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

V

v - Variable in class edu.iastate.metnet.ui.OverviewPanel

v - Variable in class edu.iastate.reload.ui.OverviewPanel

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

we shoudl check the graph at the model level rather than from the user interface level which is hard to infer the graph structure

ValidityMetaphor - Class in edu.iastate.metnet.graphmodel

highlight the nodes and edges that have problems

ValidityMetaphor(GraphValidity, Map) - Constructor for class edu.iastate.metnet.graphmodel.ValidityMetaphor

default constructor

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

matched non-null vertex size

value - Variable in class edu.iastate.metnet.db.ReturnCode

value - Variable in class edu.iastate.metnet.model.DisplayObject

valueChanged(TreeSelectionEvent) - Method in class edu.iastate.metnet.birdseyeview.TreePanel

Required by TreeSelectionListener interface.

valueChanged(ListSelectionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

valueChanged(ListSelectionEvent) - Method in class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel

valueChanged(TreeSelectionEvent) - Method in class edu.iastate.metnet.metaomgraph.MetaOmHelpListener

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

Called when a new gene list is selected.

valueChanged(ListSelectionEvent) - Method in class edu.iastate.metnet.soft.SOFTParserOptionPanel

valueChanged(TreeSelectionEvent) - Method in class edu.iastate.metnet.ui.CategoryEditForm

update the pathway table content when a selection in the tree is changed

valueChanged(GraphSelectionEvent) - Method in class edu.iastate.metnet.ui.NodeSelectionForm

valueChanged(GraphSelectionEvent) - Method in class edu.iastate.metnet.ui.SelectionListener

valueChanged(GraphSelectionEvent) - Method in class edu.iastate.metnet.ui.VersionSaver

get the version data selection

valueChanged(GraphSelectionEvent) - Method in class edu.iastate.reload.ui.SelectionListener

callback graph listener

valueForPathChanged(TreePath, Object) - Method in class edu.iastate.metnet.model.CategoryTreeModel

VerbNode - Class in fcmodeler.pathbinder.gui

VerbNode(String, String) - Constructor for class fcmodeler.pathbinder.gui.VerbNode

verbose(boolean) - Method in class edu.iastate.jtm.assistant.GoogleScholar

VerbPanel - Class in fcmodeler.pathbinder.gui

VerbPanel(MySqlConnector) - Constructor for class fcmodeler.pathbinder.gui.VerbPanel

verifyChecksum(File, File) - Method in class fcmodeler.pathbinder.MedLeaseClient

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

VersionEditor - Class in edu.iastate.metnet.ui

general version data browser and selector

VersionEditor(VersionListener, MyVersionGraph) - Constructor for class edu.iastate.metnet.ui.VersionEditor

default constructor

VersionEncoder - Class in edu.iastate.metnet.graphmodel

create Dot format file to describe the graph data in memory.

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

VersionGraph - Class in edu.iastate.metnet.graphmodel

extend the JGraph by applying the metaphor description based on the content of the pathway XXX (cancelled) may we need a different but same feature class for version editor only.

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

VersionGraph(GraphModel) - Constructor for class edu.iastate.metnet.graphmodel.VersionGraph

VersionGraph(GraphModel, BasicMarqueeHandler) - Constructor for class edu.iastate.metnet.graphmodel.VersionGraph

VersionGraph(GraphModel, GraphLayoutCache) - Constructor for class edu.iastate.metnet.graphmodel.VersionGraph

VersionGraph(GraphModel, GraphLayoutCache, BasicMarqueeHandler) - Constructor for class edu.iastate.metnet.graphmodel.VersionGraph

VersionGraphMetaphor - Class in edu.iastate.metnet.graphmodel

get the version graph metaphor, by default, simple black on white

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

default costructor

VersionGraphModel - Class in edu.iastate.metnet.graphmodel

hold the version graph model through jgrapht

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

default constructor

VersionGraphModel(MyVersionGraph) - Constructor for class edu.iastate.metnet.graphmodel.VersionGraphModel

constructor

VersionListener - Interface in edu.iastate.metnet.graphmodel

VersionSaver - Class in edu.iastate.metnet.ui

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

default constructor

VersionSaver(VersionEditor) - Constructor for class edu.iastate.metnet.ui.VersionSaver

default constructor

VersionyLayoutAlgorithm - Class in edu.iastate.metnet.graphmodel

hierachical layout.

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

VERTICAL - Static variable in class edu.iastate.metnet.metaomgraph.chart.RangeMarker

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

view - Variable in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm.TreeNode

ViewComboBoxListener - Class in edu.iastate.metnet.birdseyeview

The ViewComboBoxListener Class handles changes to the view combo box.

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

Constructor.

ViewFactory - Class in edu.iastate.metnet.birdseyeview

The ViewFactory Class is a static factory class that creates AbstractView subclasses.

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

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

ViewInfo - Class in edu.iastate.metnet.birdseyeview

The ViewInfo Class holds information about the different Bird's Eye Views such as ID, name, etc.

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

Constructor.

ViewPanel - Class in edu.iastate.metnet.birdseyeview

The ViewPanel Class is a JPanel that holds the current Bird's Eye View display panel.

ViewPanel(BirdsEyeView, ViewInfo, String) - Constructor for class edu.iastate.metnet.birdseyeview.ViewPanel

Constructor.

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

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

viewSize - Static variable in class edu.iastate.metnet.birdseyeview.ViewPanel

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

visualize the esQuery alignment result

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

vocabulary - Variable in class edu.iastate.jtm.util.VocabularyCounter

VocabularyCounter - Class in edu.iastate.jtm.util

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

VocabularyCounter.TfDf - Class in edu.iastate.jtm.util

VocabularyCounter.TfDf(Object) - Constructor for class edu.iastate.jtm.util.VocabularyCounter.TfDf

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