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

F

facade - Variable in class edu.iastate.metnet.test.MyFacadeTest.FacadeWorker

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

FCMetaphor - Class in edu.iastate.metnet.graphmodel

default metaphor (nodeType = RNA) maps to (shape = rectangular) (nodeType = Protein) maps to (shape = diamond) (nodeType = Compound) maps to (shape = ecclipse) (location = cytosol) maps to (node fill color = 0xFFFFCC) (location = mitochondria*) maps to (node fill color = pink) (location = microbody) maps to (node fill color = grey) (location = plastid*) maps to (node fill color = green) (location = apoplast) maps to (node fill color = 0x6699FF) (location = nucleus) maps to (node outline color = yellow) (location = thylakoids*) maps to (node outline color = green) (edgeType = Catalysis) maps to (line thickness = medium) (edgeType = Catalysis) maps to (line color = blue) (edgeType = Enzymatic) maps to (line thickness = medium) (edgeType = OR) maps to (line thickness = medium-narrow) (edgeType = OR) maps to (line color = yellow) (edgeType = Regulation/Positive regulation) maps to (line color = green) (edgeType = Regulation/Positive regulation) maps to (line thickness = medium-narrow) (edgeType = Regulation/Negative regulation) maps to (line color = red) (edgeType = Regulation/Negative regulation) maps to (line thickness = medium-narrow) (certainty = indirect evidence) maps to (line type = dash-dot) (certainty = several line*) maps to (line type = dotted) (certainty = wild hypo*) maps to (line type = dotted)

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

default constructor

FCMetaphor(Collection) - Constructor for class edu.iastate.metnet.graphmodel.FCMetaphor

default constructor

FCMetaphor(Collection, Collection) - Constructor for class edu.iastate.metnet.graphmodel.FCMetaphor

default constructor

fcmodeler - package fcmodeler

fcmodeler.pathbinder - package fcmodeler.pathbinder

fcmodeler.pathbinder.gui - package fcmodeler.pathbinder.gui

fcmodeler.pathbinder.updater - package fcmodeler.pathbinder.updater

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

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

fetchFasta(File, File) - Method in class edu.iastate.jtm.jmed.EFetch

fetchFasta(File, File) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

fetchPlain(File, File) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given PMIDs in a file.

fetchPlain(File, String, int) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a PMID file.

fetchPlain(String[], int, File) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a list of PMIDs.

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

Fetch abstracts given a list of PMIDs.

fetchPlain(Limits, File) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a query history.

fetchPlain(Limits, String, int) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a query history.

fetchPlain(File, File) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given PMIDs in a file.

fetchPlain(File, String, int) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a PMID file.

fetchPlain(String[], int, File) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a list of PMIDs.

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

Fetch abstracts given a list of PMIDs.

fetchPlain(Limits, File) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a query history.

fetchPlain(Limits, String, int) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a query history.

fetchStream(String[], Limits) - Method in class edu.iastate.jtm.jmed.EFetch

fetchStream(String[]) - Method in class edu.iastate.jtm.jmed.EFetch

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

fetchStream(String[], int, int, Limits) - Method in class edu.iastate.jtm.jmed.EFetch

fetchStream(Limits) - Method in class edu.iastate.jtm.jmed.EFetch

Retrieve abstracts from query history.

fetchStream(String[], Limits) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

fetchStream(String[]) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

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

fetchStream(String[], int, int, Limits) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

fetchStream(Limits) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Retrieve abstracts from query history.

fetchXml(File, File, boolean) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given PMIDs in a file.

fetchXml(File, String, int, boolean) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a PMID file.

fetchXml(String[], int, File, boolean) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a list of PMIDs.

fetchXml(String[], int, String, int, boolean) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a list of PMIDs.

fetchXml(Limits, File, boolean) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a query history.

fetchXml(Limits, String, int, boolean) - Method in class edu.iastate.jtm.jmed.EFetch

Fetch abstracts given a query history.

fetchXml(File, File, boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given PMIDs in a file.

fetchXml(File, String, int, boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a PMID file.

fetchXml(String[], int, File, boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a list of PMIDs.

fetchXml(String[], int, String, int, boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a list of PMIDs.

fetchXml(Limits, File, boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a query history.

fetchXml(Limits, String, int, boolean) - Method in class edu.iastate.jtm.jmed.PubMedFetcher

Fetch abstracts given a query history.

field() - Method in class edu.iastate.jtm.jmed.Query.SimpleTerm

field - Variable in class edu.iastate.metnet.metaomgraph.TreeSearcher.Query

The field to search for.

FieldNotFoundException - Exception in edu.iastate.metnet.birdseyeview

The FieldNotFoundException Class handles exceptions in which a desired field was not found in Birds Eye View data.

FieldNotFoundException(String) - Constructor for exception edu.iastate.metnet.birdseyeview.FieldNotFoundException

Constructor.

file - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

The underlying java.io.RandomAccessFile.

file - Variable in class edu.iastate.metnet.soft.RandomAccessFile

The underlying java.io.RandomAccessFile.

FileBar - Class in edu.iastate.jtm.gui

FileBar(int, String, JFileChooser, boolean) - Constructor for class edu.iastate.jtm.gui.FileBar

FileBar(JFileChooser, boolean) - Constructor for class edu.iastate.jtm.gui.FileBar

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

fileData - Variable in class edu.iastate.metnet.dataManager.DataManager

FileData - Class in edu.iastate.metnet.dataManager

Chosen File data is loaded into this class

FileData(String[][], String[]) - Constructor for class edu.iastate.metnet.dataManager.FileData

FileFilterImpl - Class in edu.iastate.metnet.dataManager

File filter class, to ensure that only csv files are visible

FileFilterImpl() - Constructor for class edu.iastate.metnet.dataManager.FileFilterImpl

fileFormat - Variable in class edu.iastate.metnet.birdseyeview.BirdsEyeView

filename - Variable in class edu.iastate.metnet.analysis.DefaultJExcelClient

filePanel - Variable in class edu.iastate.metnet.dataManager.DataManager

filePosition - Variable in class edu.iastate.metnet.metaomgraph.RandomAccessFile

The offset in bytes from the file start, of the next read or write operation.

filePosition - Variable in class edu.iastate.metnet.soft.RandomAccessFile

The offset in bytes from the file start, of the next read or write operation.

FileSplitter - Class in edu.iastate.jtm.util

Split a big file into small ones.

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

filesTable - Variable in class edu.iastate.metnet.dataManager.DataManager

FilesTableMouseListener - Class in edu.iastate.metnet.dataManager

Listener for file table.

FilesTableMouseListener(DataManager) - Constructor for class edu.iastate.metnet.dataManager.FilesTableMouseListener

fillMetalPattern(Component, Graphics, int, int, int, int, Color, Color) - Static method in class edu.iastate.reload.skin.MetalUtilsX

Fills a rectangle with the typical Metal pattern.

fillMetalPattern(Component, Graphics, int, int, int, int, Color, Color) - Static method in class javax.swing.plaf.metal.MetalUtils

Fills a rectangle with the typical Metal pattern.

fillMetalPattern2D(Graphics2D, int, int, int, int, Color, Color) - Static method in class edu.iastate.reload.skin.MetalUtilsX

Fills a rectangle with the typical Metal pattern using Java2D.

fillMetalPattern2D(Graphics2D, int, int, int, int, Color, Color) - Static method in class javax.swing.plaf.metal.MetalUtils

Fills a rectangle with the typical Metal pattern using Java2D.

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

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

FilterableTableModel - Class in edu.iastate.metnet.metaomgraph

FilterableTableModel(TableModel) - Constructor for class edu.iastate.metnet.metaomgraph.FilterableTableModel

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

given a set of interaction and remove all catalysis type interaction

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

given a set of interaction and remove all catalysis type interaction

filterDefined() - Method in class fcmodeler.pathbinder.gui.TaxonomyPanel

FilterEntry - Class in fcmodeler.pathbinder

FilterEntry(String, String, String, int, int) - Constructor for class fcmodeler.pathbinder.FilterEntry

FilterPanel - Class in fcmodeler.pathbinder.updater

FilterPanel(StatusBar, JFileChooser) - Constructor for class fcmodeler.pathbinder.updater.FilterPanel

filterToRows(int[]) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

filterToRows(Collection<Integer>) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

FilterUpdater - Class in fcmodeler.pathbinder

FilterUpdater(MySqlConnector) - Constructor for class fcmodeler.pathbinder.FilterUpdater

Creates a new instance of Tax2Pmid

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

This method finalizes the gene list by creating the gene container panel based on the list.

finalTableName() - Method in class fcmodeler.pathbinder.PmidFilter

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

find the blockunit containing the name, the name may contain double comma or tab delimer

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

find the blockunit containing the name, the name may contain double comma or tab delimer

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

find the blockunit containing the name, the name may contain double comma or tab delimer

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

find the blockunit containing the name, the name may contain double comma or tab delimer

findAscentdant(Object) - Method in class edu.iastate.metnet.dao.RelationMap

find the root of the ascendant

findAssociatedInteraction(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

find the associated interaction based on two nodes (do not consider catalysis and regulation

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

find the associated interaction based on two nodes (do not consider catalysis and regulation

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

extract locus only information

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

extract locus only information

findAtGeneLocusObject(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

test the prepared statement to handle the escape sequence in SQL language and enhance the query performance if it is used more than 60-200 times.

findAtGeneLocusObject(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

test the prepared statement to handle the escape sequence in SQL language and enhance the query performance if it is used more than 60-200 times.

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

extract the list of locus object

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

extract the list of locus object

findAtGeneLocusObjectList(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

extract the list of locus object, test PHYA-3'

findAtGeneLocusObjectList(String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

extract the list of locus object, test PHYA-3'

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

extract the list of locus object by fulltext search

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

extract the list of locus object by fulltext search

findBlockunitInstance(Collection) - Method in class edu.iastate.metnet.export.GraphExporterImpl

findBlockunitInstance(Collection) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

get the blockunit map

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

get the map id->blockunit

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

get the instance and join if necessary

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

get the map id->blockunit

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

get the instance and join if necessary

findBlockunitInstance(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

get the instance and join if necessary

findBlockunitInstance(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

get the instance and join if necessary

findBlockunitInstance(Collection) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

get the instance and join if necessary

findBlockunitInstance(Integer) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

get the instance and join if necessary

findBlockunitInstance(Integer) - Method in class edu.iastate.metnet.ui.BlockunitFinder

delegate the finding blockunit

findBlockunitInstance(Collection) - Method in class edu.iastate.metnet.ui.BlockunitFinder

find the blockunit instance

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

get the recommend name and synonym based on the ec number

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

get the recommend name and synonym based on the ec number

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

get the product based on the ec number

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

get the product based on the ec number

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

get the substrate based on the ec number

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

get the substrate based on the ec number

findByGeneId(String, String) - Method in class edu.iastate.metnet.hivemindService.CompareInPathBinder

findByGeneNames(String, String) - Method in class edu.iastate.metnet.hivemindService.CompareInPathBinder

Search for common sentences using gene names

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

get the chebi compounds list

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

get the chebi compounds list

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

get the chebi names list

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

get the chebi names list

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

find the chebi id of the specified name from the chebi ontology

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

find the chebi id of the specified name from the chebi ontology

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

find the chebi id of the specified name from the chebi ontology

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

find the chebi id of the specified name from the chebi ontology

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

get the codelocation object list

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

get the codelocation object list

findCodelocationList() - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

get the codelocation object list

findCodelocationList() - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

get the codelocation object list

findCommunityInteractionList(Collection, int) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

get the community interaction in p-step

findCommunityInteractionList(Collection, int) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

get the community interaction in p-step

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

get the confidence object list

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

get the confidence object list

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

Locates the given data column header.

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

get the data source object list

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

get the data source object list

findDescendant(Object) - Method in class edu.iastate.metnet.dao.RelationMap

find the descendant of the node not limit to the leaves

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

find the substrates of the interaction

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

find the substrates of the interaction

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

special finder for enzymatic reaction and similar ones

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

special finder for enzymatic reaction and similar ones

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

find the live entity based on the name

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

find the live entity based on the name

findEntity(CharSequence) - Method in class edu.iastate.jtm.EntityFinder

Find entities in a string.

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

get all entity which contain "similar" name

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

get all entity which contain "similar" name in the prodvided list

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

get all entity which contain "similar" name

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

get all entity which contain "similar" name in the prodvided list

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

get the map id->entity

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

get the instance and join if necessary

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

get the map id->entity

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

get the instance and join if necessary

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

get the entity type object list

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

get the entity type object list

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

get the entity with location contains the similar name

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

find the entitywithlocation according to the 4 criteria

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

get the entity with location contains the similar name

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

find the entitywithlocation according to the 4 criteria

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

find enzyme of the enzymatic interaction

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

find enzyme of the enzymatic interaction

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

find the blockunit match the name exactly

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

find the blockunit match the name exactly

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

find the entityt match the name exactly

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

find the entity based on the name and type

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

find the entityt match the name exactly

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

find the entity based on the name and type

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

find the blockunit containing the name, the name may contain double comma or tab delimer

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

get the blockunit which contain the similar name and same entitytype and location

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

find the blockunit containing the name, the name may contain double comma or tab delimer

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

get the blockunit which contain the similar name and same entitytype and location

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

search the interaction according to the entitywithlocation name

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

search the interaction according to the entitywithlocation name

findGenes() - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph

find the gene object in the graph model

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

find the group of the owner

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

find the group of the owner

findHiddenLink(Entity[], Entity[]) - Method in class fcmodeler.pathbinder.HiddenLink

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

find all blockunit as a version graph

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

find all blockunit as a version graph

findHistoryFlatInteraction(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

get the instance of the history flat interaction

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

get the instance of the history flat interaction

findHistoryFlatLiveEntity(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

get the instance of the history flat live entity

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

get the instance of the history flat live entity

findHistoryFlatPathway(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

get the instance of the history flat pathway

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

get the instance of the history flat pathway

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

find the interaction list based on the substrate and product name

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

find the interaction list based on the substrate and product name

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

find all associated interaction for the blockunit

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

find all associated interaction for the blockunit

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

find all associated interaction for the name

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

find all associated interaction for the name

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

find basic interaction informations

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

search the interaction according to the entitywithlocation name

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

find basic interaction informations

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

search the interaction according to the entitywithlocation name

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

find all involved interaction except catalysis type

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

find all involved interaction except catalysis type

findInteractionList(Collection) - Method in class edu.iastate.metnet.ui.BlockunitFinder

find the interaction information object

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

get the interaction type object list

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

get the interaction type object list

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

find the involved pathway from the blockunit

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

find the involved pathway from the blockunit

findInvolvedPathways(Collection, Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade

collect all pathway objects related to the selected entitywithlocation

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

collect all pathway objects related to the selected entitywithlocation

findLatestControlLiveEntity(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

find the latest control interaction

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

find the latest control interaction

findLatestInteractionPart(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

find the latest record id list of the interaction part.

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

find the latest record id list of the interaction part.

findLatestPathwayPart(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

find the latest record id list of the pathway part.

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

find the latest record id list of the pathway part.

findLiveEntityList(boolean, String, String, String) - Method in class edu.iastate.metnet.export.GraphExporterImpl

findLiveEntityList(boolean, String, String, String) - Method in interface edu.iastate.metnet.hiveface.GraphExporter

find the live entities according to the specified query condition

findLiveEntityList(boolean, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetService

find the live entities according to the specified query condition

findLiveEntityList(boolean, String, String, String) - Method in interface edu.iastate.metnet.interfaces.MyMetnetServiceLocal

find the live entities according to the specified query condition

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

get the location object list

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

get the location object list

findLongForm(CharSequence, CharSequence, boolean) - Method in class edu.iastate.jtm.AbbreviationChecker

findLongForm(CharSequence, CharSequence) - Method in class edu.iastate.jtm.AbbreviationChecker

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

findNormalInteractionStructure(Collection, Collection) - Method in interface edu.iastate.metnet.interfaces.MyFacade

an optimized version of checkInteraction, should not containing interaction in the parameters.

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

an optimized version of checkInteraction, should not containing interaction in the parameters.

findNormalInteractionStructureX(Map, Map) - Method in interface edu.iastate.metnet.interfaces.MyFacade

an extension version of finding interaction structure.

findNormalInteractionStructureX(Map, Map) - Method in interface edu.iastate.metnet.interfaces.MyFacadeLocal

an extension version of finding interaction structure.

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

get the organism object list

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

get the organism object list

findOrInsert(String, String) - Static method in class edu.iastate.metnet.db.TableAbbreviationRules

if exists, return the ruleID, if not, create a new one, and return the the ruleID

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

find or insert the abbreviation rule

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

find or insert the abbreviation rule

findOrphans(PathwayModel) - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph

findPath(String) - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree

Finds the first node in this tree whose name starts with the given String.

findPath(TreeNode, String) - Method in class edu.iastate.metnet.metaomgraph.MetaOmHelpListener

findPathwayObjectList(Collection, boolean) - Method in class edu.iastate.metnet.ui.BlockunitFinder

find the pathway object list

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

get all pathway blockid in the database for displaying in pathway selector

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

get all pathway blockid in the database for displaying in pathway selector

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

find the pathway blockid based on the name, this can be pathway name or entity name

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

find the pathway blockid based on the name, this can be pathway name or entity name

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

find the entity id list for the name

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

find the entity id list for the name

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

find the sid list according to the search name

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

find the sid list according to the search name

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

find the synonym for the given search name list

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

find the synonym for the given search name list

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

get the reference type object list

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

get the reference type object list

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

findRNAs() - Method in class edu.iastate.metnet.graphmodel.JMetaphorGraph

get RNA object in graph model

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

get the rule object list

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

get the rule object list

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

find the name which appear in name/synonym/abbreviation EXACTLY.

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

find the name which appear in name/synonym/abbreviation EXACTLY.

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

find the entity id list for the name

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

find the entity id list for the name

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

find the sid list according to the search name

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

find the sid list according to the search name

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

find the synonym for the given search name list.

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

find the synonym for the given search name list.

findTrivialMetabolite(Integer, Integer) - Method in interface edu.iastate.metnet.interfaces.MyFacade

find the trivial metabolite that take part in one or more pathways

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

find the trivial metabolite that take part in one or more pathways

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

find the product of the interaction

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

find the product of the interaction

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

special finder for enzymatic reaction and similar ones

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

special finder for enzymatic reaction and similar ones

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

search by example

findUser(User) - Method in interface edu.iastate.metnet.interfaces.MyPaper

search by example

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

find the User instance based on the username

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

find the User instance based on the username

finished() - Method in class edu.iastate.jtm.gui.SwingWorker

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

finished() - Method in class edu.iastate.metnet.metaomgraph.AnimatedSwingWorker

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

finished() - Method in class edu.iastate.metnet.metaomgraph.MetaOmGraph.NewProjectWorker

If the project was created successfully, this sets up the extra information (row names, column names, extended info) and displays the project table.

finished() - Method in class edu.iastate.metnet.metaomgraph.SwingWorker

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

finished() - Method in class edu.iastate.metnet.test.MyFacadeTest.FacadeWorker

finished() - Method in class edu.iastate.metnet.test.MyPaperTest.PaperWorker

finished() - Method in class edu.iastate.metnet.ui.BlockunitWorker

save the result to main sink

finished() - Method in class edu.iastate.metnet.ui.CompileWorker

save the result to main sink

finished() - Method in class edu.iastate.metnet.ui.InteractionWorker

save the result to main sink

finished() - Method in class edu.iastate.metnet.ui.PathwayObjectWorker

save the result to main sink

finished() - Method in class edu.iastate.metnet.utils.SwingWorker

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

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

Called on the event dispatching thread (not on the worker thread) after the construct method has returned.

finishTime - Variable in class edu.iastate.metnet.hibernate.BackgroundTask

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

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

update the graph visualization if there are some changes in the graph model

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

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

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

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

Calls the stateChanged() method of all registered ChangeListeners.

fireTableChanged(TableModelEvent) - Method in class edu.iastate.metnet.metaomgraph.FilterableTableModel

fireTreeNodesChanged(TreeModelEvent) - Method in class edu.iastate.metnet.model.TreeModelSupport

fireTreeNodesInserted(TreeModelEvent) - Method in class edu.iastate.metnet.model.TreeModelSupport

fireTreeNodesRemoved(TreeModelEvent) - Method in class edu.iastate.metnet.model.TreeModelSupport

fireTreeStructureChanged(TreeModelEvent) - Method in class edu.iastate.metnet.model.TreeModelSupport

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

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

firstAuthor(String) - Method in class edu.iastate.jtm.jmed.MedCitation

firstAuthor() - Method in class edu.iastate.jtm.jmed.MedCitation

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

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

FirstForm - Class in edu.iastate.reload.ui

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

Creates new form FirstForm

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

first position of the edge

flag - Static variable in class edu.iastate.metnet.birdseyeview.ExploRaseExpFrame

FlatFileConverter - Class in edu.iastate.metnet.metaomgraph.utils

Class for converting String values based on data in a flat file.

FlatFileConverter(InputStream) - Constructor for class edu.iastate.metnet.metaomgraph.utils.FlatFileConverter

Constructs the hashtable by reading values from the text file locusconvert.txt.

FlippingSquaresThrobber - Class in edu.iastate.metnet.metaomgraph.throbber

FlippingSquaresThrobber() - Constructor for class edu.iastate.metnet.metaomgraph.throbber.FlippingSquaresThrobber

floatValue() - Method in class edu.iastate.metnet.metaomgraph.CorrelationValue

floatValue() - Method in class edu.iastate.metnet.metaomgraph.SortableData

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

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

Copy the contents of the buffer to the disk.

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

Copy the contents of the buffer to the disk.

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

FolderChange - Class in edu.iastate.metnet.model

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

FolderChange(DefaultExcelSheet, double) - Constructor for class edu.iastate.metnet.model.FolderChange

forceInsert() - Method in class edu.iastate.metnet.aracyc.AracycCompound

forceInsert() - Method in class edu.iastate.metnet.aracyc.ClassTree

forceRNode() - Method in class edu.iastate.metnet.mapbuilder.InteractionInfo

Forces this interaction to use a reaction node.

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

formalize the composition for those multi-enzyme reactions

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

formalize the composition for those multi-enzyme reactions

format(double, StringBuffer, FieldPosition) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel.ExperimentFormat

This version of format will return either the full column name, or a shortened column name, based on the state of shortenItem

format(long, StringBuffer, FieldPosition) - Method in class edu.iastate.metnet.metaomgraph.chart.MetaOmChartPanel.ExperimentFormat

This version of format will always return the full column name, regardless of the state of shortenItem.

formatSentences(boolean, boolean) - Method in class fcmodeler.pathbinder.gui.SentencePane

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

external database link editor window instance

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

abbreivation rule editor window instance

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

pathway basic property editor window instance

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

synonym candidate approval editor window instance

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

reference and comment editor window instance

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

synonym and abbreviation editor window instance

FromMetaOmGraph(MetaOmProject) - Method in class edu.iastate.metnet.hivemindService.ExportToBirdsEyeView

sends all data from MetaOmGraph to BirdseyeView

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

fromXML(Element) - Method in class edu.iastate.metnet.metaomgraph.chart.CustomSortDialog.CustomSortObject

fromXML(Element) - Method in class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel.QuerySet

fromXML(Element) - Method in class edu.iastate.metnet.metaomgraph.TreeSearcher.Query

fromXML(Element) - Method in interface edu.iastate.metnet.metaomgraph.XMLizable

Initializes this object from an XML Element.

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

FULL - Static variable in interface edu.iastate.jtm.util.Queue

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

full insert blockunit and entity and entitywithcontext, since the data can be from expert data or aracyc, so source and username are parameters also

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

full insert blockunit and entity and entitywithcontext, since the data can be from expert data or aracyc, so source and username are parameters also

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

function category

functionConfidence - Variable in class edu.iastate.metnet.model.EntityConfidenceObservable

FuzzyTrieNode - Class in edu.iastate.jtm.dic

Biochemical name characters: Letters (case insensitive) Digits Enclosing marks: ()[] Separators: ,+-'/SPACE Other characters: treated as same special char

FuzzyTrieNode() - Constructor for class edu.iastate.jtm.dic.FuzzyTrieNode