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

N

n2sort() - Method in class edu.iastate.jtm.gui.TableSorter

n2sort() - Method in class edu.iastate.metnet.model.TableSorter

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

name

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

COMMON-NAME

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

COMMON-NAME

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

the name

name - Variable in class edu.iastate.metnet.dao.CategoryNode

class name or pathway name

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

blockunit name

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

name of the data

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

interaction name

name - Variable in class edu.iastate.metnet.dao.NameSource

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

pathway name

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

the name of the entity

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

search string for node

name - Variable in class edu.iastate.metnet.graphmodel.SearchNameMetaphor

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

search string for node

name - Variable in class edu.iastate.metnet.model.NodeSelectionModel

name - Variable in class fcmodeler.pathbinder.Entity

name() - Method in class fcmodeler.pathbinder.Entity

NameCharType - Class in edu.iastate.jtm.util

NameCharType() - Constructor for class edu.iastate.jtm.util.NameCharType

NameService - Class in edu.iastate.metnet.ui

the synonym window

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

the constructor, initialize the table model of blockunit list

nameSource - Variable in class edu.iastate.metnet.dao.ChebiOntologyName

NameSource - Class in edu.iastate.metnet.dao

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

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

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

NE_CORNER - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

NE_CORNER - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder

negativeSequence - Static variable in class edu.iastate.metnet.utils.Utils

save the sequence

NetworkEditForm - Class in edu.iastate.reload.ui

NetworkEditForm() - Constructor for class edu.iastate.reload.ui.NetworkEditForm

Creates new form NetworkEditorForm

NetworkEditForm(boolean) - Constructor for class edu.iastate.reload.ui.NetworkEditForm

NetworkEditHelper - Class in edu.iastate.metnet.graphmodel

helper function for NetworkEditForm

NetworkEditHelper(JGraph) - Constructor for class edu.iastate.metnet.graphmodel.NetworkEditHelper

default constructor

NetworkEncoder - Class in edu.iastate.metnet.graphmodel

encode the network in editing

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

NEW_CORRELATION_CAUSE - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmProject

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

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

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

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

true if remained after merge

newData(String, ArrayList, ArrayList, ArrayList) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

This method processes the new data so it can be displayed.

newExperiment(int) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

This method calls the load controller to load data from a different experiment using the current probe name and variance data.

newgetMetNetInfo(Object[]) - Static method in class edu.iastate.metnet.metaomgraph.utils.Utils

NewProjectDialog - Class in edu.iastate.metnet.metaomgraph

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

NewProjectDialog(Frame) - Constructor for class edu.iastate.metnet.metaomgraph.NewProjectDialog

NewProjectDialog(Dialog) - Constructor for class edu.iastate.metnet.metaomgraph.NewProjectDialog

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

newVariances(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

This method processes the new variances.

newVariant(double, int) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView

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

This method sets the new view.

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

This method sets the GO button and labels button visibility based on the new view.

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

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

This method notifies the children that the view has changed.

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

This method handles changes to the view by clearing out the annotations.

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

This method creates the new view based on the new view info.

next - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.PolyLine

next position

nextGUID() - Static method in class edu.iastate.metnet.utils.GUID

nextLine() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Advances to the next line of text.

nextLine() - Method in class edu.iastate.metnet.soft.RandomAccessFile

Advances to the next line of text.

nextNode - Variable in class edu.iastate.metnet.launch.ListNode

nextPortObject() - Method in class edu.iastate.metnet.graphmodel.NetworkEditHelper

create unique port number

nextPortObject() - Method in class edu.iastate.metnet.ui.StructureQueryHelper

create unique port number

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

nextText() - Method in interface edu.iastate.jtm.gui.Highlightable

nextText() - Method in class edu.iastate.jtm.gui.HighlightableTextPane

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

Find next unit from the input.

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

Find next unit from the input.

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

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

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

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

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

drag to create a node

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

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

default node distance

NodeInfo - Class in edu.iastate.metnet.mapbuilder

Stores information about nodes.

NodeInfo(String, String, String, String, String, String, String) - Constructor for class edu.iastate.metnet.mapbuilder.NodeInfo

NodeSelectionController - Class in edu.iastate.metnet.controller

NodeSelectionController(NodeSelectionForm) - Constructor for class edu.iastate.metnet.controller.NodeSelectionController

nodeSelectionController - Variable in class edu.iastate.metnet.ui.NodeSelectionForm

NodeSelectionForm - Class in edu.iastate.metnet.ui

NodeSelectionForm(PathwayEditor) - Constructor for class edu.iastate.metnet.ui.NodeSelectionForm

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

NodeSelectionModel - Class in edu.iastate.metnet.model

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

nodeTable - Variable in class edu.iastate.jtm.gui.XmlTreeModel

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

store the id and cellview, id maybe the blockid for normal node or guid for multi-node

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

store the id and cellview, id maybe the blockid for normal node or guid for multi-node

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

store the id and cellview, id maybe the blockid for normal node or guid for multi-node

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

store the id and cellview, id maybe the blockid for normal node or guid for multi-node

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

store the id and cellview, id maybe the blockid for normal node or guid for multi-node

noFocusBorder - Variable in class edu.iastate.jtm.gui.RowHeaderRenderer

NONE - Static variable in class edu.iastate.metnet.metaomgraph.utils.Utils

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

NoneditableTableModel - Class in edu.iastate.metnet.newgui

Class used to create a non-editable table.

NoneditableTableModel(Object[][], String[]) - Constructor for class edu.iastate.metnet.newgui.NoneditableTableModel

Constructs a non-editable table with the given data/columns.

NoneditableTableModel - Class in edu.iastate.metnet

Creates a table that displays the data appropriately formatted (ints as ints, booleans as checkboxes, etc.), and which does not allow inline editing by default.

NoneditableTableModel(Object[][], String[]) - Constructor for class edu.iastate.metnet.NoneditableTableModel

Constructs a NoneditableTableModel from the given data/headers.

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

normalize(String) - Method in class edu.iastate.jtm.jmed.QueryParser

NoSuchNodeException - Exception in edu.iastate.metnet.dao

special exception for pathway structure

NoSuchNodeException() - Constructor for exception edu.iastate.metnet.dao.NoSuchNodeException

NoSuchNodeException(String) - Constructor for exception edu.iastate.metnet.dao.NoSuchNodeException

NoSuchNodeException - Exception in edu.iastate.metnet.export

special exception for pathway structure

NoSuchNodeException() - Constructor for exception edu.iastate.metnet.export.NoSuchNodeException

NoSuchNodeException(String) - Constructor for exception edu.iastate.metnet.export.NoSuchNodeException

NOT - Static variable in class edu.iastate.jtm.jmed.Query.Operator

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

NOT_FOUND - Static variable in class edu.iastate.jtm.jmed.PubMedQuerier

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

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

nothing is ready to create

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

change the pathway structure history.

notifyPathwayStructureChange(Collection, String) - Method in interface edu.iastate.metnet.interfaces.MyPaper

change the pathway structure history.

notImplemented(String) - Static method in class edu.iastate.jtm.assistant.Controller

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

NW_CORNER - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder

NW_CORNER - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder