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

T

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

TableAbbreviationRules - Class in edu.iastate.metnet.db

+-----------+--------------+------+-----+---------+----------------+ | Field | Type | Null | Key | Default | Extra | +-----------+--------------+------+-----+---------+----------------+ | ruleid | int(11) | | PRI | [NULL] | auto_increment | | shortterm | varchar(255) | | | | | | longterm | varchar(255) | | | | | +-----------+--------------+------+-----+---------+----------------+

TableBlockUnitConfidence - Class in edu.iastate.metnet.db

+--------------------+---------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +--------------------+---------+------+-----+---------+-------+ | BlockID | int(11) | | PRI | 0 | | | LocationConfidence | int(11) | YES | | 0 | | | FunctionConfidence | int(11) | YES | | 0 | | +--------------------+---------+------+-----+---------+-------+

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

tableCandidate - Variable in class edu.iastate.metnet.ui.SynonymCandidate

tableChanged(TableModelEvent) - Method in class edu.iastate.jtm.gui.TableMap

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

tableChanged(TableModelEvent) - Method in class edu.iastate.metnet.model.TableMap

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

TableClassRelation - Class in edu.iastate.metnet.db

+----------+---------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +----------+---------+------+-----+---------+-------+ | ParentID | int(11) | | | 0 | | | ChildID | int(11) | | | 0 | | +----------+---------+------+-----+---------+-------+

TableCodeClass - Class in edu.iastate.metnet.db

+------------+--------------+------+-----+---------+----------------+ | Field | Type | Null | Key | Default | Extra | +------------+--------------+------+-----+---------+----------------+ | ClassID | int(11) | | PRI | [NULL] | auto_increment | | CommonName | varchar(255) | | | | | | AracycID | varchar(255) | | | | | +------------+--------------+------+-----+---------+----------------+

TableCodeConfidence - Class in edu.iastate.metnet.db

+--------------+--------------+------+-----+---------+----------------+ | Field | Type | Null | Key | Default | Extra | +--------------+--------------+------+-----+---------+----------------+ | Code | int(11) | | PRI | [NULL] | auto_increment | | Value | double | YES | | 0 | | | Description | varchar(255) | YES | | | | | Presentation | varchar(255) | YES | | | | +--------------+--------------+------+-----+---------+----------------+

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

TableDataModel - Class in edu.iastate.metnet.dataManager

Model class for JTable

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

TableDataModel(int, int) - Constructor for class edu.iastate.metnet.dataManager.TableDataModel

TableMap - Class in edu.iastate.jtm.gui

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

TableMap - Class in edu.iastate.metnet.model

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

TableMarker - Class in edu.iastate.jtm.gui

TableMarker(JTable, Markable, int) - Constructor for class edu.iastate.jtm.gui.TableMarker

tableModel - Variable in class edu.iastate.metnet.metaomgraph.TableSorter

tableModel - Variable in class edu.iastate.metnet.ui.AbbreviationRules

tablePanel - Static variable in class edu.iastate.metnet.MetNetLAFTest

tablePanel - Variable in class edu.iastate.metnet.ui.SynonymCandidate

tableRules - Variable in class edu.iastate.metnet.ui.AbbreviationRules

TableSorter - Class in edu.iastate.jtm.gui

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

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

TableSorter - Class in edu.iastate.metnet.metaomgraph

TableSorter() - Constructor for class edu.iastate.metnet.metaomgraph.TableSorter

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

TableSorter(TableModel, JTableHeader) - Constructor for class edu.iastate.metnet.metaomgraph.TableSorter

TableSorter - Class in edu.iastate.metnet.model

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

TableSorter(TableModel) - Constructor for class edu.iastate.metnet.model.TableSorter

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

TableUtil - Class in edu.iastate.jtm.gui

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

TabularFileReader - Class in edu.iastate.metnet.aracyc

TabularFileReader() - Constructor for class edu.iastate.metnet.aracyc.TabularFileReader

TabularFileReaderEx - Class in edu.iastate.metnet.aracyc

same as TabularFileReader except implementing the data structure by Map of MultiMap

TabularFileReaderEx() - Constructor for class edu.iastate.metnet.aracyc.TabularFileReaderEx

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

tag - Variable in class edu.iastate.metnet.test.MyPaperTest.PaperWorker

taigaSearch(String) - Method in class edu.iastate.metnet.hivemindService.Browser

links to Arabidosis images search page.

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

TairAffy25kArrayElements - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_affy25k_array_elements' table.

TairAffy25kArrayElements() - Constructor for class edu.iastate.metnet.hibernate.TairAffy25kArrayElements

Simple constructor of TairAffy25kArrayElements instances.

TairAffy25kArrayElements(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairAffy25kArrayElements

Constructor of TairAffy25kArrayElements instances given a simple primary key.

TairAffy8kArrayElements - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_affy8k_array_elements' table.

TairAffy8kArrayElements() - Constructor for class edu.iastate.metnet.hibernate.TairAffy8kArrayElements

Simple constructor of TairAffy8kArrayElements instances.

TairAffy8kArrayElements(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairAffy8kArrayElements

Constructor of TairAffy8kArrayElements instances given a simple primary key.

TairAfgcArrayElements - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_afgc_array_elements' table.

TairAfgcArrayElements() - Constructor for class edu.iastate.metnet.hibernate.TairAfgcArrayElements

Simple constructor of TairAfgcArrayElements instances.

TairAfgcArrayElements(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairAfgcArrayElements

Constructor of TairAfgcArrayElements instances given a simple primary key.

TairAgiToUniprot - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_agi_to_uniprot' table.

TairAgiToUniprot() - Constructor for class edu.iastate.metnet.hibernate.TairAgiToUniprot

Simple constructor of TairAgiToUniprot instances.

TairAgiToUniprot(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairAgiToUniprot

Constructor of TairAgiToUniprot instances given a simple primary key.

TairAracycDump - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_aracyc_dump' table.

TairAracycDump() - Constructor for class edu.iastate.metnet.hibernate.TairAracycDump

Simple constructor of TairAracycDump instances.

TairAracycDump(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairAracycDump

Constructor of TairAracycDump instances given a simple primary key.

TairAthGoGoslim - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_ath_go_goslim' table.

TairAthGoGoslim() - Constructor for class edu.iastate.metnet.hibernate.TairAthGoGoslim

Simple constructor of TairAthGoGoslim instances.

TairAthGoGoslim(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairAthGoGoslim

Constructor of TairAthGoGoslim instances given a simple primary key.

TairReference - Interface in edu.iastate.metnet.hiveface

interface for access TAIR reference information

TairReferenceObject - Class in edu.iastate.metnet.dao

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

TairSequencedGenes - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_sequenced_genes' table.

TairSequencedGenes() - Constructor for class edu.iastate.metnet.hibernate.TairSequencedGenes

Simple constructor of TairSequencedGenes instances.

TairSequencedGenes(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairSequencedGenes

Constructor of TairSequencedGenes instances given a simple primary key.

TairTargetpAnalysis - Class in edu.iastate.metnet.hibernate

A class that represents a row in the 'tair_targetp_analysis' table.

TairTargetpAnalysis() - Constructor for class edu.iastate.metnet.hibernate.TairTargetpAnalysis

Simple constructor of TairTargetpAnalysis instances.

TairTargetpAnalysis(Integer) - Constructor for class edu.iastate.metnet.hibernate.TairTargetpAnalysis

Constructor of TairTargetpAnalysis instances given a simple primary key.

targetId - Variable in class edu.iastate.metnet.dao.ZEdge

target blockid

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

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

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

TAXONOMY - Static variable in class edu.iastate.jtm.jmed.Entrez

TaxonomyPanel - Class in fcmodeler.pathbinder.gui

TaxonomyPanel(MySqlConnector, JFileChooser, LocationPanel) - Constructor for class fcmodeler.pathbinder.gui.TaxonomyPanel

taxSql - Static variable in class fcmodeler.pathbinder.FilterUpdater

tblInteraction - Variable in class edu.iastate.metnet.ui.InteractionSelector

interaction list table

TDF - Static variable in class edu.iastate.jtm.util.VocabularyCounter

tearDown() - Method in class edu.iastate.biocyc.test.ArabReaderTest

tearDown() - Method in class edu.iastate.biocyc.test.BlockunitTest

tearDown() - Method in class edu.iastate.biocyc.test.RiceReaderTest

tearDown() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

tearDown() - Method in class edu.iastate.metnet.test.MD5DigestTest

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

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

tearDown() - Method in class edu.iastate.metnet.test.MySolverTest

tearDown() - Method in class edu.iastate.metnet.test.UtilsTest

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

current template interaction's version id

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

term - Variable in class edu.iastate.jtm.util.VocabularyCounter.TfDf

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

The value to search for.

term - Variable in class fcmodeler.pathbinder.HiddenLink.Link

termChanged(Query.Term) - Method in class edu.iastate.jtm.jmed.Query

termId - Variable in class fcmodeler.pathbinder.gui.EntityPanel.InteractionScore

the temp term interaction score expression

termSelected(Query.Term) - Method in class edu.iastate.jtm.assistant.CompositeTermPanel

termSelected(Query.Term) - Method in interface edu.iastate.jtm.assistant.QueryListener

termSelected(Query.Term) - Method in class edu.iastate.jtm.assistant.SimpleTermPanel

test(String[]) - Method in class edu.iastate.metnet.aracyc.ClassesDatReader

test(String[]) - Method in class edu.iastate.metnet.aracyc.CompoundsDatReader

testAtGeneSearchObject5() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

testBevGetAllLocationInfo() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoBioProcesses() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoChildren() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoFunctions() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoGeneProductID() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoNodeName() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoNodesWithinDistance() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetGoTermAncestors() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetLocations() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetLocusIDs() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetMetnetEntityID() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetPathways() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetPolypeptides() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBevGetProteinComplexes() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test BirdsEyeView functions

testBigMap() - Method in class edu.iastate.biocyc.test.RiceReaderTest

put all maps together, there should be 109417 instances

testBiologicalType() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the biological type

testBlocks(String) - Static method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Test the block operations of the RandomAccessFile class.

testBlocks(String) - Static method in class edu.iastate.metnet.soft.RandomAccessFile

Test the block operations of the RandomAccessFile class.

testBytes(String, int) - Static method in class edu.iastate.metnet.metaomgraph.RandomAccessFile

Test the byte operations of the RandomAccessFile class.

testBytes(String, int) - Static method in class edu.iastate.metnet.soft.RandomAccessFile

Test the byte operations of the RandomAccessFile class.

testCheckOrInsertEntity() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testCheckOrInsertEntitywithcontext() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testCheckOrInsertEntitywithlocation() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testClassNetwork() - Method in class edu.iastate.biocyc.test.ArabReaderTest

test the class network

testClassNetwork() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the class network

testCollectClassType() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test our interesting classes

testConstructMatrix() - Method in class edu.iastate.metnet.test.MySolverTest

testConstructRowVector() - Method in class edu.iastate.metnet.test.MySolverTest

testConstructVector() - Method in class edu.iastate.metnet.test.MySolverTest

testConvertGraph() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the graph conversion

testDelete() - Method in class edu.iastate.metnet.test.HibernateTest

testDuplicatedClassName() - Method in class edu.iastate.biocyc.test.RiceReaderTest

get duplicated class name

testDuplicatedCompoundName() - Method in class edu.iastate.biocyc.test.RiceReaderTest

get duplicated compound name

testDuplicatedGeneName() - Method in class edu.iastate.biocyc.test.RiceReaderTest

get duplicated gene name

testDuplicatedProteinName() - Method in class edu.iastate.biocyc.test.RiceReaderTest

get duplicated protein name

testGeneLocation() - Method in class edu.iastate.biocyc.test.RiceReaderTest

testGetAllLocation() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get the subcellular compartment list

testGetAtGeneSearchAttributeList() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'getAtGeneSearchAttributeList()'

testGetAtGeneSearchObject() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'getAtGeneSearchObject()'

testGetAtGeneSearchObject2() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'getAtGeneSearchObject()'

testGetAtGeneSearchObject3() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'getAtGeneSearchObject()'

testGetAtGeneSearchObject4() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'getAtGeneSearchObject()'

testGetBlockunit() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get the blockunit object

testGetComplex4Component() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the p-neighborhood graph.

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

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

testGetDataSourceList() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testGetDescendentValue() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testGetECList() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testGetEntityTypeList() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testGetFullGeneAnnotationList() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test time used for retrieve 1000 atgenesearch object

testGetGraphModelByEntity() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'edu.iastate.metnet.hiveface.GraphExporter.getGraphModelByEntity(GobiNode)'

testGetGraphModelByEntityList() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'edu.iastate.metnet.hiveface.GraphExporter.getGraphModelByEntityList(ArrayList)'

testGetGraphModelMapByEntityList() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

Test method for 'edu.iastate.metnet.hiveface.GraphExporter.getGraphModelByEntityList(ArrayList)'

testGetLocation4Entity() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get the subcelllar location

testGetLocationList() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testGetMD5Digest() - Method in class edu.iastate.metnet.test.MD5DigestTest

testGetMetaboliteMap() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the metabolite id and name map

testGetMetaboliteObject() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get the metabolite object.

testGetOrganismList() - Method in class edu.iastate.metnet.test.BlockunitFinderTest

testGetPathwayElementMap() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the pathway element mapping

testGetPathwayInfo() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the pathway information retrieve function

testGetPathwayLocusMap() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the pathway locus mapping

testGetPathwayMetaboliteMap() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the pathway metabolite mapping

testGetPolypeptide4Gene() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the p-neighborhood graph.

testInsert() - Method in class edu.iastate.metnet.test.HibernateTest

testIsCompatible() - Method in class edu.iastate.metnet.test.MySolverTest

testJ2EEconnection() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the J2EE connection

testMysqlOldPassword() - Method in class edu.iastate.metnet.test.UtilsTest

testNestedNetwork() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the nested network

testPathwayCategory() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test the feature to extract the information pathway category

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

test if the pathway name exists

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

test if the pathway name exists

testProteinType() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the protein, if it is a polypeptide or a protein complex

testPubchemCasFilter() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get cas from pubchem synonym.

testPubchemCid2Name() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get pubchem name.

testPubchemName2Cid() - Method in class edu.iastate.metnet.hivetest.GraphExporterTest

test to get pubchem cid.

testReactionNetwork() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the reaction network

testReadClass() - Method in class edu.iastate.biocyc.test.RiceReaderTest

read compound data

testReadEnzrxn() - Method in class edu.iastate.biocyc.test.RiceReaderTest

read the control interaction

testReadGene() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the read of gene.

testReadPathway() - Method in class edu.iastate.biocyc.test.RiceReaderTest

read the pathway test

testReadProtein() - Method in class edu.iastate.biocyc.test.RiceReaderTest

read the protein data

testReadReaction() - Method in class edu.iastate.biocyc.test.RiceReaderTest

read the reaction data

testRewriteGraph() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the rewrite graph

testSolve() - Method in class edu.iastate.metnet.test.MySolverTest

testTrimString() - Method in class edu.iastate.biocyc.test.RiceReaderTest

test the string trim feature

testUpdate() - Method in class edu.iastate.metnet.test.HibernateTest

testVisualization() - Method in class edu.iastate.biocyc.test.RiceReaderTest

visualize the whole graph in the cytoscape

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

TEXT - Static variable in class edu.iastate.metnet.metaomgraph.GraphFileFilter

Mode to accept .txt and .csv files

TextArea - Class in edu.iastate.metnet.birdseyeview

The TextArea Class is a simple text area class that will ensure line wrapping of the text and prohibit editing of text.

TextArea(String, Color, Color, Font) - Constructor for class edu.iastate.metnet.birdseyeview.TextArea

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

TextPanel - Class in edu.iastate.metnet.birdseyeview

The TextPanel Class holds rows of AnnotationTextPanel objects.

TextPanel(ArrayList, Dimension) - Constructor for class edu.iastate.metnet.birdseyeview.TextPanel

Constructor.

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

TF - Static variable in class edu.iastate.jtm.util.VocabularyCounter

tf - Variable in class edu.iastate.jtm.util.VocabularyCounter.TfDf

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

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

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

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

tid - Variable in class fcmodeler.pathbinder.HiddenLink.Link

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

Wait at most msecs to access the constructed result.

TipRenderer - Class in fcmodeler.pathbinder.gui

TipRenderer() - Constructor for class fcmodeler.pathbinder.gui.TipRenderer

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

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

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

title - Variable in class edu.iastate.metnet.dao.TairReferenceObject

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

The label used to display the title.

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

titledBorder1 - Variable in class edu.iastate.metnet.ui.AbbreviationRules

titledBorder2 - Variable in class edu.iastate.metnet.ui.AbbreviationRules

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

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycClass

instance map contains the unique id key and biocyc element value

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycCompound

instance map contains the unique id key and biocyc element value

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycEnzrxn

instance map contains the unique id key and biocyc element value

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycGene

instance map contains the unique id key and biocyc element value

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycPathway

instance map contains the unique id key and biocyc element value

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycProtein

instance map contains the unique id key and biocyc element value

toBiocycMap(Map) - Static method in class edu.iastate.biocyc.dao.txt.BiocycReaction

instance map contains the unique id key and biocyc element value

toFloatList(float[]) - Method in class edu.iastate.metnet.analysis.MySolver

toFloatList(float[][]) - Method in class edu.iastate.metnet.analysis.MySolver

toFullString() - Method in class fcmodeler.pathbinder.Entity

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

This method does nothing by default.

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

This method turns the map labels on/off given the flag.

toggleMapLabels(boolean) - Method in class edu.iastate.metnet.birdseyeview.ButtonPanel

This method modifies the labels button depending on the parameter.

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

toggleMapLabels(boolean) - Method in class edu.iastate.metnet.birdseyeview.RootPanel

This method calls the view panel and button panel to turn the map labels on/off.

toggleMapLabels(boolean) - Method in class edu.iastate.metnet.birdseyeview.ViewPanel

This method notifies the current view about the 'toggle map labels' instruction.

TokenAnalyzer - Class in edu.iastate.jtm

Check surface clue to see whether a token is a possible biochemical name.

TokenAnalyzer() - Constructor for class edu.iastate.jtm.TokenAnalyzer

tokenBuffer - Variable in class edu.iastate.jtm.dic.AbstractDictionary

tokenize(String) - Static method in class edu.iastate.jtm.TokenAnalyzer

tokenProcessor - Variable in class edu.iastate.jtm.dic.AbstractDictionary

TokenProcessor - Class in edu.iastate.jtm.util

Remove punctuations from left and right of a token.

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

tooltipTemplate - Variable in class edu.iastate.metnet.model.AbstractBlockunitDecorator

the internal tooltip

toPresentation() - Method in class edu.iastate.metnet.dao.MyVersionGraph

get the stringization of this instance, same as toString() but use different method name to prevent name conflication

toString() - Method in class edu.iastate.jtm.assistant.QueryBuilder.QueryTemplate

toString() - Method in class edu.iastate.jtm.gui.XmlTreeNode

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

toString() - Method in class edu.iastate.jtm.jmed.MeshDescriptor

toString() - Method in class edu.iastate.jtm.jmed.Query.Field

toString() - Method in class edu.iastate.jtm.jmed.Query.Operator

toString() - Method in class edu.iastate.jtm.PorterStemmer

After a word has been stemmed, it can be retrieved by toString(), or a reference to the internal buffer can be retrieved by getResultBuffer and getResultLength (which is generally more efficient.)

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

toString() - Method in class edu.iastate.metnet.birdseyeview.AnnotationTextPanel

This method returns a string with the name, type, locations, and pathways for the annotation.

toString() - Method in exception edu.iastate.metnet.birdseyeview.BirdsEyeViewException

toString() - Method in exception edu.iastate.metnet.birdseyeview.FieldNotFoundException

toString() - Method in class edu.iastate.metnet.birdseyeview.PathwayTreeNode

toString() - Method in class edu.iastate.metnet.dao.AbstractMultiPathwayElementNode

toString() - Method in class edu.iastate.metnet.dao.CategoryNode

control the representation in the graph

toString() - Method in class edu.iastate.metnet.dao.ChebiOntologyName

for representation in the tree node model

toString() - Method in class edu.iastate.metnet.dao.InputNode

display information

toString() - Method in class edu.iastate.metnet.dao.MetnetBlockUnit

toString() - Method in class edu.iastate.metnet.dao.MetnetInteraction

do not display anything in the JGraph

toString() - Method in class edu.iastate.metnet.dao.MetnetLiveEntity

display the name of the entity, if it is polypptide, display the abbreviation, which may be the gene symbol

toString() - Method in class edu.iastate.metnet.dao.MultiInteractionNode

we do not need a name for dummy interaction node

toString() - Method in class edu.iastate.metnet.dao.MyVersionNode

display the information

toString() - Method in class edu.iastate.metnet.export.AtGeneSearchObjectImpl

toString() - Method in class edu.iastate.metnet.graphmodel.MyTreeAlgorithm

Returns the name of this algorithm in human readable form.

toString() - Method in class edu.iastate.metnet.hibernate.Codeconfidence

toString() - Method in class edu.iastate.metnet.hibernate.Codedatasource

toString() - Method in class edu.iastate.metnet.hibernate.Codeentitytype

toString() - Method in class edu.iastate.metnet.hibernate.Codeinteractiontype

toString() - Method in class edu.iastate.metnet.hibernate.Codelocation

toString() - Method in class edu.iastate.metnet.hibernate.Codeorganism

toString() - Method in class edu.iastate.metnet.hibernate.Codereferencetype

toString() - Method in class edu.iastate.metnet.hibernate.Coderule

get the presentation for tablemodel

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

toString() - Method in class edu.iastate.metnet.metaomgraph.ExtendedInfoTree.InfoNode

Returns the name of the node.

toString() - Method in class edu.iastate.metnet.metaomgraph.GeneList

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

Create a string representation of this object.

toString() - Method in class edu.iastate.metnet.model.CodeRulePresentation

for combobox presentation

toString() - Method in class edu.iastate.metnet.model.DisplayObject

the display string of the current object

toString() - Method in class edu.iastate.metnet.model.XMLMutableTreeNode

presentation of the node

toString() - Method in class edu.iastate.metnet.soft.Entity

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

Create a string representation of this object.

toString() - Method in class edu.iastate.metnet.ui.HelpWindow.HelpPage

toString() - Method in class fcmodeler.pathbinder.Entity

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

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

toString() - Method in class fcmodeler.pathbinder.HiddenLink.Link

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

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

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

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

Converts this object to an XML Element.

treeCollapsed(TreeExpansionEvent) - Method in class edu.iastate.metnet.ui.CategoryEditForm

treeExpanded(TreeExpansionEvent) - Method in class edu.iastate.metnet.ui.CategoryEditForm

TreeModelSupport - Class in edu.iastate.metnet.model

copy from http://java.sun.com/products/jfc/tsc/articles/jtree/

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

TreePanel - Class in edu.iastate.metnet.birdseyeview

TreePanel(ArrayList) - Constructor for class edu.iastate.metnet.birdseyeview.TreePanel

TreePanel(Dimension, BirdsEyeView) - Constructor for class edu.iastate.metnet.birdseyeview.TreePanel

treePanel - Static variable in class edu.iastate.metnet.MetNetLAFTest

TreeSearcher - Class in edu.iastate.metnet.metaomgraph

Searches a tree rooted at a DefaultMutableTreeNode.

TreeSearcher(DefaultMutableTreeNode) - Constructor for class edu.iastate.metnet.metaomgraph.TreeSearcher

TreeSearcher.Query - Class in edu.iastate.metnet.metaomgraph

Specifies a search for a TreeSearcher object.

TreeSearcher.Query() - Constructor for class edu.iastate.metnet.metaomgraph.TreeSearcher.Query

Default constructor.

TreeSearcher.Query(String, String, boolean) - Constructor for class edu.iastate.metnet.metaomgraph.TreeSearcher.Query

Constructor.

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

Panel for constructing TreeSearcher.Query objects.

TreeSearchQueryConstructionPanel(MetaOmProject) - Constructor for class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel

TreeSearchQueryConstructionPanel.QuerySet - Class in edu.iastate.metnet.metaomgraph.chart

TreeSearchQueryConstructionPanel.QuerySet(TreeSearcher.Query[], boolean) - Constructor for class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel.QuerySet

TreeSearchQueryConstructionPanel.QuerySet() - Constructor for class edu.iastate.metnet.metaomgraph.chart.TreeSearchQueryConstructionPanel.QuerySet

TreeUtil - Class in edu.iastate.jtm.gui

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

Trie - Class in edu.iastate.jtm.dic

An implementation of trie data structure.

Trie(TrieNode) - Constructor for class edu.iastate.jtm.dic.Trie

Creates a new instance of Trie.

TrieDictionary - Class in edu.iastate.jtm.dic

A dictionary backed with a trie.

TrieDictionary(Trie) - Constructor for class edu.iastate.jtm.dic.TrieDictionary

Creates a new instance of TrieDictionary

TrieDictionary(Trie, boolean) - Constructor for class edu.iastate.jtm.dic.TrieDictionary

TrieDictionary(Trie, SlidingWindow, boolean, boolean) - Constructor for class edu.iastate.jtm.dic.TrieDictionary

TrieNode - Interface in edu.iastate.jtm.dic

Define the behaviors of a node in a trie.

trim(String, char, char) - Static method in class edu.iastate.biocyc.io.AttributeFileReaderEx

cut the header and the tail of the string, do not consider if it is already a trimmed one

trivialListModel - Variable in class edu.iastate.metnet.ui.AmorphousQueryForm

list of trivial node

TrivialMetabolite - Class in edu.iastate.metnet.dao

contains the information of trivial metabolites that have highly connections

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

default constructor

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

default constructor

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

default constructor

TrivialNodePanel - Class in edu.iastate.metnet.mapbuilder

TrivialNodePanel() - Constructor for class edu.iastate.metnet.mapbuilder.TrivialNodePanel

TrivialSelector - Class in edu.iastate.metnet.ui

Choose trivial selector

TrivialSelector(Object) - Constructor for class edu.iastate.metnet.ui.TrivialSelector

Creates new form TrivialSelector

TrivialTableModel - Class in edu.iastate.metnet.model

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

default constructor

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

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

txtLongTerm - Variable in class edu.iastate.metnet.ui.AbbreviationRules

txtName - Variable in class edu.iastate.metnet.ui.InteractionSelector

search string

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

txtShortTerm - Variable in class edu.iastate.metnet.ui.AbbreviationRules

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

type, either class or pathway, we will not inherit the node type any more

type - Variable in class edu.iastate.metnet.dao.InteractionInformation

interaction type