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.

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