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P

p - Variable in class edu.iastate.jtm.util.VocabularyCounter.TfDf
 
PA - Static variable in class edu.iastate.jtm.jmed.Query.Field
 
PAGE - Static variable in class edu.iastate.jtm.jmed.Limits
 
paint(Graphics) - Method in class edu.iastate.jtm.gui.SplashWindow
Paints the image on the window.
paint(Graphics) - Method in class edu.iastate.metnet.graphmodel.MultiVertexView.MultiVertexRenderer
cutomized the color for multi-pathway node.
paintChildren(Graphics) - Method in class edu.iastate.metnet.ui.OverviewPanel
 
paintChildren(Graphics) - Method in class edu.iastate.reload.ui.OverviewPanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.birdseyeview.cellview.GenePanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.birdseyeview.ColorPanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.birdseyeview.GenePanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.birdseyeview.ImagePanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.ColorChooseButton
Paints the component.
paintComponent(Graphics) - Method in class edu.iastate.metnet.dataManager.JMultilineLabel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeSelector
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.PolygonPanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.ScrollingTexturePanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.SimpleChipAnimationPanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.test.AffyChipAnimationPanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.test.ColorBrickPanel
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.metaomgraph.throbber.Throbber
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.MetNetTitlePane
Paints a representation of the current state of the internal frame.
paintComponent(Graphics) - Method in class edu.iastate.metnet.StripedTable.myColorRenderer
 
paintComponent(Graphics) - Method in class edu.iastate.metnet.ui.Blip
Paints the current frame.
paintGradient(Graphics, int, int, int, int, int, String) - Static method in class edu.iastate.reload.skin.MetalUtilsX
Paints the typical Metal gradient.
paintGradient(Graphics, int, int, int, int, double, double, Color, Color, Color, int) - Static method in class edu.iastate.reload.skin.MetalUtilsX
Paints the typical Metal gradient.
paintGradient(Graphics, int, int, int, int, int, String) - Static method in class javax.swing.plaf.metal.MetalUtils
Paints the typical Metal gradient.
paintGradient(Graphics, int, int, int, int, double, double, Color, Color, Color, int) - Static method in class javax.swing.plaf.metal.MetalUtils
Paints the typical Metal gradient.
paintHorizontalGradient(Graphics, int, int, int, int, double, double, Color, Color, Color) - Static method in class edu.iastate.reload.skin.MetalUtilsX
Paints a horizontal gradient.
paintHorizontalGradient(Graphics, int, int, int, int, double, double, Color, Color, Color) - Static method in class javax.swing.plaf.metal.MetalUtils
Paints a horizontal gradient.
paintTitleBackground(Graphics) - Method in class edu.iastate.metnet.MetNetTitlePane
This method paints the TitlePane's background.
paintVerticalGradient(Graphics, int, int, int, int, double, double, Color, Color, Color) - Static method in class edu.iastate.reload.skin.MetalUtilsX
Paints a vertical gradient.
paintVerticalGradient(Graphics, int, int, int, int, double, double, Color, Color, Color) - Static method in class javax.swing.plaf.metal.MetalUtils
Paints a vertical gradient.
PANEL_BUFFER - Static variable in class edu.iastate.metnet.ui.OverviewPanel
 
PANEL_BUFFER - Static variable in class edu.iastate.reload.ui.OverviewPanel
 
panelBottom - Variable in class edu.iastate.metnet.ui.AbbreviationRules
 
panelBottom - Variable in class edu.iastate.metnet.ui.SearchDialog
 
PanelLocationsFactory - Class in edu.iastate.metnet.birdseyeview.cellview
The PanelLocationsFactory Class handles the functionality surrounding the locations of gene panels in the cell view relative to the parent component (i.e.
PanelLocationsFactory(Database) - Constructor for class edu.iastate.metnet.birdseyeview.cellview.PanelLocationsFactory
Constructor.
panelOne - Variable in class edu.iastate.metnet.ui.AbbreviationRules
 
panelQuery - Variable in class edu.iastate.metnet.ui.SearchDialog
 
panelTop - Variable in class edu.iastate.metnet.ui.AbbreviationRules
 
panelTwo - Variable in class edu.iastate.metnet.ui.AbbreviationRules
 
pannerContainerRectangle - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
pannerContainerRectangle - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
pannerContainerRectangleCopy - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
pannerContainerRectangleCopy - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
pannerResizeDecoration - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
pannerResizeDecoration - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
pannerViewRectangle - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
pannerViewRectangle - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
pannerViewRectangleCopy - Variable in class edu.iastate.metnet.ui.OverviewPanel.PannerViewfinder
 
pannerViewRectangleCopy - Variable in class edu.iastate.reload.ui.OverviewPanel.PannerViewfinder
 
paper - Variable in class edu.iastate.metnet.test.MyPaperTest.PaperWorker
 
paper - Static variable in class edu.iastate.metnet.utils.MyPaperFactory
session client
ParenFinder - Class in edu.iastate.jtm.util
Find balanced parentheses in a string.
ParenFinder() - Constructor for class edu.iastate.jtm.util.ParenFinder
Creates a new instance of ParenFinder
ParenFinder(CharType) - Constructor for class edu.iastate.jtm.util.ParenFinder
 
ParenFinder(char, char) - Constructor for class edu.iastate.jtm.util.ParenFinder
 
ParenParser - Class in edu.iastate.jtm.util
Parse parentheses into a DOM tree.
ParenParser(CharType) - Constructor for class edu.iastate.jtm.util.ParenParser
 
ParenParser(boolean) - Constructor for class edu.iastate.jtm.util.ParenParser
 
ParenParser() - Constructor for class edu.iastate.jtm.util.ParenParser
 
parent - Variable in class edu.iastate.jtm.dic.AbstractTrieNode
 
parent - Variable in class edu.iastate.metnet.ui.CategoryChooseForm
parent form
parent - Variable in class edu.iastate.metnet.ui.CategoryCreateForm
parent window
parent - Variable in class edu.iastate.metnet.ui.CategoryRenameForm
parent form
parent - Variable in class edu.iastate.metnet.ui.SearchDialog
 
PARSE - Variable in class edu.iastate.biocyc.io.AttributeFileReaderEx
file line scanner status
parse(String) - Static method in class edu.iastate.jtm.jmed.Query.SimpleTerm
 
parse(String) - Method in class edu.iastate.jtm.jmed.QueryParser
 
parse(CharSequence) - Method in class edu.iastate.jtm.SentenceParser
Parse a string into sentences.
parse(CharSequence, boolean) - Method in class edu.iastate.jtm.SentenceParser
Parse a string into sentences.
parse(CharSequence) - Method in class edu.iastate.jtm.util.ParenParser
 
PARSE - Variable in class edu.iastate.metnet.aracyc.AttributeFileReader
file line scanner status
PARSE - Variable in class edu.iastate.metnet.aracyc.AttributeFileReaderEx
file line scanner status
parse(String, ParsePosition) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel.ExperimentFormat
 
parse(String) - Static method in class fcmodeler.pathbinder.Entity
 
parse(String) - Static method in class fcmodeler.pathbinder.FilterEntry
 
parseAll(String) - Method in class fcmodeler.pathbinder.HintParse
 
parseCSVFile(File) - Method in class edu.iastate.metnet.dataManager.DataManager
 
parseDate(String) - Method in class fcmodeler.pathbinder.HintParse
 
parseDouble(String, String) - Method in class edu.iastate.metnet.utils.Utils
 
parseExcelFile(String) - Method in class edu.iastate.metnet.analysis.DefaultJExcelClient
 
parseExcelSheet(Sheet) - Method in class edu.iastate.metnet.analysis.DefaultExcelSheet
 
parseFile(LinkedList) - Method in class edu.iastate.metnet.aracyc.AttributeFileReader
parse the file lines and turn into maps
parseFile(LinkedList) - Method in class edu.iastate.metnet.aracyc.AttributeFileReaderEx
parse the file lines and turn into maps
parseFile(LinkedList) - Method in class edu.iastate.metnet.aracyc.ClassesDatReader
 
parseFile(LinkedList) - Method in class edu.iastate.metnet.aracyc.CompoundsDatReader
 
parseFile(LinkedList) - Method in class edu.iastate.metnet.aracyc.TabularFileReader
 
parseFile(LinkedList) - Method in class edu.iastate.metnet.aracyc.TabularFileReaderEx
parse the file lines and get the map of multimap
parseQuery(String) - Method in class edu.iastate.jtm.assistant.QueryBuilder
 
parseTranslation(Element, int) - Method in class edu.iastate.jtm.assistant.Highlighter
 
partChoice - Variable in class edu.iastate.metnet.ui.AddInteractionForm
indicate which part table (from or to) that user are working on, so when the user click the removePart button, program know remove which selection.
PARTIAL_ENTRY - Static variable in class edu.iastate.jtm.dic.AbstractDictionary
 
partialAllowed - Variable in class edu.iastate.jtm.dic.AbstractDictionary
 
PARTIALMATCH - Static variable in class edu.iastate.jtm.dic.AbstractDictionary
 
PASSWORD_KEY - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication
password node in the configure file
path - Variable in class edu.iastate.metnet.dao.ZEdge
path containing control points
pathBinder - Static variable in class fcmodeler.pathbinder.gui.PbFrame
 
pathBinder() - Method in class fcmodeler.pathbinder.HiddenLink
 
PathBinder - Class in fcmodeler.pathbinder
 
PathBinder(MySqlConnector) - Constructor for class fcmodeler.pathbinder.PathBinder
 
pathBinderBlockunit() - Method in class edu.iastate.metnet.controller.NodeSelectionController
 
PathBinderUpdater - Class in fcmodeler.pathbinder.updater
 
PathBinderUpdater() - Constructor for class fcmodeler.pathbinder.updater.PathBinderUpdater
 
pathway - Variable in class edu.iastate.metnet.birdseyeview.PathwayTreeNode
 
Pathway - Class in edu.iastate.metnet.birdseyeview.pathwayview
The Pathway Class encapsulates the functionality of one pathway component in the pathway view.
Pathway(String, ArrayList, String, boolean, BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.pathwayview.Pathway
Constructor.
pathway - Variable in class edu.iastate.metnet.graphmodel.PathwayModel
current pathway object
Pathway - Class in edu.iastate.metnet.launch
Pathway class containing pathway name and pathway id
Pathway(String, int) - Constructor for class edu.iastate.metnet.launch.Pathway
 
PathwayA - Class in edu.iastate.metnet.dao
 
PathwayA() - Constructor for class edu.iastate.metnet.dao.PathwayA
 
PathwayA(Integer) - Constructor for class edu.iastate.metnet.dao.PathwayA
 
PathwayAlignment - Interface in edu.iastate.metnet.dao
alignment data structure
PathwayAlignmentImpl - Class in edu.iastate.metnet.dao
implementation of alignment
PathwayAlignmentImpl() - Constructor for class edu.iastate.metnet.dao.PathwayAlignmentImpl
 
PathwayAlignmentImpl(PathwayGraph, PathwayGraph) - Constructor for class edu.iastate.metnet.dao.PathwayAlignmentImpl
 
PathwayCategoryNode - Interface in edu.iastate.metnet.hiveface
category and pathway node.
PathwayCategoryNodeImpl - Class in edu.iastate.metnet.export
used to delegate my own data access object so no need to change the class CategoryNode.
PathwayCategoryNodeImpl(CategoryNode) - Constructor for class edu.iastate.metnet.export.PathwayCategoryNodeImpl
default constructor
PathwayChoiceModel - Class in edu.iastate.biocyc.ui
 
PathwayChoiceModel(ListModel) - Constructor for class edu.iastate.biocyc.ui.PathwayChoiceModel
 
PathwayChoiceTableModel - Class in edu.iastate.metnet.ui
pathway choice table model
PathwayChoiceTableModel(ListModel) - Constructor for class edu.iastate.metnet.ui.PathwayChoiceTableModel
default constructor
PathwayCompartmentPrefix - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
 
PathwayDecorator - Class in edu.iastate.metnet.model
provide decorator function for pathway
PathwayDecorator() - Constructor for class edu.iastate.metnet.model.PathwayDecorator
 
PathwayDecorator(Blockunit) - Constructor for class edu.iastate.metnet.model.PathwayDecorator
 
pathwaydotCapacity - Variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
 
pathwayEditor - Static variable in class edu.iastate.metnet.ui.MainWindow2
pathway editor window instance
pathwayEditor - Variable in class edu.iastate.metnet.ui.NodeSelectionForm
 
PathwayEditor - Class in edu.iastate.metnet.ui
main window for pathway preview
PathwayEditor() - Constructor for class edu.iastate.metnet.ui.PathwayEditor
default constructor
PathwayElementMetaphor - Class in edu.iastate.metnet.graphmodel
metaphor for selected element.
PathwayElementMetaphor(Set) - Constructor for class edu.iastate.metnet.graphmodel.PathwayElementMetaphor
default constructor
PathwayElementNode - Interface in edu.iastate.metnet.dao
hold the data of the element in a version of pathway
PathwayGeneThread - Class in edu.iastate.metnet.threads
Thread that download all pathway data from MetNetDB and arranges it into hashtable
PathwayGeneThread() - Constructor for class edu.iastate.metnet.threads.PathwayGeneThread
 
PathwayGraph - Interface in edu.iastate.metnet.dao
 
PathwayGraphImpl - Class in edu.iastate.metnet.dao
a simple pathway graph to detect the structure change.
PathwayGraphImpl() - Constructor for class edu.iastate.metnet.dao.PathwayGraphImpl
default constructor
PathwayHighlightForm - Class in edu.iastate.metnet.ui
decide which pathway needs to be highlighted
PathwayHighlightForm(Object, List) - Constructor for class edu.iastate.metnet.ui.PathwayHighlightForm
Creates new form PathwayHighlightForm
PathwayInfo - Interface in edu.iastate.metnet.hiveface
get the pathway information
PathwayInfoImpl - Class in edu.iastate.metnet.export
 
PathwayInfoImpl(PathwayObject) - Constructor for class edu.iastate.metnet.export.PathwayInfoImpl
 
pathwayList - Variable in class edu.iastate.metnet.dao.InteractionInformation
the involved pathways
pathwayList - Variable in class edu.iastate.metnet.ui.PathwaySelector2
pathway object list
pathwayListModel - Variable in class edu.iastate.metnet.ui.AmorphousQueryForm
pathway data list model
pathwayListModel - Variable in class edu.iastate.reload.ui.DBSearchForm
pathway list model
PathwayModel - Class in edu.iastate.metnet.graphmodel
special graph model, which only add interaction nodes, and automatically add entitywithlocation nodes and edges related to these nodes
PathwayModel(DirectedGraph, Map) - Constructor for class edu.iastate.metnet.graphmodel.PathwayModel
construct the model based on the networks
PathwayModel(DirectedGraph, Map, MultiKeyMap) - Constructor for class edu.iastate.metnet.graphmodel.PathwayModel
create a pathway model from network
PathwayModel(Map) - Constructor for class edu.iastate.metnet.graphmodel.PathwayModel
set up the mixture of the pathway based on the ID
PathwayObject - Class in edu.iastate.metnet.dao
store basic pathway information for pathway selector
PathwayObject() - Constructor for class edu.iastate.metnet.dao.PathwayObject
 
pathwayObject - Variable in class edu.iastate.metnet.export.PathwayInfoImpl
pathway object
pathwayObject - Variable in class edu.iastate.metnet.model.PathwayObjectChoice
pathway object
PathwayObjectChoice - Class in edu.iastate.metnet.model
pathway object selection
PathwayObjectChoice(PathwayObject) - Constructor for class edu.iastate.metnet.model.PathwayObjectChoice
default constructor
PathwayObjectTableModel - Class in edu.iastate.reload.model
display pathway table model
PathwayObjectTableModel(ListModel) - Constructor for class edu.iastate.reload.model.PathwayObjectTableModel
 
PathwayObjectWorker - Class in edu.iastate.metnet.ui
 
PathwayObjectWorker(Collection, Vector, boolean) - Constructor for class edu.iastate.metnet.ui.PathwayObjectWorker
default constructor
Pathwayparts - Class in edu.iastate.metnet.hibernate
A class that represents a row in the 'pathwayparts' table.
Pathwayparts() - Constructor for class edu.iastate.metnet.hibernate.Pathwayparts
Simple constructor of Pathwayparts instances.
Pathwayparts(PathwaypartsKey) - Constructor for class edu.iastate.metnet.hibernate.Pathwayparts
Constructor of Pathwayparts instances given a composite primary key.
PathwaypartsKey - Class in edu.iastate.metnet.hibernate
A class representing a composite primary key id for the pathwayparts table.
PathwaypartsKey() - Constructor for class edu.iastate.metnet.hibernate.PathwaypartsKey
Simple constructor of PathwaypartsKey instances.
PathwayPrefix - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
 
PathwaySelectionFrame - Class in edu.iastate.metnet.dataManager
Frame that lists pathway names for the selected gene ids.
PathwaySelectionFrame - Class in edu.iastate.metnet.metaomgraph
 
PathwaySelector2 - Class in edu.iastate.metnet.ui
 
PathwaySelector2(Object, boolean) - Constructor for class edu.iastate.metnet.ui.PathwaySelector2
the pathway selector
PathwayService - Class in edu.iastate.metnet.hivemindService
HiveMind Service to get Pathway Category Tree
PathwayService() - Constructor for class edu.iastate.metnet.hivemindService.PathwayService
 
pathwaySink - Variable in class edu.iastate.metnet.ui.PathwayObjectWorker
the pathway object result for this thread
PathwaySubmitListener - Class in edu.iastate.metnet.birdseyeview
 
PathwaySubmitListener() - Constructor for class edu.iastate.metnet.birdseyeview.PathwaySubmitListener
 
PathwaySubmitListener - Class in edu.iastate.metnet.dataManager
 
PathwaySubmitListener() - Constructor for class edu.iastate.metnet.dataManager.PathwaySubmitListener
 
PathwaySubmitListener - Class in edu.iastate.metnet.metaomgraph
 
PathwaySubmitListener() - Constructor for class edu.iastate.metnet.metaomgraph.PathwaySubmitListener
 
PathwayTableModel - Class in edu.iastate.metnet.model
List the basic pathway information for pathway selector, especially the user information and source information.
PathwayTableModel(ListModel) - Constructor for class edu.iastate.metnet.model.PathwayTableModel
 
PathwayTreeNode - Class in edu.iastate.metnet.birdseyeview
The Panle shows the tree of pathway as a menu for user to choose so that the genes belonging to this pathway will be shown in cell view or other views.
PathwayTreeNode(String) - Constructor for class edu.iastate.metnet.birdseyeview.PathwayTreeNode
 
PathwayView - Class in edu.iastate.metnet.birdseyeview.pathwayview
The PathwayView Class displays the Bird's Eye View of the pathways in which the gene products participate.
PathwayView(ViewInfo, BirdsEyeView, ArrayList, Dimension, String) - Constructor for class edu.iastate.metnet.birdseyeview.pathwayview.PathwayView
Constructor.
PathwayViewID - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
 
PathwayViewName - Static variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView
 
pattern - Variable in class edu.iastate.metnet.aracyc.AracycCompound
 
pattern2D - Static variable in class edu.iastate.reload.skin.MetalUtilsX
The typical metal pattern for use with Graphics2D.
pattern2D - Static variable in class javax.swing.plaf.metal.MetalUtils
The typical metal pattern for use with Graphics2D.
PbFrame - Class in fcmodeler.pathbinder.gui
 
PbFrame(MySqlConnector) - Constructor for class fcmodeler.pathbinder.gui.PbFrame
 
pbid - Variable in class edu.iastate.biocyc.ui.PbidNode
 
pbid - Variable in class edu.iastate.metnet.dao.CategoryNode
blockid of the pathway if this is a pathway
pbid - Variable in class edu.iastate.metnet.dao.PathwayObject
the blockid
pbid - Variable in class edu.iastate.metnet.ui.AddInteractionForm
blockid of the pathway
pbidList - Variable in class edu.iastate.metnet.ui.CompileWorker
compilation list
pbidList - Variable in class edu.iastate.metnet.ui.PathwayObjectWorker
the pathway blockid for query
PbidNode - Class in edu.iastate.biocyc.ui
 
PbidNode(Integer) - Constructor for class edu.iastate.biocyc.ui.PbidNode
 
pbidSet - Variable in class edu.iastate.metnet.ui.AddPathwayForm
select pathway list for template
PbSentence - Class in fcmodeler.pathbinder
 
PbSentence(String, long) - Constructor for class fcmodeler.pathbinder.PbSentence
 
PbViewer - Class in fcmodeler.pathbinder.gui
 
PbViewer() - Constructor for class fcmodeler.pathbinder.gui.PbViewer
 
PbViewer(PathBinder) - Constructor for class fcmodeler.pathbinder.gui.PbViewer
 
PbViewer(PbSentence[], Set, Set, Set, Set, Set, Set, String[], String[]) - Constructor for class fcmodeler.pathbinder.gui.PbViewer
 
PCASSAY - Static variable in class edu.iastate.jtm.jmed.Entrez
 
PCCOMPOUND - Static variable in class edu.iastate.jtm.jmed.Entrez
 
PCSUBSTANCE - Static variable in class edu.iastate.jtm.jmed.Entrez
 
PDATE - Static variable in class edu.iastate.jtm.jmed.Limits
 
PEARSON - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmAnalyzer
 
PEARSON_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmTablePanel
 
pearsonCorrelation(Object[], boolean, Double) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
Calculates the Pearson Correlation of this calculator's base data with another set of data.
pearsonCorrelation(double[], boolean, Double) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
 
pearsonCorrelationStandard(double[]) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
 
pearsonCorrelationWithSkips(double[], Double) - Method in class edu.iastate.metnet.metaomgraph.CorrelationCalc
 
peek() - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile
Returns the character at the current pointer without advancing the pointer.
peek() - Method in class edu.iastate.metnet.soft.RandomAccessFile
Returns the character at the current pointer without advancing the pointer.
peekDic - Variable in class edu.iastate.jtm.EntityFinder
 
peekRegex - Variable in class edu.iastate.jtm.EntityFinder
 
performEnterAction(KeyEvent) - Method in class edu.iastate.metnet.ui.TrivialSelector
perform the enter key
permitOrganismList(String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
get all organism that the user allowed to edit
permitOrganismList(String) - Method in interface edu.iastate.metnet.interfaces.MyPaper
get all organism that the user allowed to edit
PG - Static variable in class edu.iastate.jtm.jmed.Query.Field
 
PL - Static variable in class edu.iastate.jtm.jmed.Query.Field
 
Platform - Class in edu.iastate.metnet.soft
 
Platform(String) - Constructor for class edu.iastate.metnet.soft.Platform
 
PlatformService - Class in edu.iastate.metnet.ui
 
PlatformService(List) - Constructor for class edu.iastate.metnet.ui.PlatformService
 
plugins - Variable in class edu.iastate.metnet.launch.RunCytoscape
 
pluralDetector - Variable in class edu.iastate.jtm.EntityFinder
 
PluralDetector - Class in edu.iastate.jtm
Lookup a noun's singular form against a dictionary.
PluralDetector(File) - Constructor for class edu.iastate.jtm.PluralDetector
Creates a new instance of PluralDetector.
PluralDetector(URL) - Constructor for class edu.iastate.jtm.PluralDetector
 
PluralDetector() - Constructor for class edu.iastate.jtm.PluralDetector
 
PLUS - Static variable in class edu.iastate.jtm.util.NameCharType
 
PMC - Static variable in class edu.iastate.jtm.jmed.Entrez
 
pmid() - Method in class edu.iastate.jtm.jmed.MedCitation
 
PmidFilter - Class in fcmodeler.pathbinder
Take care of creating temporary filter table.
PmidFilter(MySqlConnector) - Constructor for class fcmodeler.pathbinder.PmidFilter
 
pmidPool - Static variable in class edu.iastate.jtm.assistant.Controller
 
pmidTablePanel - Static variable in class edu.iastate.jtm.assistant.Controller
 
PmidTablePanel - Class in edu.iastate.jtm.assistant
 
PmidTablePanel(CitationPool) - Constructor for class edu.iastate.jtm.assistant.PmidTablePanel
 
PNG - Static variable in class edu.iastate.metnet.metaomgraph.GraphFileFilter
Mode to accept .png files
PointInfoPanel - Class in edu.iastate.metnet.metaomgraph.chart
 
PointInfoPanel(MetaOmChartPanel) - Constructor for class edu.iastate.metnet.metaomgraph.chart.PointInfoPanel
 
pointNumber() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode
This method return the number of points in genepanel
poly - Variable in class edu.iastate.metnet.metaomgraph.throbber.PolygonThrobber
 
PolygonPanel - Class in edu.iastate.metnet.metaomgraph
 
PolygonPanel(int, int) - Constructor for class edu.iastate.metnet.metaomgraph.PolygonPanel
 
PolygonPanel.BouncingPolygon - Class in edu.iastate.metnet.metaomgraph
 
PolygonPanel.BouncingPolygon(int, int, int, int, int) - Constructor for class edu.iastate.metnet.metaomgraph.PolygonPanel.BouncingPolygon
 
PolygonThrobber - Class in edu.iastate.metnet.metaomgraph.throbber
 
PolygonThrobber() - Constructor for class edu.iastate.metnet.metaomgraph.throbber.PolygonThrobber
 
polyPanel - Variable in class edu.iastate.metnet.metaomgraph.AboutFrame
 
Polypeptide - Class in edu.iastate.metnet.birdseyeview
The Polypeptide Class is a subclass of protein which defines its type.
Polypeptide(Integer, String) - Constructor for class edu.iastate.metnet.birdseyeview.Polypeptide
Constructor.
PolypeptideType - Static variable in class edu.iastate.metnet.birdseyeview.Annotation
 
POPSET - Static variable in class edu.iastate.jtm.jmed.Entrez
 
PorterStemmer - Class in edu.iastate.jtm
PorterStemmer, implementing the Porter Stemming Algorithm The Stemmer class transforms a word into its root form.
PorterStemmer() - Constructor for class edu.iastate.jtm.PorterStemmer
Creates a new instance of PorterStemmer
post(String[], int, int, Limits) - Method in class edu.iastate.jtm.jmed.EPost
 
post(String[], Limits) - Method in class edu.iastate.jtm.jmed.EPost
 
post(String[]) - Method in class edu.iastate.jtm.jmed.EPost
 
postInitData() - Method in class edu.iastate.metnet.ui.PathwayEditor
initialize data after ui initialization
predGuidSet - Variable in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode
pred multi-node
PredictedLocation - Interface in edu.iastate.metnet.datamodel.attributes
Interface represents PredictedLocation
preferences - Variable in class edu.iastate.metnet.aracyc.ConsoleApplication
preference setting
preferredLayoutSize(Container) - Method in class edu.iastate.metnet.birdseyeview.GenePanelLayout
 
preInitData() - Method in class edu.iastate.metnet.ui.PathwayEditor
initialize data before ui initialization
prepare(String, String, String[]) - Static method in class edu.iastate.metnet.utils.Utils
replace the mark in the template string
prepare(String, String, String, String) - Static method in class edu.iastate.metnet.utils.Utils
 
prepare(String, String, String, String, String) - Static method in class edu.iastate.metnet.utils.Utils
 
prepare(String, String, String, String, String, String) - Static method in class edu.iastate.metnet.utils.Utils
 
prepare(String, String, String) - Static method in class edu.iastate.metnet.utils.Utils
 
prepare(String, String) - Static method in class edu.iastate.metnet.utils.Utils
 
prepare(String, String[]) - Static method in class edu.iastate.metnet.utils.Utils
prepare the template with default mark as ?
prepareRenderer(TableCellRenderer, int, int) - Method in class edu.iastate.metnet.StripedTable
Shades alternate rows in different colors.
prepareStatement(String) - Method in class edu.iastate.jtm.util.MySqlConnector
 
PRIMARY1 - Static variable in class edu.iastate.reload.skin.OceanThemeX
The OceanTheme value for primary1.
PRIMARY1 - Static variable in class javax.swing.plaf.metal.OceanTheme
The OceanTheme value for primary1.
PRIMARY2 - Static variable in class edu.iastate.reload.skin.OceanThemeX
The OceanTheme value for primary1.
PRIMARY2 - Static variable in class javax.swing.plaf.metal.OceanTheme
The OceanTheme value for primary1.
PRIMARY3 - Static variable in class edu.iastate.reload.skin.OceanThemeX
The OceanTheme value for primary1.
PRIMARY3 - Static variable in class javax.swing.plaf.metal.OceanTheme
The OceanTheme value for primary1.
print(Map) - Method in class edu.iastate.biocyc.io.AttributeFileReaderEx
the map structure should contain the unique as the key, then another map as the value.
print(PrintStream, boolean) - Method in class edu.iastate.jtm.dic.Trie
Print all entries in this trie.
print(Map) - Method in class edu.iastate.metnet.aracyc.AbstractAracycFileReader
the map structure should contain the unique as the key, then another map as the value.
print() - Method in class edu.iastate.metnet.aracyc.ClassTree
 
print(Object, int) - Method in class edu.iastate.metnet.aracyc.ClassTree
 
print(Map) - Method in interface edu.iastate.metnet.aracyc.IAracycFileReader
 
print() - Method in class edu.iastate.metnet.launch.List
 
printAll() - Method in class edu.iastate.jtm.SentenceParser
 
printHelp() - Method in class edu.iastate.metnet.launch.RunCytoscape
 
printIndexMapping() - Method in class edu.iastate.jtm.dic.AbstractTrieNode
 
printIndexMapping() - Method in interface edu.iastate.jtm.dic.TrieNode
 
printParenthesesPositions() - Method in class edu.iastate.jtm.util.ParenFinder
Print out.
printSizes(Component) - Static method in class edu.iastate.jtm.gui.SpringUtilities
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
printStrides() - Method in class edu.iastate.jtm.util.SlidingWindow
 
PROBE - Static variable in class edu.iastate.jtm.jmed.Entrez
 
ProbeNames - Static variable in class edu.iastate.metnet.birdseyeview.LoadController
 
processEnded(int) - Method in interface edu.iastate.jtm.util.ProcessListener
 
processFile(File) - Method in class fcmodeler.pathbinder.MetaCrawler
 
processFinished(String) - Method in class edu.iastate.jtm.gui.StatusBar
 
processLeft(int) - Method in class edu.iastate.jtm.util.ParenFinder
Process a LEFT character.
ProcessListener - Interface in edu.iastate.jtm.util
Listener of a process.
processReport(String, float) - Method in interface edu.iastate.jtm.util.ProcessListener
 
processResponse() - Method in class edu.iastate.jtm.jmed.UmlsSocketClient
 
processResult(InputStream) - Method in interface edu.iastate.jtm.jmed.EUtility.Processor
 
processRight(int) - Method in class edu.iastate.jtm.util.ParenFinder
Process a RIGHT character.
processStderr(char[], int) - Method in class edu.iastate.jtm.util.ProcessWrapper
 
processStdout(char[], int) - Method in class edu.iastate.jtm.util.ProcessWrapper
 
processUnit() - Method in class fcmodeler.pathbinder.MetaCrawler
 
ProcessWrapper - Class in edu.iastate.jtm.util
A wrapper class for a commandline process.
ProcessWrapper(String) - Constructor for class edu.iastate.jtm.util.ProcessWrapper
Creates a new instance of ProcessMoniter
ProcessWrapper.CmdNotFoundException - Exception in edu.iastate.jtm.util
 
ProcessWrapper.CmdNotFoundException(String) - Constructor for exception edu.iastate.jtm.util.ProcessWrapper.CmdNotFoundException
 
PROCITE - Static variable in class edu.iastate.jtm.assistant.Exporter
 
ProCite - Class in edu.iastate.jtm.assistant
 
ProCite() - Constructor for class edu.iastate.jtm.assistant.ProCite
 
products - Variable in class edu.iastate.metnet.dao.InteractionInformation
right part of the interactions
progress - Variable in class edu.iastate.jtm.gui.DefaultMonitorable
 
progress - Variable in class edu.iastate.metnet.newgui.MetNetStatusbar
 
ProgressMonitor - Interface in edu.iastate.jtm.util
 
PROJECT - Static variable in class edu.iastate.metnet.metaomgraph.GraphFileFilter
Mode to accept .mcg and .mog files
ProjectPropertiesPanel - Class in edu.iastate.metnet.metaomgraph
 
ProjectPropertiesPanel(MetaOmProject) - Constructor for class edu.iastate.metnet.metaomgraph.ProjectPropertiesPanel
 
prompt() - Method in class edu.iastate.metnet.aracyc.GraphStatistics
prompt command line to let user do input and observe output
promptPassphrase(String) - Method in class edu.iastate.jtm.util.RemoteControl
 
promptPassword(String) - Method in class edu.iastate.jtm.util.RemoteControl
 
promptToSave() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph
Prompts the user to save the active project.
promptYesNo(String) - Method in class edu.iastate.jtm.util.RemoteControl
 
Properties - Class in edu.iastate.metnet.dataManager
Class stores properties of File chosen by user.
Properties(String, int, int, Date) - Constructor for class edu.iastate.metnet.dataManager.Properties
 
Properties() - Constructor for class edu.iastate.metnet.dataManager.Properties
 
PROPERTIES_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.MetaOmGraph
 
PropertiesMetalTheme - Class in edu.iastate.metnet.ui
This class allows you to load a theme from a file.
PropertiesMetalTheme(InputStream) - Constructor for class edu.iastate.metnet.ui.PropertiesMetalTheme
pass an inputstream pointing to a properties file.
propertyChange(PropertyChangeEvent) - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView
Invoked when task's progress property changes.
propertyChange(PropertyChangeEvent) - Method in class edu.iastate.metnet.event.UISwitchListener
 
propertyChange(PropertyChangeEvent) - Method in class edu.iastate.metnet.ui.OverviewPanel
 
propertyChange(PropertyChangeEvent) - Method in class edu.iastate.reload.ui.OverviewPanel
 
PROPERTYNAME_CHANGED - Static variable in class com.jgoodies.binding.extras.ChangeTracker
The name of the read-only bound bean property that indicates whether one of the observed properties has changed.
PropertyTable - Class in edu.iastate.metnet.ui
 
PropertyTable() - Constructor for class edu.iastate.metnet.ui.PropertyTable
 
props - Variable in class edu.iastate.metnet.launch.RunCytoscape
 
propsItem - Variable in class edu.iastate.metnet.dataManager.DataManager
 
PropsWindow - Class in edu.iastate.metnet.dataManager
Window that shows properties of a file
PropsWindow(Properties) - Constructor for class edu.iastate.metnet.dataManager.PropsWindow
 
PROTEIN - Static variable in class edu.iastate.jtm.jmed.Entrez
 
Protein - Class in edu.iastate.metnet.birdseyeview
The Protein class is an abstract class that encapsulates the name, metnet entity ID, and type of a protein.
Protein(Integer, String, String) - Constructor for class edu.iastate.metnet.birdseyeview.Protein
Constructor.
ProteinComplex - Class in edu.iastate.metnet.birdseyeview
The ProteinComplex Class is a subclass of protein which defines its type.
ProteinComplex(Integer, String) - Constructor for class edu.iastate.metnet.birdseyeview.ProteinComplex
Constructor.
ProteinComplexType - Static variable in class edu.iastate.metnet.birdseyeview.Annotation
 
PrototypeAnnotations - Class in edu.iastate.metnet.birdseyeview
The PrototypeAnnotations Class provides annotation data for the prototype of the Bird's Eye View API.
PrototypeAnnotations() - Constructor for class edu.iastate.metnet.birdseyeview.PrototypeAnnotations
 
PS - Static variable in class edu.iastate.jtm.jmed.Query.Field
 
PT - Static variable in class edu.iastate.jtm.jmed.Query.Field
 
PTYPE - Static variable in class edu.iastate.jtm.jmed.Limits
 
pubchemCasFilter(Collection) - Method in class edu.iastate.metnet.export.GraphExporterImpl
 
pubchemCasFilter(Collection) - Method in interface edu.iastate.metnet.hiveface.GraphExporter
obtain CAS from a list of name.
pubchemCasFilter(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade
filter out the cas number from synonyms
pubchemCasFilter(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
filter out the cas number from synonyms
pubchemCasFilter(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService
filter out the cas number from synonyms
pubchemCasFilter(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal
filter out the cas number from synonyms
pubchemCid2Name(Collection) - Method in class edu.iastate.metnet.export.GraphExporterImpl
 
pubchemCid2Name(Collection) - Method in interface edu.iastate.metnet.hiveface.GraphExporter
obtain pubchem synonym from compound id list
pubchemCid2Name(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade
get the pubchem synonym from pubchem cid
pubchemCid2Name(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
get the pubchem synonym from pubchem cid
pubchemCid2Name(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService
get the pubchem synonym from pubchem cid
pubchemCid2Name(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal
get the pubchem synonym from pubchem cid
pubchemName2Cid(Collection) - Method in class edu.iastate.metnet.export.GraphExporterImpl
 
pubchemName2Cid(Collection) - Method in interface edu.iastate.metnet.hiveface.GraphExporter
obtain pubchem compound id from name.
pubchemName2Cid(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade
this function search the table pubchem_cid_synonym to get the cid based on the name.
pubchemName2Cid(Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal
this function search the table pubchem_cid_synonym to get the cid based on the name.
pubchemName2Cid(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService
this function search the table pubchem_cid_synonym to get the cid based on the name.
pubchemName2Cid(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal
this function search the table pubchem_cid_synonym to get the cid based on the name.
PUBDATE - Static variable in class edu.iastate.jtm.jmed.Limits
 
PUBLICATION - Static variable in class edu.iastate.jtm.assistant.GoogleScholar
 
publicationId - Variable in class edu.iastate.metnet.dao.TairReferenceObject
 
PUBMED - Static variable in class edu.iastate.jtm.jmed.Entrez
 
PubMedAssistant - Class in edu.iastate.jtm.assistant
 
PubMedAssistant() - Constructor for class edu.iastate.jtm.assistant.PubMedAssistant
 
PubMedFetcher - Class in edu.iastate.jtm.jmed
Retrive abstracts from Medline given a list of PMIDs or last query's history.
PubMedFetcher() - Constructor for class edu.iastate.jtm.jmed.PubMedFetcher
Create a new instance of PubMedFetcher with default buffer size.
PubMedFetcher(int) - Constructor for class edu.iastate.jtm.jmed.PubMedFetcher
Create a new instance of PubMedFetcher with specified buffer size.
PubMedFetcher(MedlineParser) - Constructor for class edu.iastate.jtm.jmed.PubMedFetcher
Create a new instance of PubMedFetcher with default buffer size and a specified MedlineParser.
PubMedFetcher(String, String) - Constructor for class edu.iastate.jtm.jmed.PubMedFetcher
Create a new instance of PubMedFetcher with a tool name and email address.
pubmedId - Variable in class edu.iastate.metnet.dao.TairReferenceObject
 
PubMedQuerier - Class in edu.iastate.jtm.jmed
Get number of hits and/or PMID list from PubMed.
PubMedQuerier(int) - Constructor for class edu.iastate.jtm.jmed.PubMedQuerier
 
PubMedQuerier() - Constructor for class edu.iastate.jtm.jmed.PubMedQuerier
 
PubMedQuerier(SAXReader, int) - Constructor for class edu.iastate.jtm.jmed.PubMedQuerier
 
PubMedQuerier(SAXReader) - Constructor for class edu.iastate.jtm.jmed.PubMedQuerier
 
PubMedQuerier(int, String, String) - Constructor for class edu.iastate.jtm.jmed.PubMedQuerier
 
PubMedQuerier(String, String) - Constructor for class edu.iastate.jtm.jmed.PubMedQuerier
 
PubMedSampler - Class in edu.iastate.jtm.jmed
Randomly sample PubMed files.
PubMedSampler() - Constructor for class edu.iastate.jtm.jmed.PubMedSampler
 
PubMedTimer - Class in edu.iastate.jtm.jmed
Keep track of time intervals between two consective PubMed inqueries.
PUNC - Static variable in class edu.iastate.jtm.util.SlidingWindow
 
put(String, Object) - Method in class edu.iastate.jtm.dic.Trie
Put a key and value pair in the trie.
put(CharSequence, Object, boolean) - Method in class edu.iastate.jtm.dic.Trie
Put a key and value pair in the trie.
put(int, char) - Method in class edu.iastate.jtm.util.RunningBuffer
 
put(String, int, int) - Method in class edu.iastate.jtm.util.RunningBuffer
 
put(String) - Method in class edu.iastate.jtm.util.RunningBuffer
 
put(char) - Method in class edu.iastate.jtm.util.RunningBuffer
 
put(char[], int, int) - Method in class edu.iastate.jtm.util.RunningBuffer
 
put(CharBuffer) - Method in class edu.iastate.jtm.util.RunningBuffer
 
put(String, ArrayList) - Method in class edu.iastate.metnet.aracyc.AracycEntity
common interface for all
putEntry(String, Object) - Method in class edu.iastate.jtm.dic.AbstractDictionary
 
putEntry(String, Object) - Method in class edu.iastate.jtm.dic.HashDictionary
 
putEntry(String, Object) - Method in class edu.iastate.jtm.dic.TrieDictionary
 
putMapping(Object, CellView) - Method in class edu.iastate.metnet.ui.OverviewPanel.ViewRedirector
 
putMapping(Object, CellView) - Method in class edu.iastate.reload.ui.OverviewPanel.ViewRedirector
 
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