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

R

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

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

radioInteractionType - Variable in class edu.iastate.metnet.ui.SearchDialog

radioNodeName - Variable in class edu.iastate.metnet.ui.SearchDialog

RandomAccessFile - Class in edu.iastate.metnet.metaomgraph

A buffered drop-in replacement for java.io.RandomAccessFile.

RandomAccessFile(int) - Constructor for class edu.iastate.metnet.metaomgraph.RandomAccessFile

RandomAccessFile(String, int) - Constructor for class edu.iastate.metnet.metaomgraph.RandomAccessFile

Create a new buffered random-access file with a default buffer size.

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

Creates a random access file stream to read from, and optionally to write to, a file with the specified name.

RandomAccessFile(String, String, int) - Constructor for class edu.iastate.metnet.metaomgraph.RandomAccessFile

Creates a random access file stream to read from, and optionally to write to, a file with the specified name.

RandomAccessFile(File, String) - Constructor for class edu.iastate.metnet.metaomgraph.RandomAccessFile

Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.

RandomAccessFile(String, int, int) - Constructor for class edu.iastate.metnet.metaomgraph.RandomAccessFile

Create a new buffered random-access file with a specified buffer size.

RandomAccessFile - Class in edu.iastate.metnet.soft

A buffered drop-in replacement for java.io.RandomAccessFile.

RandomAccessFile(int) - Constructor for class edu.iastate.metnet.soft.RandomAccessFile

RandomAccessFile(String, int) - Constructor for class edu.iastate.metnet.soft.RandomAccessFile

Create a new buffered random-access file with a default buffer size.

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

Creates a random access file stream to read from, and optionally to write to, a file with the specified name.

RandomAccessFile(String, String, int) - Constructor for class edu.iastate.metnet.soft.RandomAccessFile

Creates a random access file stream to read from, and optionally to write to, a file with the specified name.

RandomAccessFile(File, String) - Constructor for class edu.iastate.metnet.soft.RandomAccessFile

Creates a random access file stream to read from, and optionally to write to, the file specified by the File argument.

RandomAccessFile(String, int, int) - Constructor for class edu.iastate.metnet.soft.RandomAccessFile

Create a new buffered random-access file with a specified buffer size.

RandomLayoutAlgorithm - Class in edu.iastate.metnet.graphmodel

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

randomSample(int, int, long) - Method in class edu.iastate.jtm.jmed.PubMedSampler

RangeMarker - Class in edu.iastate.metnet.metaomgraph.chart

Class that holds information about a sort beyond the order.

RangeMarker(int, int, String, int) - Constructor for class edu.iastate.metnet.metaomgraph.chart.RangeMarker

RangeMarker(int, int, String, int, Color) - Constructor for class edu.iastate.metnet.metaomgraph.chart.RangeMarker

Constructor.

RangeSelector - Class in edu.iastate.metnet.metaomgraph.chart

RangeSelector(MetaOmChartPanel) - Constructor for class edu.iastate.metnet.metaomgraph.chart.RangeSelector

RC_DUPLICATE - Static variable in class edu.iastate.metnet.db.ReturnCode

RC_INSERTED - Static variable in class edu.iastate.metnet.db.ReturnCode

RC_OK - Static variable in class edu.iastate.metnet.db.ReturnCode

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

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

reactionRateMap - Variable in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

hold the chemical reaction rates

read(String) - Method in class edu.iastate.biocyc.io.AttributeFileReaderEx

read in the file and turn into map data structure like ATP=> {UID=>[ATP], SYNONYM=>[ATPase, ADP]}

read(InputStream) - Method in class edu.iastate.biocyc.io.AttributeFileReaderEx

read data from the input stream

read(String) - Method in class edu.iastate.metnet.aracyc.AbstractAracycFileReader

empty function need to be implemented by subclass

read(InputStream) - Method in class edu.iastate.metnet.aracyc.AbstractAracycFileReader

read(String) - Method in class edu.iastate.metnet.aracyc.AttributeFileReader

read in the file and turn into map data structure like ATP=> {UID=>[ATP], SYNONYM=>[ATPase, ADP]}

read(String) - Method in class edu.iastate.metnet.aracyc.AttributeFileReaderEx

read in the file and turn into map data structure like ATP=> {UID=>[ATP], SYNONYM=>[ATPase, ADP]}

read(InputStream) - Method in class edu.iastate.metnet.aracyc.AttributeFileReaderEx

read(String) - Method in interface edu.iastate.metnet.aracyc.IAracycFileReader

read the file into map structure, use UNIQUE-ID as the key

read(InputStream) - Method in interface edu.iastate.metnet.aracyc.IAracycFileReader

read(String) - Method in class edu.iastate.metnet.aracyc.TabularFileReader

read(String) - Method in class edu.iastate.metnet.aracyc.TabularFileReaderEx

read files and get the map of multimap

read(InputStream) - Method in class edu.iastate.metnet.aracyc.TabularFileReaderEx

READ - Static variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Read from the file.

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

Read a byte of data from the file, blocking until data is available.

read(byte[], int, int) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Read up to len bytes into an array, at a specified offset.

read(byte[]) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Read up to b.length( ) bytes into an array.

READ - Static variable in class edu.iastate.metnet.soft.RandomAccessFile

Read from the file.

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

Read a byte of data from the file, blocking until data is available.

read(byte[], int, int) - Method in class edu.iastate.metnet.soft.RandomAccessFile

Read up to len bytes into an array, at a specified offset.

read(byte[]) - Method in class edu.iastate.metnet.soft.RandomAccessFile

Read up to b.length( ) bytes into an array.

read_(long, byte[], int, int) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

read_(long, byte[], int, int) - Method in class edu.iastate.metnet.soft.RandomAccessFile

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

Reads a boolean from this file.

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

Reads a boolean from this file.

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

Reads a signed 8-bit value from this file.

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

Reads a signed 8-bit value from this file.

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

Reads a Unicode character from this file.

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

Reads a Unicode character from this file.

readConfigureFile() - Method in class edu.iastate.metnet.db.Environment

read the configuration file?

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

Reads a double from this file.

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

Reads a double from this file.

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

Reads a float from this file.

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

Reads a float from this file.

readFromFile(File, boolean) - Method in class edu.iastate.jtm.dic.AbstractDictionary

readFromFile(File) - Method in class edu.iastate.jtm.dic.AbstractDictionary

readFromUrl(URL, boolean) - Method in class edu.iastate.jtm.dic.AbstractDictionary

readFully(byte[]) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Reads b.length bytes from this file into the byte array.

readFully(byte[], int, int) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Reads exactly len bytes from this file into the byte array.

readFully(byte[]) - Method in class edu.iastate.metnet.soft.RandomAccessFile

Reads b.length bytes from this file into the byte array.

readFully(byte[], int, int) - Method in class edu.iastate.metnet.soft.RandomAccessFile

Reads exactly len bytes from this file into the byte array.

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

Reads a signed 32-bit integer from this file.

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

Reads a signed 32-bit integer from this file.

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

Reads the next line of text from this file.

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

Reads the next line of text from this file.

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

Reads a signed 64-bit integer from this file.

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

Reads a signed 64-bit integer from this file.

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

Reads a signed 16-bit number from this file.

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

Reads a signed 16-bit number from this file.

readString(char, boolean) - Method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Fetches everything up to the next delimiter character, \n character, or EOF.

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

Fetches everything up to the next delimiter character, \n character, or EOF.

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

Fetches everything up to the next tab character, \n character, or EOF

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

Reads an unsigned 8-bit number from this file.

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

Reads an unsigned 8-bit number from this file.

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

Reads an unsigned 16-bit number from this file.

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

Reads an unsigned 16-bit number from this file.

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

Reads in a string from this file.

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

Reads in a string from this file.

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

concrete one history of the pathway into the database so we can use it for comparison or other purposed like a normal pathway

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

concrete one history of the pathway into the database so we can use it for comparison or other purposed like a normal pathway

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

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

realView - Variable in class edu.iastate.metnet.ui.OverviewPanel.ViewRedirector

realView - Variable in class edu.iastate.reload.ui.OverviewPanel.ViewRedirector

rebuildViewToModel() - Method in class edu.iastate.metnet.metaomgraph.TableSorter

receive(char[], int, int) - Method in interface edu.iastate.jtm.util.RemoteReceiver

receiveInteraction(InteractionInformation) - Method in class edu.iastate.reload.ui.NetworkEditForm

add interaction to the graph

receiveLiveEntity(Blockunit) - Method in class edu.iastate.reload.ui.NetworkEditForm

add live entity to the graph

receiveLiveEntityList(List) - Method in class edu.iastate.metnet.ui.AmorphousQueryForm

used for entity selector for querying network

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

receive the live entity list

receivePathway(HashMap) - Method in class edu.iastate.metnet.ui.AbstractMetnetWindow

used for pathway editor

receivePathway(HashMap) - Method in class edu.iastate.metnet.ui.AddInteractionForm

get the pathway's BlocID and list it in the the pathway table

receivePathway(HashMap) - Method in class edu.iastate.metnet.ui.AddPathwayForm

receive the selection and update the current interaction list

receivePathway(HashMap) - Method in interface edu.iastate.metnet.ui.IMetnetWindow

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

accept the pathway and visualize it

receivePathway(PathwayModel) - Method in class edu.iastate.reload.ui.NetworkEditForm

receive a pathway model directly

receivePathwayList(List) - Method in class edu.iastate.metnet.ui.AmorphousQueryForm

used for entity selector for querying network

receiveReactionID(String, boolean) - Method in class edu.iastate.metnet.ui.AddInteractionForm

get the BlockID from Edit Entity window or Edit Pathway window and show all the information of the specified interaction.

receiveSpecies(Collection) - Method in class edu.iastate.metnet.ui.CategoryEditForm

obtain the species for filter

receiveTrivialList(List) - Method in class edu.iastate.metnet.ui.AmorphousQueryForm

used for metabolite selector for querying network

receiveVersionDataObject(Object) - Method in interface edu.iastate.metnet.graphmodel.VersionListener

receiveVersionDataObject(Object) - Method in class edu.iastate.metnet.ui.AddEntityForm

handle the version data update

receiveVersionDataObject(Object) - Method in class edu.iastate.metnet.ui.AddInteractionForm

handle the version data update

receiveVersionDataObject(Object) - Method in class edu.iastate.metnet.ui.AddPathwayForm

handle the version data update

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

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

depends on the controlled interaction?

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

depends on the controlled interaction?

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

recognize the interaction and create it if necesaary.

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

recognize the interaction and create it if necesaary.

recognizeNormalLiveEntity(String, String, String, String, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyFacade

recognize the live entity and create the live entity if necessary, since the data can be from expert data or aracyc, so source and username are parameters also.

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

recognize the live entity and create the live entity if necessary, since the data can be from expert data or aracyc, so source and username are parameters also.

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

unique id in the graph

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

record if of the history

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

record id of the data

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

record id, for internal usage

redisplayGenesToNodes(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoBioProcessView

redisplayGenesToNodes(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoFunctionView

redisplayGenesToNodes(ArrayList) - Method in class edu.iastate.metnet.birdseyeview.goview.GoView

redrawAnnotations() - Method in class edu.iastate.metnet.metaomgraph.chart.ChartAnnotator

Redraws the annotations on the chart

ReferenceEditForm - Class in edu.iastate.reload.ui

ReferenceEditForm(ArrayListModel, Blockunitref) - Constructor for class edu.iastate.reload.ui.ReferenceEditForm

Creates new form ReferenceEditForm

ReferenceObject - Class in edu.iastate.metnet.dao

ReferenceObject(Integer, String, String, String, boolean) - Constructor for class edu.iastate.metnet.dao.ReferenceObject

ReferenceObject(String, String, String) - Constructor for class edu.iastate.metnet.dao.ReferenceObject

referenceOrigin - Variable in class edu.iastate.reload.ui.ReferenceEditForm

original reference value

ReferenceTableModel - Class in edu.iastate.metnet.model

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

ReferenceTableModel - Class in edu.iastate.reload.model

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

refresh() - Method in class edu.iastate.metnet.metaomgraph.chart.PointInfoPanel

refresh() - Method in class edu.iastate.metnet.model.AbbreviationRulesModel

refreshCharts() - Static method in class edu.iastate.metnet.metaomgraph.MetaOmGraph

refreshCustomSortMenu() - Method in class edu.iastate.metnet.metaomgraph.chart.ChartToolBar

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

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

RefService - Class in edu.iastate.metnet.ui

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

constructor

refType - Variable in class edu.iastate.metnet.dao.ReferenceObject

refValue - Variable in class edu.iastate.metnet.dao.ReferenceObject

register(Object, int) - Method in class edu.iastate.jtm.util.VocabularyCounter

Add a new word to the vocabulary, or update count of a registered word.

registerComponent(JComponent) - Method in class edu.iastate.metnet.newgui.MetNetHelpBar

Registers a component with this help bar.

registerComponent(JComponent) - Method in class edu.iastate.metnet.newgui.MetNetStatusbar

Registers the given JComponent with this statusbar so that its ToolTipText is displayed here rather than in a tooltip.

RegisterForm - Class in edu.iastate.metnet.ui

new interface for registration

RegisterForm(Frame) - Constructor for class edu.iastate.metnet.ui.RegisterForm

Creates new form RegisterForm

RegisterForm(Dialog) - Constructor for class edu.iastate.metnet.ui.RegisterForm

Creates new form RegisterForm

RegisterForm2 - Class in edu.iastate.metnet.ui

this registration form is deprecated by class RegisterForm, which contains the species that can be edited by the curator.

RegisterForm2(Frame) - Constructor for class edu.iastate.metnet.ui.RegisterForm2

main class

RegisterForm2(Dialog) - Constructor for class edu.iastate.metnet.ui.RegisterForm2

main class

regularPolygon(int, int, int, int, double) - Static method in class edu.iastate.metnet.metaomgraph.throbber.SpinningPolygonThrobber

Create a regular closed polygon, (all sides equal length, all interior angles equal).

RelationMap - Class in edu.iastate.metnet.dao

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

RelationObject - Class in edu.iastate.metnet.graphmodel

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

releaseWriteLock() - Static method in class edu.iastate.metnet.ui.MainWindow2

release the write lock

reloadData() - Method in class edu.iastate.metnet.birdseyeview.AbstractView

Subclasses must reload the annotation data and modify their displays accordingly.

reloadData() - Method in class edu.iastate.metnet.birdseyeview.cellview.CellView

reloadData() - Method in class edu.iastate.metnet.birdseyeview.goview.GoView

reloadData() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.PathwayView

remanent - Variable in class edu.iastate.reload.ui.MyMarqueeHandler

A boolean telling wether or not a button creating an Edge or a Vertex should be remanent or not.

RemoteControl - Class in edu.iastate.jtm.util

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

RemoteControl(String, String, String) - Constructor for class edu.iastate.jtm.util.RemoteControl

remoteDelete(Object) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remote delete a database object

remoteDelete(Object) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remote delete a database object

remoteInsert(Object) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remote insert a database object

remoteInsert(Object, Serializable) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remote insert a database object

remoteInsert(Object) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remote insert a database object

remoteInsert(Object, Serializable) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remote insert a database object

remoteLayout(String) - Method in interface edu.iastate.metnet.interfaces.MyFacade

run layout on the server

remoteLayout(String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

run layout on the server

RemoteReceiver - Interface in edu.iastate.jtm.util

remoteSelect(String) - Method in interface edu.iastate.metnet.interfaces.MyFacade

let hibernate run at remote side

remoteSelect(String) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

let hibernate run at remote side

remoteUpdate(Object) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remote update a database object

remoteUpdate(Object, Object) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remote update a database object which has a natural key by itself

remoteUpdate(Object) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remote update a database object

remoteUpdate(Object, Object) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remote update a database object which has a natural key by itself

remove(CharSequence) - Method in class edu.iastate.jtm.dic.Trie

Remove an entry from the trie.

remove(Object) - Method in class edu.iastate.jtm.util.VocabularyCounter

remove(int) - Method in class fcmodeler.pathbinder.gui.VerbNode

remove(MutableTreeNode) - Method in class fcmodeler.pathbinder.gui.VerbNode

REMOVE_ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

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

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

REMOVE_FILE_COMMAND - Static variable in class edu.iastate.metnet.soft.SOFTParserOptionPanel

removeActionListener(ActionListener) - Method in class edu.iastate.metnet.metaomgraph.chart.RangeSelector

removeAllGenes() - Method in class edu.iastate.metnet.birdseyeview.goview.GoNode

This method clears out the gene list.

removeAllGenes() - Method in class edu.iastate.metnet.birdseyeview.pathwayview.Pathway

This method removes all the gene data by clearing out the gene container.

removeAllNodes() - Method in class edu.iastate.metnet.birdseyeview.goview.GoLevel

This method removes all the nodes on this level.

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

This method removes the given annotation from the list.

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

RemoveBridgeNodes - Class in edu.iastate.metnet.graphmodel

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

default constructor

RemoveBridgeNodes(boolean) - Constructor for class edu.iastate.metnet.graphmodel.RemoveBridgeNodes

default constructor

removeChangeListener(ChangeListener) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Unregisters a ChangeListener from this project.

removeChebiLink(EntityOntology) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remove the entityontology

removeChebiLink(EntityOntology) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remove the entityontology

removeChild(int) - Method in class edu.iastate.jtm.dic.AbstractTrieNode

removeChild(int) - Method in interface edu.iastate.jtm.dic.TrieNode

removeChildren() - Method in class edu.iastate.jtm.dic.AbstractTrieNode

removeChildren() - Method in interface edu.iastate.jtm.dic.TrieNode

removeCitation(int) - Method in class edu.iastate.jtm.assistant.CitationPool

removeCitationListener(CitationListener) - Method in class edu.iastate.jtm.assistant.CitationPool

removeColumn(JTable, int) - Method in class edu.iastate.metnet.utils.Utils

hidden the column from JTable such as serial number, if used on multiple columns, do from largest one

removeCompositionGraphModelChangedListener(CompositionGraphModelChangedListener) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

RemoveCompositionNodes - Class in edu.iastate.metnet.graphmodel

the only difference with remove RemoveSelectedNodes is not connect the upstream nodes with downstream nodes

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

removeEditorForColumn(int) - Method in class edu.iastate.metnet.model.ColumnEditorModel

removeEditorForRow(int) - Method in class edu.iastate.metnet.model.RowEditorModel

removeEntry(String) - Method in class edu.iastate.jtm.dic.AbstractDictionary

removeEntry(String) - Method in class edu.iastate.jtm.dic.HashDictionary

removeEntry(String) - Method in class edu.iastate.jtm.dic.TrieDictionary

removeFromBack() - Method in class edu.iastate.metnet.launch.List

removeFromFront() - Method in class edu.iastate.metnet.launch.List

removeFromParent() - Method in class fcmodeler.pathbinder.gui.VerbNode

removeGroup(Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

remove the selected group

removeGroup(Integer) - Method in interface edu.iastate.metnet.interfaces.MyPaper

remove the selected group

removeJGraphEdge(Edge) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Remove the edge corresponding to this JGraph edge from the JGraphT graph.

removeJGraphTEdge(Edge) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Removes the specified JGraphT edge from being reflected by this graph model.

removeJGraphTVertex(Object) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Removes the specified JGraphT vertex from being reflected by this graph model.

removeJGraphVertex(GraphCell) - Method in class edu.iastate.metnet.graphmodel.MyJGraphModelAdapter

Remove the vertex corresponding to this JGraph vertex from the JGraphT graph.

removeLastCorrelation() - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

removeLayoutComponent(Component) - Method in class edu.iastate.metnet.birdseyeview.GenePanelLayout

removeListDataListener(ListDataListener) - Method in class com.jgoodies.binding.extras.ListModelHolder

Removes a listener from the list that's notified each time a change to the data model occurs.

removeMarkListener(MarkListener) - Method in class edu.iastate.jtm.assistant.CitationPool

removeMarkListener(MarkListener) - Method in interface edu.iastate.jtm.gui.Markable

removeMetnetBlockunit(Integer) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

removeNode(Integer) - Method in interface edu.iastate.metnet.dao.PathwayGraph

remove a node from the pathway structure

removeNode(Integer) - Method in class edu.iastate.metnet.dao.PathwayGraphImpl

removeNode(Integer) - Method in class edu.iastate.metnet.export.MyPathwayGraph

remove a node from the pathway structure

removeNodeFromParent(MutableTreeNode) - Method in class edu.iastate.jtm.gui.XmlTreeModel

removeNodeFromParent(Node) - Method in class edu.iastate.jtm.gui.XmlTreeModel

removeProcessListener(ProcessListener) - Method in class edu.iastate.jtm.util.ProcessWrapper

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

removeQueueListener(QueueListener) - Method in class edu.iastate.jtm.assistant.CitationPool

removeRelation(Integer, Integer) - Method in class edu.iastate.metnet.graphmodel.CompositionGraphModel

removeRemoteReceiver(RemoteReceiver) - Method in class edu.iastate.jtm.util.RemoteControl

RemoveSelectedNodes - Class in edu.iastate.metnet.graphmodel

RemoveSelectedNodes(Object[]) - Constructor for class edu.iastate.metnet.graphmodel.RemoveSelectedNodes

removeTreeModelListener(TreeModelListener) - Method in class edu.iastate.metnet.model.TreeModelSupport

removeUnmarked() - Method in class edu.iastate.jtm.assistant.CitationPool

removeValueChangeListener(PropertyChangeListener) - Method in class com.jgoodies.binding.extras.ListModelHolder

Removes the given PropertyChangeListener.

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

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

rename the category

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

rename the category

renameColumnHeader(int, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

renameGeneList(String, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmProject

Renames a gene list.

renderer - Static variable in class edu.iastate.metnet.graphmodel.MultiVertexView

special renderer override normal gradient painter

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

This method ensures that the window is updated after a change.

replaceQuery(String) - Method in class edu.iastate.jtm.assistant.QueryPanel

replayChildren(GoNode, boolean) - Method in class edu.iastate.metnet.birdseyeview.goview.GoView

This method displays the child nodes for the given node.

report(String, float) - Method in class edu.iastate.jtm.util.ProcessWrapper

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

repository - Variable in class edu.iastate.metnet.ui.HistoryReportForm

store the query from the database, used to filter the pathway list

repository - Variable in class edu.iastate.metnet.ui.PathwaySelector2

store the query from the database, used to filter the pathway list

RequestGene - Class in edu.iastate.metnet.hivemindService

Class used to request gene data.

RequestGeneData - Class in edu.iastate.metnet.hivemindService

HiveMind service searches for gene information given the gene ID.

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

res - Static variable in class edu.iastate.metnet.ui.PropertiesMetalTheme

reselect() - Method in class edu.iastate.metnet.metaomgraph.chart.PointInfoPanel

reset() - Method in class com.jgoodies.binding.extras.ChangeTracker

Resets this tracker's changed state to false.

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

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

reset() - Method in class edu.iastate.jtm.util.CharType

reset() - Method in class edu.iastate.jtm.util.NameCharType

reset(CharSequence) - Method in class edu.iastate.jtm.util.ParenFinder

reset() - Method in class edu.iastate.jtm.util.ParenFinder

Reset arrays.

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

reset the UI and internal model

reset() - Method in class edu.iastate.reload.ui.NetworkEditForm

reset the status of the UI and internal model

RESET_ACTION_COMMAND - Static variable in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog

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

ResetButton - Class in edu.iastate.metnet.mapbuilder

Implementation of a button which, when pressed, de-selects all the checkboxes in a given array.

ResetButton(JCheckBox[]) - Constructor for class edu.iastate.metnet.mapbuilder.ResetButton

Creates the ResetButton

resetDesc() - Method in class edu.iastate.metnet.dataManager.DataManager

resetInstance() - Static method in class edu.iastate.metnet.birdseyeview.BPathwaySelectionFrame

resetInstance() - Static method in class edu.iastate.metnet.dataManager.PathwaySelectionFrame

resetInstance() - Static method in class edu.iastate.metnet.metaomgraph.PathwaySelectionFrame

resetLocalDictionary() - Method in class edu.iastate.jtm.assistant.Highlighter

resetPanelLocations() - Method in class edu.iastate.metnet.birdseyeview.cellview.PanelLocationsFactory

This method resets all the points for all the cellular locations.

resetPoints() - Method in class edu.iastate.metnet.birdseyeview.cellview.CellularLocation

This method resets the vacant points list to make all the points vacant.

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

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

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

resetWindow(CharSequence, CharBuffer) - Method in class edu.iastate.jtm.util.SlidingWindow

reSize(Rectangle2D) - Method in class edu.iastate.reload.ui.MyMarqueeHandler

By default we don't resize the cell but this may be be overriden in order to implement an automatic resizing...

resort() - Method in class edu.iastate.metnet.metaomgraph.ListTree

resortThisNode(DefaultMutableTreeNode, boolean) - Method in class edu.iastate.metnet.metaomgraph.ListTree

resource - Static variable in class edu.iastate.metnet.ui.MainWindow2

external user prefenrece, will be overriden by preference xml file

responseBuffer - Variable in class edu.iastate.jtm.jmed.UmlsSocketClient

restoreDefaults() - Static method in class edu.iastate.metnet.MetNetOceanTheme

restoreDefaults() - Static method in class edu.iastate.reload.skin.MetNetOceanTheme

resultReady - Variable in class edu.iastate.jtm.jmed.EUtility

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

resultset from database

resultSet - Variable in class edu.iastate.metnet.ui.AddPathwayForm

result set

ResultSetAdapter - Class in edu.iastate.metnet.db

the class is called once in the lifetime

ResultSetAdapter(Statement, String) - Constructor for class edu.iastate.metnet.db.ResultSetAdapter

ResultSetAdapter(String) - Constructor for class edu.iastate.metnet.db.ResultSetAdapter

retractInterestFor(Object, String) - Method in class com.jgoodies.binding.extras.ChangeTracker

Retracts interest for the specified readable bound bean property in the given bean.

retractInterestFor(ValueModel) - Method in class com.jgoodies.binding.extras.ChangeTracker

Retracts interest for value changes in the given ValueModel.

retrieveAll(String[]) - Method in class edu.iastate.jtm.jmed.ESearch

Retrieve all PMIDs to an array.

retrieveAll() - Method in class edu.iastate.jtm.jmed.ESearch

retrieveAll(List) - Method in class edu.iastate.jtm.jmed.ESearch

retrieveAll(File) - Method in class edu.iastate.jtm.jmed.ESearch

Retrieve all PMIDs to a single file.

retrieveAll(String, int) - Method in class edu.iastate.jtm.jmed.ESearch

Retrieve all PMIDs to multiple files.

retrieveAll(String[]) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

Retrieve all PMIDs to an array.

retrieveAll(List) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

retrieveAll(File) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

Retrieve all PMIDs to a single file.

retrieveAll(String, int) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

Retrieve all PMIDs to multiple files.

retrieveBatch() - Method in class edu.iastate.jtm.jmed.ESearch

Retrieve a batch of PMIDs, and store them in a new array.

retrieveBatch(String[], int) - Method in class edu.iastate.jtm.jmed.ESearch

Retrieve a batch of PMIDs into an array starting at offset.

retrieveBatch(List) - Method in class edu.iastate.jtm.jmed.ESearch

retrieveBatch() - Method in class edu.iastate.jtm.jmed.PubMedQuerier

Retrieve a batch of PMIDs, and store them in a new array.

retrieveBatch(String[], int) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

Retrieve a batch of PMIDs into an array starting at offset.

retrieveBatch(List) - Method in class edu.iastate.jtm.jmed.PubMedQuerier

ReturnCode - Class in edu.iastate.metnet.db

store the result of database operation

ReturnCode(int, Object) - Constructor for class edu.iastate.metnet.db.ReturnCode

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

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

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

reversible - Variable in class edu.iastate.metnet.dao.InteractionObject

if reversible interaction

rewriteGraph(Map, DirectedGraph, MultiKeyMap, DirectedGraph, String, String, String) - Method in class edu.iastate.biocyc.io.BiocycImporter

the most important function in this conversion.

rewritePathway(DirectedGraph, Map, DirectedGraph, Map, String, String, String) - Method in class edu.iastate.biocyc.io.BiocycImporter

construct pathway blockunit

RGBtoHSV(int, int, int) - Static method in class edu.iastate.metnet.birdseyeview.GeneColor

This method determines the HSV values of the given color in RGB values.

RiceReaderTest - Class in edu.iastate.biocyc.test

this is only used for ricecyc data

RiceReaderTest(String) - Constructor for class edu.iastate.biocyc.test.RiceReaderTest

RIGHT - Static variable in class edu.iastate.jtm.util.NameCharType

RIGHT - Static variable in class edu.iastate.jtm.util.ParenFinder

RIGHT - Static variable in class edu.iastate.jtm.util.ParenParser

right(Element) - Method in class edu.iastate.jtm.util.ParenParser

RIGHT - Static variable in class edu.iastate.jtm.util.SlidingWindow

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

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

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

rightEbidEidMap - Variable in class edu.iastate.metnet.dao.InteractionStructure

blockid of products

rightGraph - Variable in class edu.iastate.metnet.dao.PathwayAlignmentImpl

the other pathway graph

rightId() - Method in class fcmodeler.pathbinder.FilterEntry

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

to part of the interaction

rightNode - Variable in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

define the right element node

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

REACTION (unique-id of another interaction)

rightPart - Variable in class edu.iastate.metnet.dao.MetnetInteraction

right part's blockid as Integer

rightUnit - Variable in class edu.iastate.metnet.model.AbstractMultiBlockunitDecorator

right entitywithlocation

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

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

RootID - Static variable in class edu.iastate.metnet.birdseyeview.goview.GoFunctionView

rootNode - Variable in class edu.iastate.metnet.birdseyeview.goview.GoView

rootPane - Variable in class edu.iastate.metnet.MetNetTitlePane

RootPanel - Class in edu.iastate.metnet.birdseyeview

The RootPanel Class contains the functionality for positioning and creating the Bird's Eye View GUI.

RootPanel(BirdsEyeView, Dimension, ViewInfo, ArrayList, String) - Constructor for class edu.iastate.metnet.birdseyeview.RootPanel

Constructor.

route(EdgeView) - Method in class edu.iastate.reload.ui.JGraphParallelEdgeRouter

row - Variable in class edu.iastate.metnet.metaomgraph.test.AffyChipAnimationPanel

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

RowEditorModel - Class in edu.iastate.metnet.model

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

rowEditorModel - Variable in class edu.iastate.metnet.ui.MyJTableEx

RowHeaderRenderer - Class in edu.iastate.jtm.gui

RowHeaderRenderer() - Constructor for class edu.iastate.jtm.gui.RowHeaderRenderer

RowHeaderTable - Class in edu.iastate.jtm.gui

RowHeaderTable(TableModel) - Constructor for class edu.iastate.jtm.gui.RowHeaderTable

Create a new instance of RowHeaderTable.

RowHeaderTable.TableRowHeaderRenderer - Class in edu.iastate.jtm.gui

RowHeaderTable.TableRowHeaderRenderer() - Constructor for class edu.iastate.jtm.gui.RowHeaderTable.TableRowHeaderRenderer

rowName - Variable in class edu.iastate.metnet.analysis.AbstractExcelSheet

rowName - Variable in class edu.iastate.metnet.model.AbstractPlotData

rows - Variable in class edu.iastate.metnet.model.JDBCComboModel

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

rulevec - Variable in class edu.iastate.metnet.model.AbbreviationRulesModel

run(String) - Method in class edu.iastate.jtm.util.ProcessWrapper

run() - Method in class edu.iastate.metnet.aracyc.ChangeName

run(String[]) - Method in class edu.iastate.metnet.aracyc.ConsoleApplication

require the subclass implement the run() function

run(String[]) - Method in class edu.iastate.metnet.aracyc.GraphStatistics

run() - Method in class edu.iastate.metnet.birdseyeview.BirdsEyeView.LoadAnnotation

run(ArrayList<String>, boolean) - Method in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame

run(String, int) - Static method in class edu.iastate.metnet.birdseyeview.Loader

This method reads the given file and returns a list of the fields with the given index.

run(PathwayGraph, PathwayGraph) - Method in interface edu.iastate.metnet.dao.AlignmentAlgorithm

align two pathway graph, and get the alignment result? How do we represent the alignment results

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphMetaphor

make the graph black and white

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphProcessor

process normal pathway graph model

run(MultiPathwayModel) - Method in class edu.iastate.metnet.graphmodel.AbstractGraphProcessor

process multi-pathway graph model

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.AdjacencyGraphWalker

walk through the pathway model

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.AlignmentMetaphor

apply metaphor for the graph.

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.CategoryLayoutAlgorithm

layout without any static cells

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.CategoryLayoutAlgorithm

run layout based on the underlying model type

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.CategoryMetaphor

apply the category metaphor

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.ComparativeMetaphor

apply metaphor for the graph

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.CompositionRelationMetaphor

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.EditingLayoutAlgorithm

layout without any static cells

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.EditingLayoutAlgorithm

run layout based on the underlying model type

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.EditingMetaphor

color the graph according to FCModeler

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.FCMetaphor

color the graph according to FCModeler

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.GlobalGraphWalker

walk through the graph model

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.GraphWalker

walk through pathway model

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.HierachyLayoutAlgorithm

layout without any static cells

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.HierachyLayoutAlgorithm

run layout based on the underlying model type

run(JGraph, Object[]) - Method in interface edu.iastate.metnet.graphmodel.IGraphMetaphor

run the metaphor on the selected cells.

run(PathwayModel) - Method in interface edu.iastate.metnet.graphmodel.IGraphProcessor

although it is a part of interface, we do not mandatory require the class implements them, so use abstract class hide these requirements.

run(MultiPathwayModel) - Method in interface edu.iastate.metnet.graphmodel.IGraphProcessor

although it is a part of interface, we do not mandatory require the class implements them, so use abstract class hide these requirements.

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.InputLayoutAlgorithm

layout without any static cells

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.InputLayoutAlgorithm

run layout based on the underlying model type

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.IsomorphismMetaphor

highlight the alignment

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

main entry point of the layout algorithm

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.PathwayElementMetaphor

color the graph according to FCModeler

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.RandomLayoutAlgorithm

layout without any static cells

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.RandomLayoutAlgorithm

layout with all dynamic cells

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.RemoveBridgeNodes

remove single bridge node (interaction with only one substrate and one product) from the pathway

run(MultiPathwayModel) - Method in class edu.iastate.metnet.graphmodel.RemoveBridgeNodes

we have to use two version of run() for two types of graph model.

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.RemoveCompositionNodes

remove the selected nodes, and connect the upstream nodes to all downstream nodes.

run(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.RemoveSelectedNodes

remove the selected nodes, and connect the upstream nodes to all downstream nodes.

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.SearchInteractionTypeMetaphor

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.SearchNameMetaphor

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.ValidityMetaphor

color the graph according to graph validity

run(JGraph, Object[], Object[]) - Method in class edu.iastate.metnet.graphmodel.VersionyLayoutAlgorithm

layout without any static cells

run(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.VersionyLayoutAlgorithm

run layout based on the underlying model type

run(ArrayList<String>) - Method in class edu.iastate.metnet.metaomgraph.ExploRaseFrame

run() - Method in class edu.iastate.metnet.threads.AnnotationThread

run() - Method in class edu.iastate.metnet.threads.DataThread

run() - Method in class edu.iastate.metnet.threads.ExploRaseThread

run() - Method in class edu.iastate.metnet.threads.PathwayGeneThread

run() - Method in class edu.iastate.metnet.ui.SBMLExporter

run() - Method in class edu.iastate.metnet.utils.SwingWorker2

Calls the construct method to compute the result, and then invokes the finished method on the event dispatch thread.

RunCytoscape - Class in edu.iastate.metnet.launch

This is the main startup class for Cytoscape.

RunCytoscape() - Constructor for class edu.iastate.metnet.launch.RunCytoscape

runGlobalMetaphor(JGraph, Object[]) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

label all valid interaction as red

runIntegration(String) - Static method in class edu.iastate.metnet.birdseyeview.Loader

This method reads the integrated file and outputs the experiments and probes list

runIntegVar(String, int) - Static method in class edu.iastate.metnet.birdseyeview.Loader

This method reads the integrated file and outputs the variances list

runIoC() - Method in class edu.iastate.metnet.aracyc.ScriptSink

confirm the idea of inversion of control, let user input the script component in the command line and the framework execute the script according to the predefined facility

runJDBC() - Method in class edu.iastate.metnet.aracyc.ScriptSink

some zxJDBC code

runJyhton() - Method in class edu.iastate.metnet.aracyc.ScriptSink

some useful code

RunningBuffer - Class in edu.iastate.jtm.util

Accept contents multiple times, retrieve once.

RunningBuffer(int) - Constructor for class edu.iastate.jtm.util.RunningBuffer

RunningBuffer(CharBuffer) - Constructor for class edu.iastate.jtm.util.RunningBuffer

runPartialMetaphor(JGraph, Object[], int) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

visualize the selected sub-system, for simplicity, we only change the color of the node, and ignore all edges.

runSpecialMetaphor(JGraph, Object[], Integer) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

metaphor the selection as blue

runSpecialMetaphor(JGraph, Object[], Map) - Method in class edu.iastate.metnet.graphmodel.ChemicalReactionMetaphor

change the width of the reaction based on the rate