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
 

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