodel - package edu.iastate.metnet.datamodel

edu.iastate.metnet.datamodel.attributes - package edu.iastate.metnet.datamodel.attributes

edu.iastate.metnet.datamodel.db - package edu.iastate.metnet.datamodel.db

edu.iastate.metnet.db - package edu.iastate.metnet.db

encapsualte the database operation for every table and every view

edu.iastate.metnet.event - package edu.iastate.metnet.event

3rd party class

edu.iastate.metnet.export - package edu.iastate.metnet.export

export data implementation for hivemind

edu.iastate.metnet.graphmodel - package edu.iastate.metnet.graphmodel

new graph model for metnet pathways

edu.iastate.metnet.hibernate - package edu.iastate.metnet.hibernate

persistent layer between stateless session bean and the database.

edu.iastate.metnet.hiveface - package edu.iastate.metnet.hiveface

programming interface with 3rd party tools and hivemind

edu.iastate.metnet.hivemindService - package edu.iastate.metnet.hivemindService

edu.iastate.metnet.hivetest - package edu.iastate.metnet.hivetest

edu.iastate.metnet.interfaces - package edu.iastate.metnet.interfaces

autogen from the xdoclet (ejbdoclet).

edu.iastate.metnet.launch - package edu.iastate.metnet.launch

edu.iastate.metnet.mapbuilder - package edu.iastate.metnet.mapbuilder

edu.iastate.metnet.metaomgraph - package edu.iastate.metnet.metaomgraph

edu.iastate.metnet.metaomgraph.chart - package edu.iastate.metnet.metaomgraph.chart

edu.iastate.metnet.metaomgraph.test - package edu.iastate.metnet.metaomgraph.test

edu.iastate.metnet.metaomgraph.throbber - package edu.iastate.metnet.metaomgraph.throbber

edu.iastate.metnet.metaomgraph.utils - package edu.iastate.metnet.metaomgraph.utils

edu.iastate.metnet.model - package edu.iastate.metnet.model

model of the UI window and other graph element.

edu.iastate.metnet.newgui - package edu.iastate.metnet.newgui

edu.iastate.metnet.soft - package edu.iastate.metnet.soft

edu.iastate.metnet.test - package edu.iastate.metnet.test

edu.iastate.metnet.threads - package edu.iastate.metnet.threads

edu.iastate.metnet.ui - package edu.iastate.metnet.ui

user interface for metnet application

edu.iastate.metnet.utils - package edu.iastate.metnet.utils

utility classes for metnet application

edu.iastate.reload.model - package edu.iastate.reload.model

edu.iastate.reload.skin - package edu.iastate.reload.skin

edu.iastate.reload.ui - package edu.iastate.reload.ui

EFetch - Class in edu.iastate.jtm.jmed

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

Create a new instance of EFetch with default buffer size.

ELink - Class in edu.iastate.jtm.jmed

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

ELINK_BASE - Static variable in class edu.iastate.jtm.jmed.ELink

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

EMPTY - Static variable in interface edu.iastate.jtm.util.Queue

EMPTY_QUERY - Static variable in class edu.iastate.jtm.jmed.Query

EMPTY_ROOT - Static variable in class edu.iastate.jtm.gui.XmlTreeNode

EMPTY_TREE - Static variable in class edu.iastate.jtm.gui.XmlTreeModel

EmptyListException - Exception in edu.iastate.metnet.launch

Thrown when a list/queue is poped whhen it is empty.

EmptyListException() - Constructor for exception edu.iastate.metnet.launch.EmptyListException

EmptyListException(String) - Constructor for exception edu.iastate.metnet.launch.EmptyListException

emptyModel - Static variable in class edu.iastate.reload.ui.JGraphParallelEdgeRouter

emptyTable(String) - Method in class fcmodeler.pathbinder.FilterUpdater

emptyTables() - Method in class fcmodeler.pathbinder.MedCrawler

enableExtendedInfo() - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel.MetaOmFrame

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

change the enable / diable status of the menu based on the level of the user

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

encode(JGraph, Object[]) - Static method in class edu.iastate.metnet.graphmodel.CategoryEncoder

encode the graph by encoding vertices and edges

encode(JGraph, Object[]) - Static method in class edu.iastate.metnet.graphmodel.InputEncoder

encode the graph by encoding vertices and edges

encode(JGraph, Object[]) - Static method in class edu.iastate.metnet.graphmodel.JGraphEncoder

encode the graph by encoding vertices and edges

encode(JGraph, Object[]) - Static method in class edu.iastate.metnet.graphmodel.NetworkEncoder

encode the graph by encoding vertices and edges

encode(JGraph, Object[]) - Static method in class edu.iastate.metnet.graphmodel.VersionEncoder

encode the graph by encoding vertices and edges

end(int) - Method in class edu.iastate.jtm.SentenceParser

end(int) - Method in class edu.iastate.jtm.util.ProcessWrapper

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

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

endDocument() - Method in class fcmodeler.pathbinder.echo

endElement(String, String, String) - Method in class fcmodeler.pathbinder.echo

endMatcher - Static variable in class edu.iastate.jtm.jmed.UmlsSocketClient

EndNote - Class in edu.iastate.jtm.assistant

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

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

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

True if we are at the end of the file.

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

True if we are at the end of the file.

enqueue(Object) - Method in class edu.iastate.metnet.launch.Queue

ensureBufferCapacity(CharSequence) - Method in class edu.iastate.jtm.dic.AbstractDictionary

ensureCapacity(CharSequence) - Method in class edu.iastate.jtm.util.RunningBuffer

ent - Variable in class fcmodeler.pathbinder.gui.EntityPanel.EntityScore

implement sort method to automatically sort list

entities - Static variable in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame

entities - Static variable in class edu.iastate.metnet.metaomgraph.ExploRaseFrame

Entity - Interface in edu.iastate.metnet.datamodel

The basic element of the Metnet data model.

Entity - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Entity instances.

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

Constructor of Entity instances given a simple primary key.

Entity - Class in edu.iastate.metnet.soft

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

Entity - Class in fcmodeler.pathbinder

Entity(String) - Constructor for class fcmodeler.pathbinder.Entity

Entity(String, String) - Constructor for class fcmodeler.pathbinder.Entity

Entity(String, String, int) - Constructor for class fcmodeler.pathbinder.Entity

Entityabbreviation - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Entityabbreviation instances.

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

Constructor of Entityabbreviation instances given a composite primary key.

EntityabbreviationKey - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntityabbreviationKey instances.

Entitycomment - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Entitycomment instances.

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

Constructor of Entitycomment instances given a composite primary key.

EntitycommentKey - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntitycommentKey instances.

EntityConfidenceObservable - Class in edu.iastate.metnet.model

represent the control layer rather than model data storage

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

EntityDBModel - Class in edu.iastate.metnet.model

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

EntityEditor - Class in edu.iastate.metnet.newgui

Editor for entity objects.

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

EntityFinder - Class in edu.iastate.jtm

EntityFinder(int, boolean) - Constructor for class edu.iastate.jtm.EntityFinder

Creates a new instance of EntityFinder

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

EntityFinder.Hit - Class in edu.iastate.jtm

EntityFinder.Hit() - Constructor for class edu.iastate.jtm.EntityFinder.Hit

entityId - Variable in class edu.iastate.biocyc.ui.EntityIdNode

entityId - Variable in class edu.iastate.metnet.dao.EntityNode

entity id

entityId - Variable in class edu.iastate.metnet.dao.TrivialMetabolite

the entityid of the entity

entityId - Variable in class edu.iastate.metnet.ui.AddInteractionForm

blockid of entity?

EntityIdNode - Class in edu.iastate.biocyc.ui

EntityIdNode(Integer) - Constructor for class edu.iastate.biocyc.ui.EntityIdNode

EntityImpl - Class in edu.iastate.metnet.datamodel

An entity implemented with its attributes stored in a map.

EntityImpl(String) - Constructor for class edu.iastate.metnet.datamodel.EntityImpl

entityList - Variable in class edu.iastate.metnet.ui.AddInteractionForm

entity list for the entity table, which support the finer-grained change event in list

EntityListModel - Class in edu.iastate.metnet.model

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

entityListModel - Variable in class edu.iastate.metnet.ui.EntitySelector

entity list model

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

entity location list used to filter the pathway list by locations

EntityNameModel - Class in edu.iastate.metnet.model

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

EntityNode - Class in edu.iastate.metnet.dao

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

the default constructor

EntityNode(Integer) - Constructor for class edu.iastate.metnet.dao.EntityNode

constuctor

EntityNode(Integer, Integer) - Constructor for class edu.iastate.metnet.dao.EntityNode

EntityObjectTableModel - Class in edu.iastate.reload.model

only different with EntitySearchTableModel is that the organism is removed

EntityObjectTableModel(ListModel) - Constructor for class edu.iastate.reload.model.EntityObjectTableModel

EntityOntology - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntityOntology instances.

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

Constructor of EntityOntology instances given a simple primary key.

EntityPanel - Class in fcmodeler.pathbinder.gui

EntityPanel(MySqlConnector, JFileChooser) - Constructor for class fcmodeler.pathbinder.gui.EntityPanel

EntityPanel.EntityScore - Class in fcmodeler.pathbinder.gui

EntityPanel.EntityScore() - Constructor for class fcmodeler.pathbinder.gui.EntityPanel.EntityScore

EntityPanel.InteractionScore - Class in fcmodeler.pathbinder.gui

EntityPanel.InteractionScore() - Constructor for class fcmodeler.pathbinder.gui.EntityPanel.InteractionScore

EntityPart - Class in edu.iastate.metnet.model

store the information for interactionparts

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

EntityPart(String, String, String, Integer) - Constructor for class edu.iastate.metnet.model.EntityPart

EntityPubchem - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntityPubchem instances.

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

Constructor of EntityPubchem instances given a simple primary key.

EntityPubchemName - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntityPubchemName instances.

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

Constructor of EntityPubchemName instances given a simple primary key.

Entityref - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Entityref instances.

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

Constructor of Entityref instances given a composite primary key.

EntityrefKey - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntityrefKey instances.

EntitySearchTableModel - Class in edu.iastate.reload.model

table model used in live entity search

EntitySearchTableModel(ListModel) - Constructor for class edu.iastate.reload.model.EntitySearchTableModel

table structure

EntitySelector - Class in edu.iastate.metnet.ui

EntitySelector

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

default constructor

Entitysynonym - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Entitysynonym instances.

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

Constructor of Entitysynonym instances given a composite primary key.

EntitysynonymKey - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntitysynonymKey instances.

entityType - Variable in class edu.iastate.metnet.export.GobiNodeImpl

entity type of node

entityType - Variable in class edu.iastate.metnet.hivetest.GobiNodeImpl

entity type of node

Entitywithcontext - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Entitywithcontext instances.

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

Constructor of Entitywithcontext instances given a composite primary key.

EntitywithcontextDecorator - Class in edu.iastate.metnet.model

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

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

EntitywithcontextKey - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of EntitywithcontextKey instances.

Entrez - Class in edu.iastate.jtm.jmed

Entrez database names.

Entrez() - Constructor for class edu.iastate.jtm.jmed.Entrez

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

entropy(int[], int, int, boolean) - Static method in class edu.iastate.jtm.util.InfoTheory

entropy(int[], boolean) - Static method in class edu.iastate.jtm.util.InfoTheory

entropy(double[], int, int, boolean) - Static method in class edu.iastate.jtm.util.InfoTheory

entropy(double[], boolean) - Static method in class edu.iastate.jtm.util.InfoTheory

entryCount - Variable in class edu.iastate.jtm.dic.AbstractDictionary

entryTokenizer - Variable in class edu.iastate.jtm.dic.AbstractDictionary

Environment - Class in edu.iastate.metnet.db

set up the global environment, like host, database name and other global variable

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

enzymes for enzymatic interactions

enzymeType - Variable in class edu.iastate.metnet.ui.AddInteractionForm

entity type of the enzyme, may polypeptide or protein complex so when insert the enzyme, program know if the enzyme exists already based on the name,entitytype and the location

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

EPost - Class in edu.iastate.jtm.jmed

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

equals(Object) - Method in class edu.iastate.jtm.jmed.MedCitation

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

This method compares this object to the given object.

equals(Object) - Method in class edu.iastate.metnet.birdseyeview.GenePanel

This method compares this object to the given object.

equals(Object) - Method in class edu.iastate.metnet.birdseyeview.Protein

This method overrides the Object.equals method to explicitly show equality for proteins.

equals(ViewInfo) - Method in class edu.iastate.metnet.birdseyeview.ViewInfo

This method checks the given view info object to see if its ID matches the ID of this object.

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

equals(Object) - Method in interface edu.iastate.metnet.datamodel.db.Gene

equals(Object) - Method in class edu.iastate.metnet.datamodel.db.GeneImpl

equals(Object) - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractAbbreviationrules

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunit

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitabbreviation

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitcomment

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitconfidence

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitref

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBlockunitsynonym

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaactivatingcompound

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendacofactor

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendainhibitor

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendametalion

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaproduct

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendarecommendname

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendaref

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendasubstrate

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractBrendasynonyms

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiChemicalData

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiComments

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiCompounds

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiDatabaseAccession

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiNames

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiOntology

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiReference

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiRelation

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractChebiVertices

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractClassName

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodeconfidence

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodedatasource

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodeentitytype

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodeinteractiontype

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodelocation

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodeorganism

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCodereferencetype

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractCoderule

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntity

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntityabbreviation

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntitycomment

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntityOntology

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchem

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntityPubchemName

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntityref

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntitysynonym

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractEntitywithcontext

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractExternaldb

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractGroupList

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractGroupMember

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractGroupShare

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractGtairProperty

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatInteraction

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatLiveEntity

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractHistoryFlatPathway

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractInteraction

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionparts

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractInteractionproperties

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractPathwayparts

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy25kArrayElements

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairAffy8kArrayElements

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairAfgcArrayElements

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairAgiToUniprot

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairAracycDump

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairAthGoGoslim

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairSequencedGenes

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractTairTargetpAnalysis

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.AbstractUser

Implementation of the equals comparison on the basis of equality of the primary key values.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BlockunitcommentKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BlockunitrefKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BlockunitsynonymKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendaactivatingcompoundKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendacofactorKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendainhibitorKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendametalionKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendaproductKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendasubstrateKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.BrendasynonymsKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.EntityabbreviationKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.EntitycommentKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.EntityrefKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.EntitysynonymKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.EntitywithcontextKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.ExternaldbKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.GroupMemberKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.GroupShareKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.InteractionpartsKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.hibernate.PathwaypartsKey

Implementation of the equals comparison on the basis of equality of the id components.

equals(Object) - Method in class edu.iastate.metnet.soft.Attribute

equals(Object) - Method in class fcmodeler.pathbinder.Entity

equals(Object) - Method in class fcmodeler.pathbinder.FilterEntry

error(Integer, String) - Method in class edu.iastate.metnet.graphmodel.GraphValidity

add one error

ERROR_ADJACENT_ENTITY - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

adjacent entities

ERROR_DUPLICATE_ENTITY - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

duplicate entity error message

ERROR_ENZYME_TYPE - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

enzyme type error message

ERROR_GENE_LOCATION - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

gene location error message

ERROR_INTERACTION_STRUCTURE - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

interaction structure error message

ERROR_NODE_USER_OBJECT - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

user object error message

ERROR_NOTHING - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

no errors

ERROR_ORPHAN_NODE - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

orphan node

ERROR_TRANSPORT_LOCATION - Static variable in class edu.iastate.metnet.graphmodel.GraphValidity

transport location error message

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

contain the esAlignmentList

escapeXML(String) - Static method in class edu.iastate.metnet.utils.Utils

replace all sensitive chars to special XML strings

ESearch - Class in edu.iastate.jtm.jmed

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

ESEARCH_BASE - Static variable in class edu.iastate.jtm.jmed.ESearch

esQuery(DirectedGraph) - Method in interface edu.iastate.metnet.interfaces.MyFacade

esQuery.

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

query the input graph from the selected pathways

esQuery(DirectedGraph) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

esQuery.

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

query the input graph from the selected pathways

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

run exactly structural query

esQuery2(List) - Method in class edu.iastate.metnet.ui.PathwayEditor

sort list only

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

EUtility - Class in edu.iastate.jtm.jmed

An abstract superclass for eSearch, eFetch, eLink, ...
It deals with the common issues for all services, such as min request interval, response parsing, service job queueing...
Subclasses (ESearch, ELink, EFetch, etc.) focus on dealing with user input and output of specific services.
In replace of PubMedQuerier, PubMedFetcher, PubMedTimer.

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

EUtility.Processor - Interface in edu.iastate.jtm.jmed

A processor is responsible for processing the response of a service.

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

blast evalue

exact - Variable in class edu.iastate.metnet.metaomgraph.TreeSearcher.Query

Specifies whether an exact match is required, or if a substring match will suffice.

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

exactSearch() - Method in class edu.iastate.metnet.ui.StructuralQueryForm

exact match on node label

exactSearch2() - Method in class edu.iastate.metnet.ui.StructuralQueryForm

multithread version of compilation, tested.

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

execute(String) - Method in class edu.iastate.jtm.util.RemoteControl

execute(String[]) - Method in class edu.iastate.jtm.util.RemoteControl

executeFile(File) - Method in class edu.iastate.jtm.util.MySqlConnector

Run a sql file.

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

exit() - Method in class edu.iastate.metnet.launch.LaunchMetNet

Method to exist the close the entire suite.

expand(boolean) - Method in class edu.iastate.jtm.gui.ExpandableLabel

ExpandableLabel - Class in edu.iastate.jtm.gui

ExpandableLabel(String, String, String, String) - Constructor for class edu.iastate.jtm.gui.ExpandableLabel

ExpandableLabel(String, String) - Constructor for class edu.iastate.jtm.gui.ExpandableLabel

expandAll(JTree) - Static method in class edu.iastate.jtm.gui.TreeUtil

expandFrom(JTree, TreePath) - Static method in class edu.iastate.jtm.gui.TreeUtil

expandTo(JTree, TreeNode, boolean) - Static method in class edu.iastate.jtm.gui.TreeUtil

expandToLevel(JTree, int) - Static method in class edu.iastate.jtm.gui.TreeUtil

expandWindow(CharBuffer, boolean, boolean) - Method in class edu.iastate.jtm.util.SlidingWindow

Increase window size by 1 stride.

ExperimentalData - Static variable in class edu.iastate.metnet.birdseyeview.LoadController

ExperimentChooserPanel - Class in edu.iastate.metnet.birdseyeview

The ExperimentChooserPanel Class holds the experiment chooser combo box and its associated text area.

ExperimentChooserPanel(LoadController) - Constructor for class edu.iastate.metnet.birdseyeview.ExperimentChooserPanel

Constructor.

ExperimentComboBoxListener - Class in edu.iastate.metnet.birdseyeview

The ExperimentComboBoxListener Class handles selections of experiments in the Experiment combo box.

ExperimentComboBoxListener(LoadController) - Constructor for class edu.iastate.metnet.birdseyeview.ExperimentComboBoxListener

Constructor.

ExperimentNames - Static variable in class edu.iastate.metnet.birdseyeview.LoadController

experiments - Static variable in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame

experiments - Static variable in class edu.iastate.metnet.metaomgraph.ExploRaseFrame

explode(String, String) - Static method in class edu.iastate.metnet.utils.Utils

similar to StringTokenize, split string by delim

ExploRaseBoxHandler - Class in edu.iastate.metnet.birdseyeview

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

ExploRaseBoxHandler - Class in edu.iastate.metnet.metaomgraph

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

ExploRaseExpFrame - Class in edu.iastate.metnet.birdseyeview

ExploRaseExportObj - Class in edu.iastate.metnet.hivemindService

Class represnts a export Object that is used to send data to ExploRase.

ExploRaseFrame - Class in edu.iastate.metnet.metaomgraph

ExploRaseSubmitListener - Class in edu.iastate.metnet.birdseyeview

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

ExploRaseSubmitListener - Class in edu.iastate.metnet.metaomgraph

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

exploRaseThread - Static variable in class edu.iastate.metnet.launch.LaunchMetNet

ExploRaseThread - Class in edu.iastate.metnet.threads

Thread used to fetch R command to JRI

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

ExploRaseThread(String) - Constructor for class edu.iastate.metnet.threads.ExploRaseThread

export(File, CitationManager) - Method in class edu.iastate.jtm.assistant.CitationPool

export(File, Element[]) - Method in class edu.iastate.jtm.jmed.CitationManager

exportData(ArrayList<String>, Hashtable, ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.ExportToExploRase

Methods recieves selected experiments from BEV and sends their data to ExploRase

exportDone(JComponent, Transferable, int) - Method in class edu.iastate.metnet.metaomgraph.ListTransferHandler

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

Exporter - Class in edu.iastate.jtm.assistant

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

ExportJungPathway - Class in edu.iastate.metnet.hivemindService

HiveMind Service exports pathway as JUNG graphs

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

exportMOGData(ArrayList<String>, ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.ExportToExploRase

Export selected data from MOG to ExploRase

exportMOGData(ArrayList<String>) - Method in class edu.iastate.metnet.hivemindService.ExportToExploRase

select all data from MOG to ExploRase

ExportToBirdsEyeView - Class in edu.iastate.metnet.hivemindService

HiveMind Service exports data to BirdseyeView

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

ExportToExploRase - Class in edu.iastate.metnet.hivemindService

Class exports data from a MetNet application to ExploRase

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

ExportToMetaOmGraph - Interface in edu.iastate.metnet.hivemindService

Interface implemented by HiveMind service to export data to MetaOmGraph

ExportToMetaOmGraphImpl - Class in edu.iastate.metnet.hivemindService

Class implements ExportToMetaOmGraph interface and export data to MetaOmGraph.

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

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

ExtendedInfoTree - Class in edu.iastate.metnet.metaomgraph

Class for storing the extended information of a MetaOmProject.

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

Default constructor.

ExtendedInfoTree.InfoNode - Class in edu.iastate.metnet.metaomgraph

Class that stores information for nodes in an ExtendedInfoTree.

ExtendedInfoTree.InfoNode(String, String, String) - Constructor for class edu.iastate.metnet.metaomgraph.ExtendedInfoTree.InfoNode

Constructor.

ExtendedInfoTree.InfoNode(String, String) - Constructor for class edu.iastate.metnet.metaomgraph.ExtendedInfoTree.InfoNode

Constructor that uses the same String for both the node name and the XML element name.

ExtendedInfoTreePanel - Class in edu.iastate.metnet.metaomgraph

A JPanel that contains a vertically-split JSplitPane.

ExtendedInfoTreePanel(ExtendedInfoTree) - Constructor for class edu.iastate.metnet.metaomgraph.ExtendedInfoTreePanel

Creates an ExtendedInfoTreePanel.

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

extend all monomers in the pathway to the gene level, add translation and transcription if necessary

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

extend all monomers in the pathway to the gene level, add translation and transcription if necessary

Externaldb - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of Externaldb instances.

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

Constructor of Externaldb instances given a composite primary key.

ExternaldbKey - Class in edu.iastate.metnet.hibernate

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

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

Simple constructor of ExternaldbKey instances.

extractIcon(ZipFile, String) - Static method in class edu.iastate.jtm.util.JarResources

extractPlainText(File, File) - Method in class edu.iastate.jtm.jmed.MedlineParser

Extract plain text abstracts from an XML file into a directory.

extractPlainText(File, String, int) - Method in class edu.iastate.jtm.jmed.MedlineParser

Extract plain text abstracts from an XML file into multiple directories.

extractPlainText(InputStream, File) - Method in class edu.iastate.jtm.jmed.MedlineParser

Extract plain text abstracts from an input stream into a directory.

extractPlainText(InputStream, String, int) - Method in class edu.iastate.jtm.jmed.MedlineParser

Extract plain text abstracts from an input stream into multiple directories.

extractPmids(File) - Method in class edu.iastate.jtm.jmed.MedlineParser

Extract all PMIDs to a single file.

extractPmids(String, int) - Method in class edu.iastate.jtm.jmed.MedlineParser

Extract all PMIDs to multiple files.