TRAC
A B C D E F G H I J K L M N P Q R S T U V W X

A

AboutPage - Class in edu.cornell.med.icb.trac.tapestry.pages
Backend code for the TRAC home page.
AboutPage() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.AboutPage
 
AbstractManager<T> - Class in edu.cornell.med.icb.trac
Abstract super class of JDO datastore manager classes.
AbstractManager() - Constructor for class edu.cornell.med.icb.trac.AbstractManager
Creates a new AbstractManager.
AbstractSequenceDiagramAsset - Class in edu.cornell.med.icb.trac.tapestry.rbdg
An asset used to display sequence diagrams generated by RbDg.
AbstractSequenceDiagramAsset(IRequestCycle, SequenceDiagramComponent) - Constructor for class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
 
AbstractText - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class AbstractText.
AbstractText() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
 
AbstractTextDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class AbstractTextDescriptor.
AbstractTextDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
 
activateExternalPage(Object[], IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
This is called when the page is first accessed.
activateExternalPage(Object[], IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
This is called when the page is first accessed.
ACTUALNUMBER - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
addArticle(Article) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
addArticle(int, Article) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
addAuthor(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
addAuthor(int, String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
addBindingInhibition(BindingInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
addBindingInhibition(int, BindingInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
addConstruct(Construct) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
addConstruct(int, Construct) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
addConstructSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
addCOUPLERItem(COUPLERItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
addCOUPLERItem(int, COUPLERItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
addInhibitionSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.LigandComponent
 
addInhibitionSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.SubstrateComponent
 
addLigand(Ligand) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
addLigand(int, Ligand) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
addLigandSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
addMarkedTextTypeItem(MarkedTextTypeItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
addMarkedTextTypeItem(int, MarkedTextTypeItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
addMutation(Mutation) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
addMutation(int, Mutation) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
addMutationSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
addNote(Note) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
addNote(int, Note) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
addProtection(Protection) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
addProtection(int, Protection) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
addProtectionSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
addResidue(Residue) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
addResidue(int, Residue) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
addSCAMReagent(SCAMReagent) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
addSCAMReagent(int, SCAMReagent) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
addSCAMReagentSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
addSubstrate(Substrate) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
addSubstrate(int, Substrate) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
addSubstrateSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
addSynonymsItem(SynonymsItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
addSynonymsItem(int, SynonymsItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
addTRACAbstractSetItem(TRACAbstractSetItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
addTRACAbstractSetItem(int, TRACAbstractSetItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
addTransportersItem(TransportersItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
addTransportersItem(int, TransportersItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
addTransportInhibition(TransportInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
addTransportInhibition(int, TransportInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
addUser(User) - Method in class edu.cornell.med.icb.trac.user.UserSet
 
addUser(int, User) - Method in class edu.cornell.med.icb.trac.user.UserSet
 
ALIGNMENT_DIRECTORY - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
ALIGNMENT_FILENAME - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
alignmentBoundariesFilename - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
alignmentsLink(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.AboutPage
 
annotate(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
User selected an article to annotate.
AnnotationStatus - Class in edu.cornell.med.icb.trac.article.xml
Class AnnotationStatus.
AnnotationStatus() - Constructor for class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
 
AnnotationStatusDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class AnnotationStatusDescriptor.
AnnotationStatusDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
 
Article - Class in edu.cornell.med.icb.trac.article.xml
transporter mutation article
Article() - Constructor for class edu.cornell.med.icb.trac.article.xml.Article
 
ArticleConverter - Class in edu.cornell.med.icb.trac.article
An utility class to convert Articles upon the change of schema.
ArticleConverter() - Constructor for class edu.cornell.med.icb.trac.article.ArticleConverter
 
ArticleDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ArticleDescriptor.
ArticleDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
 
ArticleDownloadService - Class in edu.cornell.med.icb.trac.tapestry.services
 
ArticleDownloadService() - Constructor for class edu.cornell.med.icb.trac.tapestry.services.ArticleDownloadService
 
ArticleList0Page - Class in edu.cornell.med.icb.trac.tapestry.pages
Allows the user to select an article to annotate.
ArticleList0Page() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
articleListLink(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.HomePage
 
ArticleManager - Class in edu.cornell.med.icb.trac.article
Class used to manage operations on Articles.
ArticleSet - Class in edu.cornell.med.icb.trac.article.xml
Class ArticleSet.
ArticleSet() - Constructor for class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
ArticleSetDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ArticleSetDescriptor.
ArticleSetDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
 
ArticleUtils - Class in edu.cornell.med.icb.trac.article
Utility classes to use with Articles.
attemptLogin(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Attempts to login.
attemptRegister(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Called when a user attempts to register for access to the system.
Authors - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class Authors.
Authors() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
AuthorsDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class AuthorsDescriptor.
AuthorsDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
 

B

BackgroundPropertySelectionModel - Class in edu.cornell.med.icb.trac.tapestry.form
 
BackgroundPropertySelectionModel(Article, Construct) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.BackgroundPropertySelectionModel
Creates a new property selection model based on the constructs in an article object.
BARGRAPHESTIMATION - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
BasicInfoComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
 
BasicInfoComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
basicInfoOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
Binding - Class in edu.cornell.med.icb.trac.article.xml
Class Binding.
Binding() - Constructor for class edu.cornell.med.icb.trac.article.xml.Binding
 
BINDING - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
BindingComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
BindingComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
BindingDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class BindingDescriptor.
BindingDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
 
BindingInhibition - Class in edu.cornell.med.icb.trac.article.xml
Class BindingInhibition.
BindingInhibition() - Constructor for class edu.cornell.med.icb.trac.article.xml.BindingInhibition
 
BindingInhibitionDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class BindingInhibitionDescriptor.
BindingInhibitionDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
 
BindingIonDependence - Class in edu.cornell.med.icb.trac.article.xml
Class BindingIonDependence.
BindingIonDependence() - Constructor for class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
 
BindingIonDependenceDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class BindingIonDependenceDescriptor.
BindingIonDependenceDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
 
bindingOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
BindingSite - Class in edu.cornell.med.icb.trac.article.xml
Class BindingSite.
BindingSite() - Constructor for class edu.cornell.med.icb.trac.article.xml.BindingSite
 
BindingSiteDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class BindingSiteDescriptor.
BindingSiteDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
 
BindingSiteInferenceNote - Class in edu.cornell.med.icb.trac.article.xml
Class BindingSiteInferenceNote.
BindingSiteInferenceNote() - Constructor for class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
 
BindingSiteInferenceNoteDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class BindingSiteInferenceNoteDescriptor.
BindingSiteInferenceNoteDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
 
BLANKCONSTRUCT - Static variable in class edu.cornell.med.icb.trac.article.ArticleUtils
Default name to use for new constructs.
Bmax - Class in edu.cornell.med.icb.trac.article.xml
Class Bmax.
Bmax() - Constructor for class edu.cornell.med.icb.trac.article.xml.Bmax
 
BMAX - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
BMAX_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
BmaxDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class BmaxDescriptor.
BmaxDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
 
Border - Class in edu.cornell.med.icb.trac.tapestry
The border component embeds various tapestry components to create a page.
Border() - Constructor for class edu.cornell.med.icb.trac.tapestry.Border
 
buildURL(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
Returns a URL for the asset, ready to be inserted into the output HTML.

C

CastorTypePropertySelectionModel<CastorType> - Class in edu.cornell.med.icb.trac.tapestry.form
Property selection model that can be used to build property selection components based on the associated castor source.
CastorTypePropertySelectionModel(Class) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.CastorTypePropertySelectionModel
Creates a new property selection model based on a castor type class.
channelActivity - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
children() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
CLEAR_STRING - Static variable in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Will trigger an action to clear the existing mutation for a particular wt residue.
clone(Serializable) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Creates a transient copy of a an object that may be persistent.
cloneArticle(Article) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Creates a transient copy of a an article that may be persistent.
collapse(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
collapseAllSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
collapsePath(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
compareTo(ConstructTreeNode) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
ConstraintsGenerator - Class in edu.cornell.med.icb.trac.constraints
 
ConstraintsGenerator() - Constructor for class edu.cornell.med.icb.trac.constraints.ConstraintsGenerator
 
Construct - Class in edu.cornell.med.icb.trac.article.xml
Class Construct.
Construct() - Constructor for class edu.cornell.med.icb.trac.article.xml.Construct
 
ConstructDataTableComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
ConstructDataTableComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
ConstructDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ConstructDescriptor.
ConstructDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
 
ConstructId - Class in edu.cornell.med.icb.trac.article.xml
Class ConstructId.
ConstructId() - Constructor for class edu.cornell.med.icb.trac.article.xml.ConstructId
 
ConstructIdDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ConstructIdDescriptor.
ConstructIdDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
 
ConstructRetriever - Class in edu.cornell.med.icb.trac.rbdg
 
ConstructRetriever() - Constructor for class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
ConstructTreeDataView - Class in edu.cornell.med.icb.trac.tapestry.model.components
Created by IntelliJ IDEA.
ConstructTreeDataView() - Constructor for class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
ConstructTreeDataViewJS - Class in edu.cornell.med.icb.trac.tapestry.model.components
Created by IntelliJ IDEA.
ConstructTreeDataViewJS() - Constructor for class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataViewJS
 
ConstructTreeFactory - Class in edu.cornell.med.icb.trac.tapestry.model
Created by IntelliJ IDEA.
ConstructTreeFactory(Article, Construct) - Constructor for class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeFactory
 
ConstructTreeModel - Class in edu.cornell.med.icb.trac.tapestry.model
Created by IntelliJ IDEA.
ConstructTreeModel(ITreeDataModel) - Constructor for class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeModel
Constructor for SimpleTreeModel.
ConstructTreeModel(ITreeDataModel, ITreeStateModel) - Constructor for class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeModel
 
ConstructTreeNode - Class in edu.cornell.med.icb.trac.tapestry.model
 
ConstructTreeNode(String, String, String) - Constructor for class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
ConstructTreeNode(IMutableTreeNode) - Constructor for class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
ConstructTreeNodeView - Class in edu.cornell.med.icb.trac.tapestry.model.components
 
ConstructTreeNodeView() - Constructor for class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
 
ConstructTreePage - Class in edu.cornell.med.icb.trac.tapestry.pages
 
ConstructTreePage() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
ConstructTreeStateModel - Class in edu.cornell.med.icb.trac.tapestry.model
Created by IntelliJ IDEA.
ConstructTreeStateModel() - Constructor for class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
Constructor for SimpleTreeStateModel.
ConstructTreeView - Class in edu.cornell.med.icb.trac.tapestry.model.components
Created by IntelliJ IDEA.
ConstructTreeView() - Constructor for class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
CONSTRUCTTYPE_BACKGROUND - Static variable in class edu.cornell.med.icb.trac.article.ArticleUtils
 
CONSTRUCTTYPE_BOTH - Static variable in class edu.cornell.med.icb.trac.article.ArticleUtils
 
CONSTRUCTTYPE_MODEL - Static variable in class edu.cornell.med.icb.trac.article.ArticleUtils
 
CONSTRUCTTYPE_MUTANT - Static variable in class edu.cornell.med.icb.trac.article.ArticleUtils
 
containsChild(ITreeNode) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
copyConstructSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
COUPLER - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class COUPLER.
COUPLER() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
COUPLERDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class COUPLERDescriptor.
COUPLERDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
 
COUPLERItem - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class COUPLERItem.
COUPLERItem() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
 
COUPLERItemDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class COUPLERItemDescriptor.
COUPLERItemDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
 
createBackgroundConstruct() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createBasicConstruct() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createBindingInhibition() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createBlankConstruct() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
Creates a new empty article in the datastore.
createData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
createDataSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
CreatedBy - Class in edu.cornell.med.icb.trac.article.xml
Class CreatedBy.
CreatedBy() - Constructor for class edu.cornell.med.icb.trac.article.xml.CreatedBy
 
CreatedByDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class CreatedByDescriptor.
CreatedByDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
 
createIsBackground() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
Create an IsBackground skeleton.
createIsMutant(String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
Create an IsMutant skeleton.
createLigand() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createMutantConstruct(String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createProtection() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createSCAM() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createSCAMReagent() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createSubstrate() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
createTransportInhibition() - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 

D

DATA_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
DECREASED - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
delete(T) - Method in class edu.cornell.med.icb.trac.AbstractManager
Removes an object from the datastore.
delete(long) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Removes an article from the datastore.
delete(T) - Method in interface edu.cornell.med.icb.trac.jdo.PersistenceManager
Removes an object from the datastore.
deleteAnnotatedByAuthor() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
 
deleteConcentration() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
 
deleteDisabled() - Method in class edu.cornell.med.icb.trac.user.User
 
deleteInhibitorBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
 
deleteIsCurator() - Method in class edu.cornell.med.icb.trac.user.User
 
deleteIsNewInference() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
 
deleteNoteSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Delete a note.
deletePmid() - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
deletePmid() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
deletePMID() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
deleteProtectable() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
 
deleteResidueNumber() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
 
deleteScore() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
deleteSubstrateBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
 
deleteYear() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
DELETION_STRING - Static variable in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
 
DESCRIPTION - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
DESCRIPTION_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
DynamicStringPropertySelectionModel - Class in edu.cornell.med.icb.trac.tapestry.form
 
DynamicStringPropertySelectionModel(String[]) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.DynamicStringPropertySelectionModel
Standard constructor.

E

edu.cornell.med.icb.trac - package edu.cornell.med.icb.trac
 
edu.cornell.med.icb.trac.alignment - package edu.cornell.med.icb.trac.alignment
 
edu.cornell.med.icb.trac.article - package edu.cornell.med.icb.trac.article
Classes that deal with articles in the trac application.
edu.cornell.med.icb.trac.article.xml - package edu.cornell.med.icb.trac.article.xml
Classes that deal with transporter mutation articles in the trac application.
edu.cornell.med.icb.trac.article.xml.descriptors - package edu.cornell.med.icb.trac.article.xml.descriptors
 
edu.cornell.med.icb.trac.constraints - package edu.cornell.med.icb.trac.constraints
 
edu.cornell.med.icb.trac.jdo - package edu.cornell.med.icb.trac.jdo
Main set of support classes for the trac jdo application.
edu.cornell.med.icb.trac.rbdg - package edu.cornell.med.icb.trac.rbdg
 
edu.cornell.med.icb.trac.tapestry - package edu.cornell.med.icb.trac.tapestry
Main set of support classes for the trac tapestry web application.
edu.cornell.med.icb.trac.tapestry.form - package edu.cornell.med.icb.trac.tapestry.form
Support classes for forms in the trac tapestry web application.
edu.cornell.med.icb.trac.tapestry.model - package edu.cornell.med.icb.trac.tapestry.model
 
edu.cornell.med.icb.trac.tapestry.model.components - package edu.cornell.med.icb.trac.tapestry.model.components
 
edu.cornell.med.icb.trac.tapestry.pages - package edu.cornell.med.icb.trac.tapestry.pages
Backend support classes for dynamic pages in the trac tapestry web application.
edu.cornell.med.icb.trac.tapestry.rbdg - package edu.cornell.med.icb.trac.tapestry.rbdg
 
edu.cornell.med.icb.trac.tapestry.services - package edu.cornell.med.icb.trac.tapestry.services
 
edu.cornell.med.icb.trac.tapestry.user - package edu.cornell.med.icb.trac.tapestry.user
Main set of support classes for the managing users in the trac tapestry web application.
edu.cornell.med.icb.trac.TRACAbstract.xml - package edu.cornell.med.icb.trac.TRACAbstract.xml
Classes that deal with TRAC abstracts that are generated by coupler project data mining work.
edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors - package edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
 
edu.cornell.med.icb.trac.transporter - package edu.cornell.med.icb.trac.transporter
 
edu.cornell.med.icb.trac.transporter.xml - package edu.cornell.med.icb.trac.transporter.xml
 
edu.cornell.med.icb.trac.transporter.xml.descriptors - package edu.cornell.med.icb.trac.transporter.xml.descriptors
 
edu.cornell.med.icb.trac.user - package edu.cornell.med.icb.trac.user
Classes that deal with users and user management within the TRAC application.
edu.cornell.med.icb.trac.user.descriptors - package edu.cornell.med.icb.trac.user.descriptors
 
edu.cornell.med.icb.trac.xml - package edu.cornell.med.icb.trac.xml
 
EffectType - Class in edu.cornell.med.icb.trac.article.xml
Class EffectType.
EffectType() - Constructor for class edu.cornell.med.icb.trac.article.xml.EffectType
 
EffectTypeComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
 
EffectTypeComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
EffectTypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class EffectTypeDescriptor.
EffectTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
 
EffectTypePropertySelectionModels - Class in edu.cornell.med.icb.trac.tapestry.form
 
EffectTypePropertySelectionModels() - Constructor for class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
efflux - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
encrypt(String) - Static method in class edu.cornell.med.icb.trac.user.UserUtils
Encrypts a string of text using a "one-way" collision-free mechanism that guarantees that no two different values will produce the same result.
enumerateArticle() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method enumerateArticle.
enumerateAuthor() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method enumerateAuthor.
enumerateBindingInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method enumerateBindingInhibition.
enumerateConstruct() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method enumerateConstruct.
enumerateCOUPLERItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method enumerateCOUPLERItem.
enumerateLigand() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method enumerateLigand.
enumerateMarkedTextTypeItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method enumerateMarkedTextTypeItem.
enumerateMutation() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method enumerateMutation.
enumerateNote() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method enumerateNote.
enumerateProtection() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method enumerateProtection.
enumerateResidue() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method enumerateResidue.
enumerateSCAMReagent() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method enumerateSCAMReagent.
enumerateSubstrate() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method enumerateSubstrate.
enumerateSynonymsItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method enumerateSynonymsItem.
enumerateTRACAbstractSetItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method enumerateTRACAbstractSetItem.
enumerateTransportersItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method enumerateTransportersItem.
enumerateTransportInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method enumerateTransportInhibition.
enumerateUser() - Method in class edu.cornell.med.icb.trac.user.UserSet
Method enumerateUser.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Bmax
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.ConstructId
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.History
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Id
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Kd
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Km
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Note
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.article.xml.Vmax
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
Overwrite equals to match getValue().equals().
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.user.User
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class edu.cornell.med.icb.trac.user.UserSet
Overrides the java.lang.Object.equals method.
exists(long) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Determines whether or not an article exists in the datastore.
expand(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
expandAllSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
expandPath(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
experimentalMethod - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
Exportable<T extends Serializable> - Interface in edu.cornell.med.icb.trac.xml
Classes implementing this interface are capable of exporting to XML.
Expression - Class in edu.cornell.med.icb.trac.article.xml
Class Expression.
Expression() - Constructor for class edu.cornell.med.icb.trac.article.xml.Expression
 
ExpressionDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ExpressionDescriptor.
ExpressionDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
 
expressionResult - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
expressionSystem - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
ExpressionSystemPropertySelectionModel - Class in edu.cornell.med.icb.trac.tapestry.form
 
ExpressionSystemPropertySelectionModel(Construct) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
Creates a new property selection model based on the constructs in an article object.
extractMutationString(IsMutant) - Static method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
extractPmid(Reader) - Static method in class edu.cornell.med.icb.trac.article.ArticleManager
Extracts a pubmed identifier from an article.
extractResidueIndexString(IsMutant) - Static method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
extractSynonym(Construct) - Static method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeFactory
 

F

FileDownloadService - Class in edu.cornell.med.icb.trac.tapestry.services
 
FileDownloadService() - Constructor for class edu.cornell.med.icb.trac.tapestry.services.FileDownloadService
 
filterMutants(List<SimpleMutant>, List<String>) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Filters mutants based on a list of string "commands".
filterMutantsBasedOnProtein(List<SimpleMutant>, List<String>) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Filter mutants based on a list of proteins.
filterMutantsBasedOnProtein(List<SimpleMutant>, String, String) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Filters mutants that match the protein type and species.
filterMutantsBmax(List<SimpleMutant>, double) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
filterMutantsKd(List<SimpleMutant>, double) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
filterMutantsKm(List<SimpleMutant>, double) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
filterMutantsVmax(List<SimpleMutant>, double) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
finalize() - Method in class edu.cornell.med.icb.trac.AbstractManager
Close the kodo managers upon garbage collection.
formSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Listener for the form submission.
formSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
Listener for the form submission.
fullIndexListFilename - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 

G

generateIDSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
generateImage(List<SimpleMutant>, String, ImageFormatType, OutputStream) - Static method in class edu.cornell.med.icb.trac.rbdg.RbdgXmlWriter
Generate a sequence diagram based on the list of mutants.
getAbstractText() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'abstractText'.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getAccessMode.
getAccessMode() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getAccessMode.
getAddConstructType() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getAddress1() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'address1'.
getAddress2() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'address2'.
getAll() - Method in class edu.cornell.med.icb.trac.AbstractManager
 
getAll() - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Gets all the articles in the database.
getAll() - Method in interface edu.cornell.med.icb.trac.jdo.PersistenceManager
Gets all the objects of type T in the database.
getAll() - Method in class edu.cornell.med.icb.trac.user.UserManager
Gets all the users in the database.
getAllBackgroundMutations(Construct, Map<Integer, String>) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
Get all the mutations of in the background construct(s) of given construct.
getAllBindingInhibitors(Article, String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getAllIterator() - Method in class edu.cornell.med.icb.trac.AbstractManager
 
getAllIterator() - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Gets a iterator over all the articles in the database.
getAllIterator() - Method in interface edu.cornell.med.icb.trac.jdo.PersistenceManager
Gets an iterator over all the object of type T in the database.
getAllIterator() - Method in class edu.cornell.med.icb.trac.user.UserManager
Gets a iterator over all the Users in the database.
getAllLigands(Article) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getAllowsChildren() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getAllSCAMProtectors(Article, String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getAllSCAMReagents(Article) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getAllSubstrates(Article) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getAllTransportInhibitors(Article, String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getAlteredIonNames() - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Returns the value of field 'alteredIonNames'.
getAnnotatedByAuthor() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Returns the value of field 'annotatedByAuthor'.
getAnnotatedCounter() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getAnnotationStatus() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Returns the value of field 'annotationStatus'.
getAnnotationStatus() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'annotationStatus'.
getArticle(int) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method getArticle.
getArticle() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method getArticle.Returns the contents of the collection in an Array.
getArticle() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getArticle() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getArticle() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getArticle() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
Get the article currently being examined.
getArticleAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method getArticleAsReference.Returns a reference to '_articleList'.
getArticleCount() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method getArticleCount.
getAuthor(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method getAuthor.
getAuthor() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method getAuthor.Returns the contents of the collection in an Array.
getAuthorAsReference() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method getAuthorAsReference.Returns a reference to '_authorList'.
getAuthorCount() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method getAuthorCount.
getAuthors() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'authors'.
getBackgroundConstruct() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getBackgroundIdName() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Returns the value of field 'backgroundIdName'.
getBackgroundName() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getBasicInfoOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getBasicInfoState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getBinding() - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Returns the value of field 'binding'.
getBinding() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
getBindingData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getBindingInhibition(int) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method getBindingInhibition.
getBindingInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method getBindingInhibition.Returns the contents of the collection in an Array.
getBindingInhibitionAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method getBindingInhibitionAsReference.Returns a reference to '_bindingInhibitionList'.
getBindingInhibitionCount() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method getBindingInhibitionCount.
getBindingIonDependence() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Returns the value of field 'bindingIonDependence'.
getBindingOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getBindingSite() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Returns the value of field 'bindingSite'.
getBindingSiteInferenceNote() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Returns the value of field 'bindingSiteInferenceNote'.
getBindingState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getBmax() - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Returns the value of field 'bmax'.
getCallback() - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Get the callback registered for this page.
getChannelActivity() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Returns the value of field 'channelActivity'.
getChildCount() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getChildren() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
Try to sort the children constructs here.
getChoiceValue() - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Returns the value of field 'choiceValue'.
getChoiceValue() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Returns the value of field 'choiceValue'.
getChoiceValue() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Returns the value of field 'choiceValue'.
getCity() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'city'.
getComponentPath() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
getCompound() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getCompound() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getCompoundModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getCompoundName() - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Returns the value of field 'compoundName'.
getCompoundName() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Returns the value of field 'compoundName'.
getCompoundName() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Returns the value of field 'compoundName'.
getConcentration() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Returns the value of field 'concentration'.
getConstruct(int) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getConstruct.
getConstruct() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getConstruct.Returns the contents of the collection in an Array.
getConstruct() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
 
getConstructAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getConstructAsReference.Returns a reference to '_constructList'.
getConstructByID(Article, String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getConstructCount() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getConstructCount.
getConstructCounter() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getConstructDisplayName(Construct) - Static method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeFactory
 
getConstructId() - Method in class edu.cornell.med.icb.trac.article.xml.Id
Returns the value of field 'constructId'.
getConstructID() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getConstructID() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getConstructName() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getConstructs() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getConstructType() - Method in class edu.cornell.med.icb.trac.article.xml.Id
Returns the value of field 'constructType'.
getContent() - Method in class edu.cornell.med.icb.trac.article.xml.Note
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Returns the value of field 'content'.
getContent() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Returns the value of field 'content'.
getCountry() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'country'.
getCOUPLER() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Returns the value of field 'COUPLER'.
getCOUPLERItem(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method getCOUPLERItem.
getCOUPLERItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method getCOUPLERItem.Returns the contents of the collection in an Array.
getCOUPLERItemAsReference() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method getCOUPLERItemAsReference.Returns a reference to '_items'.
getCOUPLERItemCount() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method getCOUPLERItemCount.
getCreatedBy() - Method in class edu.cornell.med.icb.trac.article.xml.History
Returns the value of field 'createdBy'.
getCreatedBy() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'createdBy'.
getData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getDataModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getDataSelected() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getDate() - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Returns the value of field 'date'.
getDateSubmitted() - Method in class edu.cornell.med.icb.trac.article.xml.Note
Returns the value of field 'dateSubmitted'.
getDescription() - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Returns the value of field 'description'.
getDisabled() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'disabled'.
getDisplayName() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getDisplayName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getEachNote() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getEffect() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getEffect() - Method in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
getEffectModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getEffectName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getEffectName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getEfflux() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Returns the value of field 'efflux'.
getEmail() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'email'.
getExpandSelection() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
getExperimentalMethod() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Returns the value of field 'experimentalMethod'.
getExperimentalMethod() - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Returns the value of field 'experimentalMethod'.
getExpression() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Returns the value of field 'expression'.
getExpressionResult() - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Returns the value of field 'expressionResult'.
getExpressionSystem() - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Returns the value of field 'expressionSystem'.
getFax() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'fax'.
getFile() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
Get the url of the xml article to annotate.
getFirstName() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'firstName'.
getForeachString() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getForeachString() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getFullIndexList(String) - Static method in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
getFullTransporterName(IsBackground) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getGenericName() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Returns the value of field 'genericName'.
getGlycosylationSite() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Returns the value of field 'glycosylationSite'.
getHasBindingData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getHasChild() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
 
getHasMutation() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getHasPDF() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getHasSCAMData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getHasStructuralInferenceData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getHasTransportData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getHistory() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Returns the value of field 'history'.
getId() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Returns the value of field 'id'.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getIdentity.
getIdentity() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getIdentity.
getImageFormatType() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
Get the type of asset this will generate.
getImageFormatType() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramGIFAsset
Get the type of asset this will generate.
getImageFormatType() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramSVGAsset
Get the type of asset this will generate.
getImmediateBackground(Construct, Article) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getIndex() - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Returns the value of field 'index'.
getIndex() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getIndex() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getIndex() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getIndex() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getIndex() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getIndex() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Returns the value of field 'index'.
getIndexList() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getIndexList() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
extract the list of NSS indices, of which the aligned residues have been mutated in the literature from the annotated articles.
getIndexSet() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getIndexString() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getIndices() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Returns the value of field 'indices'.
getInhibition() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getInhibitorBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Returns the value of field 'inhibitorBinding'.
getInhibitorModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getInhibitorName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getInhibitorName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getInitIndexForeachSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getInitIndexForeachSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getInitLeuTResidueIndexForeachSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getInitLeuTResidueIndexForeachSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getInitSegmentForeachSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getInitSegmentForeachSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getInstance() - Static method in class edu.cornell.med.icb.trac.article.ArticleManager
Get an article manager.
getInstance() - Static method in class edu.cornell.med.icb.trac.TRACConfiguration
Get a TRAC Configuration.
getInstance() - Static method in class edu.cornell.med.icb.trac.user.UserManager
Get a user manager.
getInterInferenceNote() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Returns the value of field 'interInferenceNote'.
getIntermolecularInteraction() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Returns the value of field 'intermolecularInteraction'.
getIntraInferenceNote() - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Returns the value of field 'intraInferenceNote'.
getIntramolecularInteraction() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Returns the value of field 'intramolecularInteraction'.
getIsBackground() - Method in class edu.cornell.med.icb.trac.article.xml.Id
Returns the value of field 'isBackground'.
getIsBackgroundConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getIsBlankConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getIsBlankConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getIsCurator() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getIsCurator() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'isCurator'.
getIsInhibitorEffect() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getIsMutant() - Method in class edu.cornell.med.icb.trac.article.xml.Id
Returns the value of field 'isMutant'.
getIsNewInference() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Returns the value of field 'isNewInference'.
getIsNumber() - Method in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
getIsRoot() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
 
getIsSelected() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
 
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getJavaClass.
getJavaClass() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getJavaClass.
getJournal() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'journal'.
getKd() - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Returns the value of field 'kd'.
getKEYWORD() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Returns the value of field 'KEYWORD'.
getKEYWORD() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Returns the value of field 'KEYWORD'.
getKeyword() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'keyword'.
getKi() - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Returns the value of field 'ki'.
getKinetics() - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Returns the value of field 'kinetics'.
getKiorIC50() - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Returns the value of field 'kiorIC50'.
getKm() - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Returns the value of field 'km'.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.BackgroundPropertySelectionModel
Returns the label at a specifed index.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.CastorTypePropertySelectionModel
Returns the label at a specifed index.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.DynamicStringPropertySelectionModel
Labels match options.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
Returns the label at a specifed index.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Returns the label at a specifed index.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
Returns the label at a specifed index.
getLabel(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.TRACStringPropertySelectionModel
Labels match options.
getLabeledCompoundName() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Returns the value of field 'labeledCompoundName'.
getLastLogin() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'lastLogin'.
getLastmodifiedBy() - Method in class edu.cornell.med.icb.trac.article.xml.History
Returns the value of field 'lastmodifiedBy'.
getLastmodifiedBy() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'lastmodifiedBy'.
getLastmodifiedTime() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'lastmodifiedTime'.
getLastName() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'lastName'.
getLastNodeSelectedConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getLastNodeSelectedConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getLeuTIndex() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getLeuTIndex() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getLigand(int) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method getLigand.
getLigand() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method getLigand.Returns the contents of the collection in an Array.
getLigand() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
getLigand() - Method in class edu.cornell.med.icb.trac.tapestry.pages.LigandComponent
 
getLigandAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method getLigandAsReference.Returns a reference to '_ligandList'.
getLigandCount() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method getLigandCount.
getLigandOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
getLigandState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
getLink(IRequestCycle, IComponent, Object[]) - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramService
Builds a URL for a service.
getLink(IRequestCycle, IComponent, Object[]) - Method in class edu.cornell.med.icb.trac.tapestry.services.ArticleDownloadService
Builds a URL for a service.
getLink(IRequestCycle, IComponent, Object[]) - Method in class edu.cornell.med.icb.trac.tapestry.services.FileDownloadService
Builds a URL for a service.
getListener() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramArea
 
getMarkedTextTypeItem(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method getMarkedTextTypeItem.
getMarkedTextTypeItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method getMarkedTextTypeItem.Returns the contents of the collection in an Array.
getMarkedTextTypeItemAsReference() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method getMarkedTextTypeItemAsReference.Returns a reference to '_items'.
getMarkedTextTypeItemCount() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method getMarkedTextTypeItemCount.
getMuResidue() - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Returns the value of field 'muResidue'.
getMuResidue(String) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getMuResidue() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getMutanttype() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getMutanttype() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getMutanttypeList() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getMutation(int) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method getMutation.
getMutation() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method getMutation.Returns the contents of the collection in an Array.
getMutationAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method getMutationAsReference.Returns a reference to '_mutationList'.
getMutationCount() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method getMutationCount.
getMutationString() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getMutRes() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getName() - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Returns the value of field 'name'.
getName() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramService
Returns the name of the service.
getName() - Method in class edu.cornell.med.icb.trac.tapestry.services.ArticleDownloadService
Get the name of the service.
getName() - Method in class edu.cornell.med.icb.trac.tapestry.services.FileDownloadService
Get the name of the service.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getNameSpacePrefix.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getNameSpaceURI.
getNewPassword() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Get the new password of the person trying to register.
getNewPasswordConfirmation() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Get the password confirmation of the person trying to update password.
getNodeImage() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
Returns the openNodeImage.
getNoMutationString() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getNoSuchIndex() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getNoSuchIndex() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getNotBlankConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getNote(int) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getNote.
getNote() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getNote.Returns the contents of the collection in an Array.
getNote() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getNoteAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getNoteAsReference.Returns a reference to '_noteList'.
getNoteCount() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method getNoteCount.
getNss() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getNss() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getNssList() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getNssList() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
extract the list of NSS names that have been mutated in the literature from the annotated articles.
getOpenBasicInfo() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getOpenBinding() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getOpenLigand() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
getOpenSCAM() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getOpenSCAMReagent() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
getOpenStructuralInference() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getOpenSubstrate() - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
getOpenTransport() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.BackgroundPropertySelectionModel
Returns the option at a specifed index.
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.CastorTypePropertySelectionModel
Returns the option at a specifed index.
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.DynamicStringPropertySelectionModel
 
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
Returns the option at a specifed index.
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Returns the option at a specifed index.
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
Returns the option at a specifed index.
getOption(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.TRACStringPropertySelectionModel
 
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.BackgroundPropertySelectionModel
Get the total number of available options.
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.CastorTypePropertySelectionModel
Get the total number of available options.
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.DynamicStringPropertySelectionModel
 
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
Get the total number of available options.
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Get the total number of available options.
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
Get the total number of available options.
getOptionCount() - Method in class edu.cornell.med.icb.trac.tapestry.form.TRACStringPropertySelectionModel
 
getOtherConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getOtherConstructIDName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getParameters() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramArea
 
getParent() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getPartnerProtein() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Returns the value of field 'partnerProtein'.
getPartnerProteinFilename(Construct) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getPartnerResidue() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Returns the value of field 'partnerResidue'.
getPartnerResidue() - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Returns the value of field 'partnerResidue'.
getPassword() - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Get the password of the person trying to login.
getPassword() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Get the password of the person trying to log in.
getPassword() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'password'.
getPasswordConfirmation() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Get the password confirmation of the person trying to register.
getPath() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
 
getPercentage() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Returns the value of field 'percentage'.
getPercentage() - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Returns the value of field 'percentage'.
getPharmacology() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Returns the value of field 'pharmacology'.
getPharmacology() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getPharmacology() - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
getPharmacologyModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getPhenotype() - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Returns the value of field 'phenotype'.
getPhone() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'phone'.
getPhosphorylationSite() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Returns the value of field 'phosphorylationSite'.
getPmid() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Returns the value of field 'pmid'.
getPmid() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Returns the value of field 'pmid'.
getPmid() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getPmid() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
Get the pubmed id of the article to annotate.
getPMID() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'PMID'.
getPMIDList() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getPMIDsByResidueIndex(String) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Get the articles that contain the constructs, which has the input index.
getPmidSet() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getPopulateTreeScript() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataViewJS
 
getPrincipalInvestigator() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'principalInvestigator'.
getProtectable() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Returns the value of field 'protectable'.
getProtection(int) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method getProtection.
getProtection() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method getProtection.Returns the contents of the collection in an Array.
getProtection() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getProtectionAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method getProtectionAsReference.Returns a reference to '_protectionList'.
getProtectionCount() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method getProtectionCount.
getProteinSequence() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Returns the value of field 'proteinSequence'.
getPublicationType() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'publicationType'.
getPubmedFilename() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'pubmedFilename'.
getRangeScript() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getRangeScript() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getRatio() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getRatio() - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
getReactive() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Returns the value of field 'reactive'.
getReactivity() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Returns the value of field 'reactivity'.
getReactivity() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getReader(String) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getReader(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
getReagentName() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Returns the value of field 'reagentName'.
getRegistrationDate() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'registrationDate'.
getRelevantState() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Returns the value of field 'relevantState'.
getRememberUsername() - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Determine whether or not the user wants to store username in a cookie.
getRememberUsername() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Determine whether or not the user wants to store username in a cookie.
getResidue() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getResidue() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getResidue(int) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method getResidue.
getResidue() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method getResidue.Returns the contents of the collection in an Array.
getResidueAsReference() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method getResidueAsReference.Returns a reference to '_residueList'.
getResidueCount() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method getResidueCount.
getResidueIndexString() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getResidueModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getResidueModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getResidueNumber(String) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getResidueNumber(Mutation) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getResidueNumber() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Returns the value of field 'residueNumber'.
getResourceAsStream(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
Accesses the localized version of the resource (if possible) and returns it as an input stream.
getRootBackground(Construct, Article) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
getRootNode() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataViewJS
 
getRootNode() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getSaturation() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Returns the value of field 'saturation'.
getSCAM() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Returns the value of field 'SCAM'.
getSCAM() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
getSCAMData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getSCAMDeterminationApproach() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Returns the value of field 'SCAMDeterminationApproach'.
getSCAMOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getSCAMReagent(int) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method getSCAMReagent.
getSCAMReagent() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method getSCAMReagent.Returns the contents of the collection in an Array.
getSCAMReagent() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
getSCAMReagent() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
getSCAMReagent() - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
 
getSCAMReagentAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method getSCAMReagentAsReference.Returns a reference to '_SCAMReagentList'.
getSCAMReagentCount() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method getSCAMReagentCount.
getSCAMReagentOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
getSCAMReagentState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
getSCAMState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getSchema() - Method in class edu.cornell.med.icb.trac.AbstractManager
Returns the current schema in use to validate the persistent class.
getSchema() - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Returns the current schema in use to validate the XML object.
getSchemaURL() - Method in class edu.cornell.med.icb.trac.AbstractManager
Returns the current schema in use to validate the persistent class.
getSchemaURL() - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Returns the current schema in use to validate the XML object.
getScore() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'score'.
getSegment() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getSegment() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getSegment() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Returns the value of field 'segment'.
getSelectedBindingInhibition() - Method in class edu.cornell.med.icb.trac.tapestry.pages.LigandComponent
 
getSelectedLigand() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
getSelectedNode() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
getSelectedNodeStyleID() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
getSelectedNoteDate() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getSelectedPath() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
 
getSelectedPMID() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getSelectedProtection() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
getSelectedSCAMReagent() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
getSelectedSubstrate() - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
getSelectedTransportInhibition() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SubstrateComponent
 
getSendEmail() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Determine whether or not the user wants a registration confirmation email sent to their account.
getSequenceDiagram() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
Returns a sequence diagram image asset (gif, svg, etc.) based on user selection.
getSessionStateManagerBinding() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the sessionStateManagerBinding.
getSessionStoreManager() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the SessionStoreManager.
getSessionStoreManagerBinding() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the SessionStoreManagerBinding.
getShortName(String) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getSource() - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Returns the value of field 'source'.
getSource() - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Returns the value of field 'source'.
getSource() - Method in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
getSourceModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.InhibitionTypeComponent
 
getSourceProtein() - Method in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
 
getSPACE() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Returns the value of field 'SPACE'.
getSPACE() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Returns the value of field 'SPACE'.
getSpecies() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getSpecies() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getSpecies() - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
getSpeciesFromTransporter(String) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
Get all the species that map to the transporter name.
getSpeciesModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getSpeciesName() - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Returns the value of field 'speciesName'.
getSPECIESNAME() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Returns the value of field 'SPECIESNAME'.
getSPECIESNAME() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Returns the value of field 'SPECIESNAME'.
getSpeciesName() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Returns the value of field 'speciesName'.
getState() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'state'.
getStatus() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Returns the value of field 'status'.
getStructuralInference() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Returns the value of field 'structuralInference'.
getStructuralInferenceData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getStructuralInferenceOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getStructuralInferenceState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getSubmittedBy() - Method in class edu.cornell.med.icb.trac.article.xml.Note
Returns the value of field 'submittedBy'.
getSubstrate(int) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method getSubstrate.
getSubstrate() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method getSubstrate.Returns the contents of the collection in an Array.
getSubstrate() - Method in class edu.cornell.med.icb.trac.tapestry.pages.SubstrateComponent
 
getSubstrate() - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
getSubstrateAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method getSubstrateAsReference.Returns a reference to '_substrateList'.
getSubstrateBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Returns the value of field 'substrateBinding'.
getSubstrateCount() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method getSubstrateCount.
getSubstrateOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
getSubstrateState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
getSwissProtID() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Returns the value of field 'swissProtID'.
getSynonym() - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Returns the value of field 'synonym'.
getSynonym() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.SynonymsItem
Returns the value of field 'synonym'.
getSynonyms() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Returns the value of field 'synonyms'.
getSynonymsItem(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method getSynonymsItem.
getSynonymsItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method getSynonymsItem.Returns the contents of the collection in an Array.
getSynonymsItemAsReference() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method getSynonymsItemAsReference.Returns a reference to '_items'.
getSynonymsItemCount() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method getSynonymsItemCount.
getTag() - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Returns the value of field 'tag'.
getTitle() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'title'.
getTitle() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'title'.
getTotalCounter() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
Get the number of TRACAbstracts.
getTRACAbstract() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getTRACAbstract() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
Get the TRACAbstract currently being examined.
getTRACAbstract() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSetItem
Returns the value of field 'TRACAbstract'.
getTRACAbstractMap() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getTracAbstractSet() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getTRACAbstractSet() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getTRACAbstractSetFilename() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getTRACAbstractSetItem(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method getTRACAbstractSetItem.
getTRACAbstractSetItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method getTRACAbstractSetItem.Returns the contents of the collection in an Array.
getTRACAbstractSetItemAsReference() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method getTRACAbstractSetItemAsReference.Returns a reference to '_items'.
getTRACAbstractSetItemCount() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method getTRACAbstractSetItemCount.
getTransient(Serializable) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
 
getTransport() - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Returns the value of field 'transport'.
getTransport() - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
getTransportData() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getTransporter() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getTransporter() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TransportersItem
Returns the value of field 'transporter'.
getTransporter(Article, Construct) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getTransporter(String) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getTransporterFilename(Article, Construct) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getTransporterFilename(String) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
getTransporterName() - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Returns the value of field 'transporterName'.
getTransporterName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getTransporterName() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getTransporterName() - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
getTRANSPORTERNAME() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Returns the value of field 'TRANSPORTERNAME'.
getTRANSPORTERNAME() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Returns the value of field 'TRANSPORTERNAME'.
getTransporterNameModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getTransporterNameModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
getTransporterNameModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
getTransporters() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'transporters'.
getTransportersItem(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method getTransportersItem.
getTransportersItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method getTransportersItem.Returns the contents of the collection in an Array.
getTransportersItemAsReference() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method getTransportersItemAsReference.Returns a reference to '_items'.
getTransportersItemCount() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method getTransportersItemCount.
getTransporterWithoutSpeciesPropertySelectionModel(String[]) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
Gets a tapestry property selection model for transporter names.
getTransportInhibition(int) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method getTransportInhibition.
getTransportInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method getTransportInhibition.Returns the contents of the collection in an Array.
getTransportInhibitionAsReference() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method getTransportInhibitionAsReference.Returns a reference to '_transportInhibitionList'.
getTransportInhibitionCount() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method getTransportInhibitionCount.
getTransportOCImage() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getTransportState() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getTreeDataModel() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeModel
 
getTreeDeep() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
getTreeModel() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the treeModel.
getTreeModel() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeFactory
Get the TreeModel that contains the nodes to be rendered.
getTreeModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Get the TreeModel that contains the nodes to be rendered.
getTreeModelBinding() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the treeModelBinding.
getTreeRow() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
getTreeRowObject() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
getTreeSessionState() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the treeSessionState.
getTreeSessionStateMgr() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Returns the wizardSessionStateMgr.
getTreeStateListener() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
getTreeStateListener() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
getTreeStateModel() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeModel
 
getTreeView() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
getTreeViewBinding() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
Returns the treeViewBinding.
getType() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getUnalteredIonNames() - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Returns the value of field 'unalteredIonNames'.
getUniprotName() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Returns the value of field 'uniprotName'.
getUnit() - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Returns the value of field 'unit'.
getUnit() - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Returns the value of field 'unit'.
getUnit() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Returns the value of field 'unit'.
getUnit() - Method in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
getUnitModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
getUpdating() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
If true, this indicates that the user is already registered and is attempting to update their registration information.
getUptake() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Returns the value of field 'uptake'.
getUptakeIonDependence() - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Returns the value of field 'uptakeIonDependence'.
getUser() - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Get the user object of the person trying to login.
getUser() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
Gets the logged-in user, or null if the user is not logged in.
getUser(int) - Method in class edu.cornell.med.icb.trac.user.UserSet
Method getUser.
getUser() - Method in class edu.cornell.med.icb.trac.user.UserSet
Method getUser.Returns the contents of the collection in an Array.
getUserAsReference() - Method in class edu.cornell.med.icb.trac.user.UserSet
Method getUserAsReference.Returns a reference to '_userList'.
getUserByEmailAddress(String) - Method in class edu.cornell.med.icb.trac.user.UserManager
Loads a user with the specified email address.
getUserByUsername(String) - Method in class edu.cornell.med.icb.trac.user.UserManager
Loads a user with the specified user name.
getUserCount() - Method in class edu.cornell.med.icb.trac.user.UserSet
Method getUserCount.
getUsername() - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Returns the value of field 'username'.
getUsername() - Method in class edu.cornell.med.icb.trac.tapestry.Border
Gets the username of the user logged into the system.
getUsername() - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Get the username of the person trying to login.
getUsername() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getUsername() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'username'.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getValidator.
getValidator() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getValidator.
getValue() - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Returns the value of field 'value'.
getValue() - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Returns the value of field 'value'.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.BackgroundPropertySelectionModel
Returns the string value of an option at a specifed index.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.CastorTypePropertySelectionModel
Returns the string value of an option at a specifed index.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.DynamicStringPropertySelectionModel
Values are indexes into the array of options.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
Returns the string value of an option at a specifed index.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Returns the string value of an option at a specifed index.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
Returns the string value of an option at a specifed index.
getValue(int) - Method in class edu.cornell.med.icb.trac.tapestry.form.TRACStringPropertySelectionModel
Values are indexes into the array of options.
getValue() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
getVmax() - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Returns the value of field 'vmax'.
getWtRes() - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
getWtResidue() - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Returns the value of field 'wtResidue'.
getWtResidue() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getWtResiduePropertySelectionModel() - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method getXMLName.
getXMLName() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method getXMLName.
getYear() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getYear() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getYear() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Returns the value of field 'year'.
getYearList() - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
getYearList() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
getZip() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'zip'.

H

HAS_DATA - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
hasAnnotatedByAuthor() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Method hasAnnotatedByAuthor.
hasConcentration() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Method hasConcentration.
hasDisabled() - Method in class edu.cornell.med.icb.trac.user.User
Method hasDisabled.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Bmax
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.ConstructId
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.History
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Id
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Kd
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Km
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Note
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.article.xml.Vmax
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
Overwrite hashCode to match getValue().hashCode().
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.user.User
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class edu.cornell.med.icb.trac.user.UserSet
Overrides the java.lang.Object.hashCode method.
hasInhibitorBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Method hasInhibitorBinding.
hasIsCurator() - Method in class edu.cornell.med.icb.trac.user.User
Method hasIsCurator.
hasIsNewInference() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Method hasIsNewInference.
hasPDF(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
hasPmid() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method hasPmid.
hasPmid() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method hasPmid.
hasPMID() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Method hasPMID.
hasProtectable() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Method hasProtectable.
hasResidueNumber() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Method hasResidueNumber.
hasScore() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Method hasScore.
hasSubstrateBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Method hasSubstrateBinding.
hasYear() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Method hasYear.
History - Class in edu.cornell.med.icb.trac.article.xml
Class History.
History() - Constructor for class edu.cornell.med.icb.trac.article.xml.History
 
HistoryDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class HistoryDescriptor.
HistoryDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
 
HomePage - Class in edu.cornell.med.icb.trac.tapestry.pages
Backend code for the TRAC home page.
HomePage() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.HomePage
 

I

Id - Class in edu.cornell.med.icb.trac.article.xml
identifies a construct, which can be both a background and a mutant
Id() - Constructor for class edu.cornell.med.icb.trac.article.xml.Id
 
IdDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IdDescriptor.
IdDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
 
IdType - Class in edu.cornell.med.icb.trac.article.xml
Class IdType.
IdType() - Constructor for class edu.cornell.med.icb.trac.article.xml.IdType
 
IdTypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IdTypeDescriptor.
IdTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
 
INCREASED - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
INDEX_NUMBER - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
total number of possible residue index.
IndexCalculator - Class in edu.cornell.med.icb.trac.alignment
Class used to calculate the index position, given the transporter sequence and residue number
indexCalculatorLink(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.HomePage
 
Indices - Class in edu.cornell.med.icb.trac.transporter.xml
Class Indices.
Indices() - Constructor for class edu.cornell.med.icb.trac.transporter.xml.Indices
 
IndicesDescriptor - Class in edu.cornell.med.icb.trac.transporter.xml.descriptors
Class IndicesDescriptor.
IndicesDescriptor() - Constructor for class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
 
InferenceNoteType - Class in edu.cornell.med.icb.trac.article.xml
Class InferenceNoteType.
InferenceNoteType() - Constructor for class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
 
InferenceNoteTypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class InferenceNoteTypeDescriptor.
InferenceNoteTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
 
INHIBITION - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
INHIBITION - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
InhibitionType - Class in edu.cornell.med.icb.trac.article.xml
Class InhibitionType.
InhibitionType() - Constructor for class edu.cornell.med.icb.trac.article.xml.InhibitionType
 
InhibitionTypeComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
InhibitionTypeComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.InhibitionTypeComponent
 
InhibitionTypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class InhibitionTypeDescriptor.
InhibitionTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
 
init() - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
init() - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
initialize() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
initialize() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
initMarshaller(Writer) - Method in class edu.cornell.med.icb.trac.AbstractManager
Initialize the marshalling writer.
insert(IMutableTreeNode) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
insert(Collection) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
InterInferenceNote - Class in edu.cornell.med.icb.trac.article.xml
Class InterInferenceNote.
InterInferenceNote() - Constructor for class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
 
InterInferenceNoteDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class InterInferenceNoteDescriptor.
InterInferenceNoteDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
 
IntermolecularInteraction - Class in edu.cornell.med.icb.trac.article.xml
include both dimerization and protein-protein interactions
IntermolecularInteraction() - Constructor for class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
 
IntermolecularInteractionDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IntermolecularInteractionDescriptor.
IntermolecularInteractionDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
 
IntraInferenceNote - Class in edu.cornell.med.icb.trac.article.xml
Class IntraInferenceNote.
IntraInferenceNote() - Constructor for class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
 
IntraInferenceNoteDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IntraInferenceNoteDescriptor.
IntraInferenceNoteDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
 
IntramolecularInteraction - Class in edu.cornell.med.icb.trac.article.xml
may be combined with intermolecularInteraction, but we can validate the entered residue information is correct--it will be very difficult for other proteins.
IntramolecularInteraction() - Constructor for class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
 
IntramolecularInteractionDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IntramolecularInteractionDescriptor.
IntramolecularInteractionDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
 
IonDependenceType - Class in edu.cornell.med.icb.trac.article.xml
Class IonDependenceType.
IonDependenceType() - Constructor for class edu.cornell.med.icb.trac.article.xml.IonDependenceType
 
IonDependenceTypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IonDependenceTypeDescriptor.
IonDependenceTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
 
ionName - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
isAllMutantConstruct(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
to verify if the construct is either the ending mutant or middle "both" construct
isAnnotatedByAuthor() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Returns the value of field 'annotatedByAuthor'.
IsBackground - Class in edu.cornell.med.icb.trac.article.xml
is a background construct for this article, if it is also a mutant, then do not enter the SwissProtId information.
IsBackground() - Constructor for class edu.cornell.med.icb.trac.article.xml.IsBackground
 
isBackgroundConstruct(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
isBackgroundConstruct() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
IsBackgroundDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IsBackgroundDescriptor.
IsBackgroundDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
 
isBlankConstruct(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
isBothConstruct(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
isCurator(User) - Static method in class edu.cornell.med.icb.trac.user.UserUtils
 
isDisabled() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'disabled'.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.AnnotationStatusDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ArticleSetDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingInhibitionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingIonDependenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BindingSiteInferenceNoteDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.BmaxDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ConstructIdDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.CreatedByDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.EffectTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ExpressionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.HistoryDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IdTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InferenceNoteTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InhibitionTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.InterInferenceNoteDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntermolecularInteractionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntraInferenceNoteDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IntramolecularInteractionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IonDependenceTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsBackgroundDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AbstractTextDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.AuthorsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.COUPLERItemDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.IndicesDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
Method isElementDefinition.
isEmailRegistered(String) - Method in class edu.cornell.med.icb.trac.user.UserManager
Indicates that the email address has already been registered in the database.
isInhibitorBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Returns the value of field 'inhibitorBinding'.
isIsCurator() - Method in class edu.cornell.med.icb.trac.user.User
Returns the value of field 'isCurator'.
isIsNewInference() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Returns the value of field 'isNewInference'.
isLeaf() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
IsMutant - Class in edu.cornell.med.icb.trac.article.xml
is a mutant construct for this article
IsMutant() - Constructor for class edu.cornell.med.icb.trac.article.xml.IsMutant
 
isMutantConstruct(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
IsMutantDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class IsMutantDescriptor.
IsMutantDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.IsMutantDescriptor
 
isNewVisit() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
isPasswordError() - Method in exception edu.cornell.med.icb.trac.user.LoginException
Returns true if the error is related to the password.
isProtectable() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Returns the value of field 'protectable'.
isRootNode(String) - Static method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeFactory
 
isSelectData() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
isSingleMutantConstruct(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
isStateful() - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramArea
Invoked by the direct service to query the component as to whether it is stateful.
isSubstrateBinding() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Returns the value of field 'substrateBinding'.
isTM(String) - Static method in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
isUniqueKeyExpanded(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
isUserLoggedIn() - Method in class edu.cornell.med.icb.trac.tapestry.Border
Indicates that a user is logged into the system.
isUserLoggedIn() - Method in class edu.cornell.med.icb.trac.tapestry.Visit
Indicates that a user is currently logged into the system.
isUsernameRegistered(String) - Method in class edu.cornell.med.icb.trac.user.UserManager
Indicates that the username has already been registered in the database.
isValid(Article) - Static method in class edu.cornell.med.icb.trac.article.ArticleManager
Indicates whether or not an article is in a valid state.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Bmax
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.ConstructId
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.History
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Id
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Kd
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Km
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Note
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.article.xml.Vmax
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.user.User
Method isValid.
isValid() - Method in class edu.cornell.med.icb.trac.user.UserSet
Method isValid.
iterateArticle() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method iterateArticle.
iterateAuthor() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method iterateAuthor.
iterateBindingInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method iterateBindingInhibition.
iterateConstruct() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method iterateConstruct.
iterateCOUPLERItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method iterateCOUPLERItem.
iterateLigand() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method iterateLigand.
iterateMarkedTextTypeItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method iterateMarkedTextTypeItem.
iterateMutation() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method iterateMutation.
iterateNote() - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method iterateNote.
iterateProtection() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method iterateProtection.
iterateResidue() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method iterateResidue.
iterateSCAMReagent() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method iterateSCAMReagent.
iterateSubstrate() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method iterateSubstrate.
iterateSynonymsItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method iterateSynonymsItem.
iterateTRACAbstractSetItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method iterateTRACAbstractSetItem.
iterateTransportersItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method iterateTransportersItem.
iterateTransportInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method iterateTransportInhibition.
iterateUser() - Method in class edu.cornell.med.icb.trac.user.UserSet
Method iterateUser.

J

JmolViewerPage - Class in edu.cornell.med.icb.trac.tapestry.pages
Class to handle pdbfile web page submission.
JmolViewerPage() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 

K

Kd - Class in edu.cornell.med.icb.trac.article.xml
Class Kd.
Kd() - Constructor for class edu.cornell.med.icb.trac.article.xml.Kd
 
KD - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
KD_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
KdDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class KdDescriptor.
KdDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.KdDescriptor
 
Ki - Class in edu.cornell.med.icb.trac.article.xml
Class Ki.
Ki() - Constructor for class edu.cornell.med.icb.trac.article.xml.Ki
 
KI_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
KiDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class KiDescriptor.
KiDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.KiDescriptor
 
Kinetics - Class in edu.cornell.med.icb.trac.article.xml
Class Kinetics.
Kinetics() - Constructor for class edu.cornell.med.icb.trac.article.xml.Kinetics
 
KineticsDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class KineticsDescriptor.
KineticsDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.KineticsDescriptor
 
KIORIC50_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
KiUnit - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
Km - Class in edu.cornell.med.icb.trac.article.xml
Class Km.
Km() - Constructor for class edu.cornell.med.icb.trac.article.xml.Km
 
KM - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
KM_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
KmDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class KmDescriptor.
KmDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.KmDescriptor
 

L

LastmodifiedBy - Class in edu.cornell.med.icb.trac.article.xml
Class LastmodifiedBy.
LastmodifiedBy() - Constructor for class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
 
LastmodifiedByDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class LastmodifiedByDescriptor.
LastmodifiedByDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.LastmodifiedByDescriptor
 
Ligand - Class in edu.cornell.med.icb.trac.article.xml
Class Ligand.
Ligand() - Constructor for class edu.cornell.med.icb.trac.article.xml.Ligand
 
LigandComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
LigandComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.LigandComponent
 
LigandDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class LigandDescriptor.
LigandDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.LigandDescriptor
 
ligandOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
load(long) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Load the article from the datastore.
login(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.Border
Invokes the login page if a user is not already logged in.
login(String, String) - Method in class edu.cornell.med.icb.trac.user.UserManager
Validates that the username and password combination matches a user entry within the database.
LoginException - Exception in edu.cornell.med.icb.trac.user
Exception thrown on a login failure.
LoginException(String, boolean) - Constructor for exception edu.cornell.med.icb.trac.user.LoginException
Constructs a new exception with the specified detail message.
LoginPage - Class in edu.cornell.med.icb.trac.tapestry.user
Allows the user to login, by providing username and password.
LoginPage() - Constructor for class edu.cornell.med.icb.trac.tapestry.user.LoginPage
 
loginUser(User, boolean, IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Sets up the User as the logged in user, creates a cookie for their username (for subsequent logins), and redirects to the appropriate page.
logout(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.Border
Invokes the logout cycle if a user is already logged in.
logout(String) - Method in class edu.cornell.med.icb.trac.user.UserManager
Logs the user out of the system.
logout() - Method in class edu.cornell.med.icb.trac.user.UserManager
Logs the user out of the system.

M

MAIL_SMTP_BCC - Static variable in class edu.cornell.med.icb.trac.TRACConfiguration
Property name of the user to bcc when sending email.
MAIL_SMTP_FROM - Static variable in class edu.cornell.med.icb.trac.TRACConfiguration
Property name of the user to use when sending email.
MAIL_SMTP_FROM_NAME - Static variable in class edu.cornell.med.icb.trac.TRACConfiguration
Property name of the name of the user to use when sending email.
MAIL_SMTP_HOST - Static variable in class edu.cornell.med.icb.trac.TRACConfiguration
Property name of the smtp host to use when sending email.
main(String[]) - Static method in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
main(String[]) - Static method in class edu.cornell.med.icb.trac.article.ArticleManager
 
main(String[]) - Static method in class edu.cornell.med.icb.trac.constraints.ConstraintsGenerator
 
main(String[]) - Static method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
main(String[]) - Static method in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
main(String[]) - Static method in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
main(String[]) - Static method in class edu.cornell.med.icb.trac.user.UserManager
 
MarkedTextType - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class MarkedTextType.
MarkedTextType() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
MarkedTextTypeDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class MarkedTextTypeDescriptor.
MarkedTextTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeDescriptor
 
MarkedTextTypeItem - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class MarkedTextTypeItem.
MarkedTextTypeItem() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
 
MarkedTextTypeItemDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class MarkedTextTypeItemDescriptor.
MarkedTextTypeItemDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.MarkedTextTypeItemDescriptor
 
marshal(Writer, boolean) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Writes all the articles in the database to the given writer object.
marshal(Writer, ArticleSet, boolean) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Writes all the articles in the database to the given writer object.
marshal(long, Writer) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Writes an article to the given writer object.
marshal(Article, Writer) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Writes an article to the given writer object.
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Bmax
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Bmax
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.ConstructId
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.ConstructId
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Expression
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Expression
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.History
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.History
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Id
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Id
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Kd
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Kd
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Ki
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Ki
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Km
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Km
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Note
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Note
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Protection
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Protection
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.article.xml.Vmax
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.article.xml.Vmax
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
 
marshal(Writer) - Method in class edu.cornell.med.icb.trac.user.User
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.user.User
 
marshal(Writer, boolean) - Method in class edu.cornell.med.icb.trac.user.UserManager
Writes all the users in the database to the given writer object.
marshal(Writer) - Method in class edu.cornell.med.icb.trac.user.UserSet
 
marshal(ContentHandler) - Method in class edu.cornell.med.icb.trac.user.UserSet
 
marshal(T, Writer) - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Writes an object to the given writer object as XML.
mutantBackgroundDelimiter - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
Mutation - Class in edu.cornell.med.icb.trac.article.xml
Class Mutation.
Mutation() - Constructor for class edu.cornell.med.icb.trac.article.xml.Mutation
 
mutationDelimiter - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
MutationDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class MutationDescriptor.
MutationDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.MutationDescriptor
 

N

NO_DATA - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
NO_TAG - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
NOCHANGE - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
nodeChange(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
Called when a node in the tree is clicked by the user.
nodeSelect(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeNodeView
Called when a node in the tree is clicked by the user.
noMutationString - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
NOTDETERMINED - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
Note - Class in edu.cornell.med.icb.trac.article.xml
Notes regarding articles
Note() - Constructor for class edu.cornell.med.icb.trac.article.xml.Note
 
NoteDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class NoteDescriptor.
NoteDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.NoteDescriptor
 
NOTREACTIVE - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 

P

pageBeginRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
Called before the page is rendered.
pageBeginRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Called before the page is rendered.
pageBeginRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
pageBeginRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
pageBeginRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
Called before the page is rendered.
pageBeginRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Sets the username from a cookie if available before rendering the page.
pageDetached(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
pageEndRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Called when the page is finished rendering.
pageEndRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
Called when the page is finished rendering.
pageEndRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
Called when the page is finished rendering.
pageEndRender(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
Called when the page is finished rendering.
pageValidate(PageEvent) - Method in class edu.cornell.med.icb.trac.tapestry.ProtectedBasePage
Checks if the user is logged in.
parseAllArticles() - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
 
parseArticle(Article) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Parse the given article to extract a list of mutants.
parseXML(File) - Static method in class edu.cornell.med.icb.trac.constraints.ConstraintsGenerator
Unmarshals and parses the XML file containing the Article, and calls writeConstraint for each construct is the article that has an IntramolecularInteraction.
partnerProtein - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
PersistenceManager<T> - Interface in edu.cornell.med.icb.trac.jdo
Interface for managing persistent objects.
Pharmacology - Class in edu.cornell.med.icb.trac.article.xml
Class Pharmacology.
Pharmacology() - Constructor for class edu.cornell.med.icb.trac.article.xml.Pharmacology
 
pharmacology - Variable in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
 
PharmacologyDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class PharmacologyDescriptor.
PharmacologyDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.PharmacologyDescriptor
 
Phenotype - Class in edu.cornell.med.icb.trac.article.xml
Class Phenotype.
Phenotype() - Constructor for class edu.cornell.med.icb.trac.article.xml.Phenotype
 
PhenotypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class PhenotypeDescriptor.
PhenotypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.PhenotypeDescriptor
 
pm - Variable in class edu.cornell.med.icb.trac.AbstractManager
JDO persistence manager in use.
pmf - Variable in class edu.cornell.med.icb.trac.AbstractManager
JDO persistence manager factory in use.
pmidSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
User submitted a pubmed id of an article to annotate.
POTENTIATION - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
ProtectedBasePage - Class in edu.cornell.med.icb.trac.tapestry
Base page used for pages that should be protected by the LoginPage page.
ProtectedBasePage() - Constructor for class edu.cornell.med.icb.trac.tapestry.ProtectedBasePage
 
Protection - Class in edu.cornell.med.icb.trac.article.xml
Class Protection.
Protection() - Constructor for class edu.cornell.med.icb.trac.article.xml.Protection
 
PROTECTION - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
ProtectionDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ProtectionDescriptor.
ProtectionDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ProtectionDescriptor
 

Q

queryLink(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.HomePage
 
QueryPage - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
QueryPage() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 

R

ratio - Variable in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
 
RbdgXmlWriter - Class in edu.cornell.med.icb.trac.rbdg
 
Reactivity - Class in edu.cornell.med.icb.trac.article.xml
Class Reactivity.
Reactivity() - Constructor for class edu.cornell.med.icb.trac.article.xml.Reactivity
 
REACTIVITY - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
REACTIVITY_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
ReactivityDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class ReactivityDescriptor.
ReactivityDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.ReactivityDescriptor
 
readAlignmentBoundaries(String) - Static method in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
RecordType - Class in edu.cornell.med.icb.trac.article.xml
Class RecordType.
RecordType() - Constructor for class edu.cornell.med.icb.trac.article.xml.RecordType
 
RecordTypeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class RecordTypeDescriptor.
RecordTypeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.RecordTypeDescriptor
 
REFERENCE_NAME - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
The reference sequence name.
refTransporter - Static variable in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
RegisterPage - Class in edu.cornell.med.icb.trac.tapestry.user
Invoked from the LoginPage page, to allow a user to register into the system on-the-fly.
RegisterPage() - Constructor for class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
 
relevantState - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
remove(IMutableTreeNode) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
removeAllArticle() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
removeAllAuthor() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
removeAllBindingInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
removeAllConstruct() - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
removeAllCOUPLERItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
removeAllLigand() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
removeAllMarkedTextTypeItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
removeAllMutation() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
removeAllNote() - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
removeAllProtection() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
removeAllResidue() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
removeAllSCAMReagent() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
removeAllSubstrate() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
removeAllSynonymsItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
removeAllTRACAbstractSetItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
removeAllTransportersItem() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
removeAllTransportInhibition() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
removeAllUser() - Method in class edu.cornell.med.icb.trac.user.UserSet
 
removeArticle(Article) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method removeArticle.
removeArticleAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method removeArticleAt.
removeAuthor(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method removeAuthor.
removeAuthorAt(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method removeAuthorAt.
removeBindingInhibition(BindingInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method removeBindingInhibition.
removeBindingInhibitionAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method removeBindingInhibitionAt.
removeConstruct(Construct) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method removeConstruct.
removeConstructAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method removeConstructAt.
removeConstructSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
removeCOUPLERItem(COUPLERItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method removeCOUPLERItem.
removeCOUPLERItemAt(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method removeCOUPLERItemAt.
removeFromParent() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
removeInhibitionSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.LigandComponent
 
removeInhibitionSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.SubstrateComponent
 
removeLigand(Ligand) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method removeLigand.
removeLigandAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Method removeLigandAt.
removeLigandSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BindingComponent
 
removeMarkedTextTypeItem(MarkedTextTypeItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method removeMarkedTextTypeItem.
removeMarkedTextTypeItemAt(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method removeMarkedTextTypeItemAt.
removeMutation(Mutation) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method removeMutation.
removeMutationAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method removeMutationAt.
removeNote(Note) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method removeNote.
removeNoteAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Method removeNoteAt.
removeProtection(Protection) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method removeProtection.
removeProtectionAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method removeProtectionAt.
removeProtectionSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
removeResidue(Residue) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method removeResidue.
removeResidueAt(int) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method removeResidueAt.
removeSCAMReagent(SCAMReagent) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method removeSCAMReagent.
removeSCAMReagentAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method removeSCAMReagentAt.
removeSCAMReagentSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
removeSubstrate(Substrate) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method removeSubstrate.
removeSubstrateAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Method removeSubstrateAt.
removeSubstrateSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
removeSynonymsItem(SynonymsItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method removeSynonymsItem.
removeSynonymsItemAt(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method removeSynonymsItemAt.
removeTRACAbstractSetItem(TRACAbstractSetItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method removeTRACAbstractSetItem.
removeTRACAbstractSetItemAt(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method removeTRACAbstractSetItemAt.
removeTransportersItem(TransportersItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method removeTransportersItem.
removeTransportersItemAt(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method removeTransportersItemAt.
removeTransportInhibition(TransportInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method removeTransportInhibition.
removeTransportInhibitionAt(int) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method removeTransportInhibitionAt.
removeUser(User) - Method in class edu.cornell.med.icb.trac.user.UserSet
Method removeUser.
removeUserAt(int) - Method in class edu.cornell.med.icb.trac.user.UserSet
Method removeUserAt.
renderComponent(IMarkupWriter, IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
renderComponent(IMarkupWriter, IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
renderComponent(IMarkupWriter, IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramArea
Invoked to actually render the component (with any parameter values already set).
resetState() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
resetState() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
resetTree - Variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
Residue - Class in edu.cornell.med.icb.trac.transporter.xml
Class Residue.
Residue() - Constructor for class edu.cornell.med.icb.trac.transporter.xml.Residue
 
ResidueDescriptor - Class in edu.cornell.med.icb.trac.transporter.xml.descriptors
Class ResidueDescriptor.
ResidueDescriptor() - Constructor for class edu.cornell.med.icb.trac.transporter.xml.descriptors.ResidueDescriptor
 
ResiduePropertySelectionModel - Class in edu.cornell.med.icb.trac.tapestry.form
Property selection model based on basic residue types and/or protein sequences.
ResiduePropertySelectionModel() - Constructor for class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Creates a new property selection model using basic residue types.
ResiduePropertySelectionModel(Transporter) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
 
ResiduePropertySelectionModel(Article, Construct, boolean) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Creates a new property selection model based on the constructs in an article object.
returnwosaveSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Return without save.
rollbackIfActive() - Method in class edu.cornell.med.icb.trac.AbstractManager
This aborts the current transaction only when the transaction is active.

S

SAME_AS_ITS_BACKGROUND - Static variable in class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
 
Saturation - Class in edu.cornell.med.icb.trac.article.xml
Class Saturation.
Saturation() - Constructor for class edu.cornell.med.icb.trac.article.xml.Saturation
 
SaturationDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class SaturationDescriptor.
SaturationDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.SaturationDescriptor
 
savereturnSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Listener for the form submission.
saveSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
Listener for the form submission.
SCAM - Class in edu.cornell.med.icb.trac.article.xml
Class SCAM.
SCAM() - Constructor for class edu.cornell.med.icb.trac.article.xml.SCAM
 
SCAM - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
SCAMComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
SCAMComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
SCAMDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class SCAMDescriptor.
SCAMDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMDescriptor
 
SCAMDeterminationApproach - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
SCAMMTS_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
SCAMOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
SCAMReagent - Class in edu.cornell.med.icb.trac.article.xml
Class SCAMReagent.
SCAMReagent() - Constructor for class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
SCAMReagentComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
SCAMReagentComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.SCAMReagentComponent
 
SCAMReagentDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class SCAMReagentDescriptor.
SCAMReagentDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.SCAMReagentDescriptor
 
SCAMReagentName - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
SCAMReagentOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.SCAMComponent
 
schema - Variable in class edu.cornell.med.icb.trac.AbstractManager
XML schema used to validate the persistent class.
schemaListsDir - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
searchSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
searchSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
SEGMENT_NUMBER - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
total number of segments.
segmentBoundaries - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
segmentNames - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
selectDataSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
selectSubmit(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
sendEmail(String, String, String, String, String) - Static method in class edu.cornell.med.icb.trac.user.UserUtils
Sends an email message to the specified recipient.
SequenceDiagramArea - Class in edu.cornell.med.icb.trac.tapestry.rbdg
A component used for image maps associated with sequence diagrams.
SequenceDiagramArea() - Constructor for class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramArea
 
SequenceDiagramComponent - Interface in edu.cornell.med.icb.trac.tapestry.rbdg
Describes a IComponent that is capable of embedding an AbstractSequenceDiagramAsset.
SequenceDiagramGIFAsset - Class in edu.cornell.med.icb.trac.tapestry.rbdg
An asset used to display sequence diagrams generated by RbDg in GIF format.
SequenceDiagramGIFAsset(IRequestCycle, SequenceDiagramComponent) - Constructor for class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramGIFAsset
 
sequenceDiagramProvider - Variable in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
The component that will hold the diagram.
sequenceDiagramService - Variable in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
The tapestry service that will do the work of generating the diagram.
SequenceDiagramService - Class in edu.cornell.med.icb.trac.tapestry.rbdg
Service that provides an image generated by rbdg.
SequenceDiagramService() - Constructor for class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramService
Create a new diagram service.
SequenceDiagramSVGAsset - Class in edu.cornell.med.icb.trac.tapestry.rbdg
An asset used to display sequence diagrams generated by RbDg in SVG format.
SequenceDiagramSVGAsset(IRequestCycle, SequenceDiagramComponent) - Constructor for class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramSVGAsset
 
service(IEngineServiceView, IRequestCycle, ResponseOutputStream) - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramService
Perform the service, interpreting the URL (from the HttpServletRequest) responding appropriately, and rendering a result page.
service(IEngineServiceView, IRequestCycle, ResponseOutputStream) - Method in class edu.cornell.med.icb.trac.tapestry.services.ArticleDownloadService
Writes the article information to the response output steam as xml.
service(IEngineServiceView, IRequestCycle, ResponseOutputStream) - Method in class edu.cornell.med.icb.trac.tapestry.services.FileDownloadService
Writes the specified file contents to the response output steam.
setAbstractText(AbstractText) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'abstractText'.
setAddress1(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'address1'.
setAddress2(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'address2'.
setAlteredIonNames(String) - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Sets the value of field 'alteredIonNames'.
setAnnotatedByAuthor(boolean) - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Sets the value of field 'annotatedByAuthor'.
setAnnotationStatus(AnnotationStatus) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Sets the value of field 'annotationStatus'.
setAnnotationStatus(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'annotationStatus'.
setArticle(int, Article) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
setArticle(Article[]) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
setArticle(List<Article>) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Sets the value of '_articleList' by copying the given Vector.
setArticle(Article) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setArticle(Article) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
Set the article currently being examined.
setArticleAsReference(List<Article>) - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Deprecated.  
setAuthor(int, String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
setAuthor(String[]) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
setAuthor(List<String>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Sets the value of '_authorList' by copying the given Vector.
setAuthorAsReference(List<String>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Deprecated.  
setAuthors(Authors) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'authors'.
setBackgroundConstruct(Construct) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setBackgroundIdName(String) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Sets the value of field 'backgroundIdName'.
setBackgroundName(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setBasicInfoState(Set<String>) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setBinding(Binding) - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Sets the value of field 'binding'.
setBindingData(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setBindingInhibition(int, BindingInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
setBindingInhibition(BindingInhibition[]) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
setBindingInhibition(List<BindingInhibition>) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Sets the value of '_bindingInhibitionList' by copying the given Vector.
setBindingInhibitionAsReference(List<BindingInhibition>) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Deprecated.  
setBindingIonDependence(BindingIonDependence) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Sets the value of field 'bindingIonDependence'.
setBindingSite(BindingSite) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Sets the value of field 'bindingSite'.
setBindingSiteInferenceNote(BindingSiteInferenceNote) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Sets the value of field 'bindingSiteInferenceNote'.
setBindingState(Set<String>) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setBmax(Bmax) - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Sets the value of field 'bmax'.
setBothType(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
setCallback(ICallback) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Set the callback for this page.
setChannelActivity(String) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Sets the value of field 'channelActivity'.
setCity(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'city'.
setCompoundName(String) - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Sets the value of field 'compoundName'.
setCompoundName(String) - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Sets the value of field 'compoundName'.
setCompoundName(String) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Sets the value of field 'compoundName'.
setConcentration(float) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Sets the value of field 'concentration'.
setConstruct(int, Construct) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
setConstruct(Construct[]) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
setConstruct(List<Construct>) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Sets the value of '_constructList' by copying the given Vector.
setConstruct(Construct) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setConstruct(Construct) - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
 
setConstructAsReference(List<Construct>) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Deprecated.  
setConstructId(ConstructId) - Method in class edu.cornell.med.icb.trac.article.xml.Id
Sets the value of field 'constructId'.
setConstructID(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setConstructName(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setConstructType(String) - Method in class edu.cornell.med.icb.trac.article.xml.Id
Sets the value of field 'constructType'.
setContent(String) - Method in class edu.cornell.med.icb.trac.article.xml.Note
Sets the value of field 'content'.
setContent(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Sets the value of field 'content'.
setContent(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Sets the value of field 'content'.
setCountry(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'country'.
setCOUPLER(COUPLER) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Sets the value of field 'COUPLER'.
setCOUPLERItem(int, COUPLERItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
setCOUPLERItem(COUPLERItem[]) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
setCOUPLERItem(List<COUPLERItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Sets the value of '_items' by copying the given Vector.
setCOUPLERItemAsReference(List<COUPLERItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Deprecated.  
setCreatedBy(CreatedBy) - Method in class edu.cornell.med.icb.trac.article.xml.History
Sets the value of field 'createdBy'.
setCreatedBy(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'createdBy'.
setData(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setDate(Date) - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Sets the value of field 'date'.
setDateSubmitted(Date) - Method in class edu.cornell.med.icb.trac.article.xml.Note
Sets the value of field 'dateSubmitted'.
setDescription(String) - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Sets the value of field 'description'.
setDisabled(boolean) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'disabled'.
setEachNote(Note) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setEffect(EffectType) - Method in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
setEfflux(String) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Sets the value of field 'efflux'.
setEmail(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'email'.
setExperimentalMethod(String) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Sets the value of field 'experimentalMethod'.
setExperimentalMethod(String) - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Sets the value of field 'experimentalMethod'.
setExpression(Expression) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Sets the value of field 'expression'.
setExpressionResult(String) - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Sets the value of field 'expressionResult'.
setExpressionSystem(String) - Method in class edu.cornell.med.icb.trac.article.xml.Expression
Sets the value of field 'expressionSystem'.
setFax(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'fax'.
setFile(IUploadFile) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
Set the url of the xml article to annotate.
setFirstName(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'firstName'.
setGenericName(String) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Sets the value of field 'genericName'.
setGlycosylationSite(Object) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Sets the value of field 'glycosylationSite'.
setHasPDF(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setHistory(History) - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Sets the value of field 'history'.
setId(Id) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Sets the value of field 'id'.
setIndex(Article) - Method in class edu.cornell.med.icb.trac.article.ArticleConverter
 
setIndex(String) - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Sets the value of field 'index'.
setIndex(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setIndex(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
setIndex(String) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setIndex(String) - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Sets the value of field 'index'.
setIndices(Indices) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Sets the value of field 'indices'.
setInhibitorBinding(boolean) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Sets the value of field 'inhibitorBinding'.
setInterInferenceNote(InterInferenceNote) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Sets the value of field 'interInferenceNote'.
setIntermolecularInteraction(IntermolecularInteraction) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Sets the value of field 'intermolecularInteraction'.
setIntraInferenceNote(IntraInferenceNote) - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Sets the value of field 'intraInferenceNote'.
setIntramolecularInteraction(IntramolecularInteraction) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Sets the value of field 'intramolecularInteraction'.
setIsBackground(IsBackground) - Method in class edu.cornell.med.icb.trac.article.xml.Id
Sets the value of field 'isBackground'.
setIsCurator(boolean) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'isCurator'.
setIsMutant(IsMutant) - Method in class edu.cornell.med.icb.trac.article.xml.Id
Sets the value of field 'isMutant'.
setIsNewInference(boolean) - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Sets the value of field 'isNewInference'.
setJournal(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'journal'.
setKd(Kd) - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
Sets the value of field 'kd'.
setKEYWORD(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Sets the value of field 'KEYWORD'.
setKEYWORD(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Sets the value of field 'KEYWORD'.
setKeyword(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'keyword'.
setKi(Ki) - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Sets the value of field 'ki'.
setKinetics(Kinetics) - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Sets the value of field 'kinetics'.
setKiorIC50(String) - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
Sets the value of field 'kiorIC50'.
setKm(Km) - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Sets the value of field 'km'.
setLabeledCompoundName(String) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Sets the value of field 'labeledCompoundName'.
setLastLogin(Date) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'lastLogin'.
setLastmodifiedBy(LastmodifiedBy) - Method in class edu.cornell.med.icb.trac.article.xml.History
Sets the value of field 'lastmodifiedBy'.
setLastmodifiedBy(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'lastmodifiedBy'.
setLastmodifiedTime(Date) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'lastmodifiedTime'.
setLastName(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'lastName'.
setLastNodeSelectedConstruct(Construct) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setLastNodeSelectedConstruct(Construct) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setLigand(int, Ligand) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
setLigand(Ligand[]) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
setLigand(List<Ligand>) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Sets the value of '_ligandList' by copying the given Vector.
setLigandAsReference(List<Ligand>) - Method in class edu.cornell.med.icb.trac.article.xml.Binding
Deprecated.  
setMarkedTextTypeItem(int, MarkedTextTypeItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
setMarkedTextTypeItem(MarkedTextTypeItem[]) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
setMarkedTextTypeItem(List<MarkedTextTypeItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Sets the value of '_items' by copying the given Vector.
setMarkedTextTypeItemAsReference(List<MarkedTextTypeItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Deprecated.  
setMuResidue(String) - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Sets the value of field 'muResidue'.
setMuResidue(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
setMutantType(Construct) - Static method in class edu.cornell.med.icb.trac.article.ArticleUtils
 
setMutanttype(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
setMutanttype(String) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setMutation(int, Mutation) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
setMutation(Mutation[]) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
setMutation(List<Mutation>) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Sets the value of '_mutationList' by copying the given Vector.
setMutationAsReference(List<Mutation>) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Deprecated.  
setMutRes(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setName(String) - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Sets the value of field 'name'.
setNewPassword(String) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set the new password of the person trying to register.
setNewPasswordConfirmation(String) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set the password confirmation of the person trying to update password.
setNewVisit(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setNoSuchIndex(String) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setNote(int, Note) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
setNote(Note[]) - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
setNote(List<Note>) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Sets the value of '_noteList' by copying the given Vector.
setNote(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setNoteAsReference(List<Note>) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Deprecated.  
setNss(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
setNss(String) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setParent(IMutableTreeNode) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
setPartnerProtein(String) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Sets the value of field 'partnerProtein'.
setPartnerResidue(String) - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Sets the value of field 'partnerResidue'.
setPartnerResidue(String) - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Sets the value of field 'partnerResidue'.
setPassword(String) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Set the password of the person trying to login.
setPassword(String) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set the password of the person trying to log in.
setPassword(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'password'.
setPasswordConfirmation(String) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set the password confirmation of the person trying to register.
setPercentage(String) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Sets the value of field 'percentage'.
setPercentage(String) - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Sets the value of field 'percentage'.
setPharmacology(Pharmacology) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Sets the value of field 'pharmacology'.
setPharmacology(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
setPharmacology(String) - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
setPhenotype(Phenotype) - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Sets the value of field 'phenotype'.
setPhone(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'phone'.
setPhosphorylationSite(Object) - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Sets the value of field 'phosphorylationSite'.
setPmid(long) - Method in class edu.cornell.med.icb.trac.article.xml.Article
Sets the value of field 'pmid'.
setPmid(long) - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Sets the value of field 'pmid'.
setPmid(long) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setPmid(long) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
Set the pubmed id of the article to annotate.
setPMID(long) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'PMID'.
setPmidSet(Set<Long>) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setPrincipalInvestigator(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'principalInvestigator'.
setProtectable(boolean) - Method in class edu.cornell.med.icb.trac.article.xml.Protection
Sets the value of field 'protectable'.
setProtection(int, Protection) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
setProtection(Protection[]) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
setProtection(List<Protection>) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Sets the value of '_protectionList' by copying the given Vector.
setProtectionAsReference(List<Protection>) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Deprecated.  
setProteinSequence(String) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Sets the value of field 'proteinSequence'.
setPublicationType(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'publicationType'.
setPubmedFilename(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'pubmedFilename'.
setRatio(double) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
setRatio(double) - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
setReactive(String) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Sets the value of field 'reactive'.
setReactivity(Reactivity) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Sets the value of field 'reactivity'.
setReagentName(String) - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Sets the value of field 'reagentName'.
setRegistrationDate(Date) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'registrationDate'.
setRelevantState(String) - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
Sets the value of field 'relevantState'.
setRememberUsername(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Set whether or not the user wants to store username in a cookie.
setRememberUsername(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set whether or not the user wants to store username in a cookie.
setResidue(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
setResidue(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
setResidue(int, Residue) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
setResidue(Residue[]) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
setResidue(List<Residue>) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Sets the value of '_residueList' by copying the given Vector.
setResidueAsReference(List<Residue>) - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Deprecated.  
setResidueNumber(int) - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Sets the value of field 'residueNumber'.
setSaturation(Saturation) - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
Sets the value of field 'saturation'.
setSCAM(SCAM) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Sets the value of field 'SCAM'.
setSCAMData(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setSCAMDeterminationApproach(String) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Sets the value of field 'SCAMDeterminationApproach'.
setSCAMReagent(int, SCAMReagent) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
setSCAMReagent(SCAMReagent[]) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
setSCAMReagent(List<SCAMReagent>) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Sets the value of '_SCAMReagentList' by copying the given Vector.
setSCAMReagent(SCAMReagent) - Method in class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
 
setSCAMReagentAsReference(List<SCAMReagent>) - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
Deprecated.  
setSCAMState(Set<String>) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setSchema(String) - Method in class edu.cornell.med.icb.trac.AbstractManager
Set the schema used to validate the article.
setSchema(String) - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Set the schema used to validate the XML object.
setSchemaURL(URL) - Method in class edu.cornell.med.icb.trac.AbstractManager
Set the schema used to validate the persistent class.
setSchemaURL(URL) - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Set the schema used to validate the XML object.
setScore(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'score'.
setSegment(String) - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Sets the value of field 'segment'.
setSelectData(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setSelectedNode(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeStateModel
 
setSelectedPMID(long) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
setSendEmail(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set whether or not the user wants a registration confirmation email sent to their account.
setSessionStateManagerBinding(IBinding) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Sets the sessionStateManagerBinding.
setSessionStoreManagerBinding(IBinding) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Sets the SessionStoreManagerBinding.
setSource(String) - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Sets the value of field 'source'.
setSource(String) - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Sets the value of field 'source'.
setSPACE(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Sets the value of field 'SPACE'.
setSPACE(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Sets the value of field 'SPACE'.
setSpecies(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setSpecies(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
setSpecies(String) - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
setSpeciesName(String) - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Sets the value of field 'speciesName'.
setSPECIESNAME(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Sets the value of field 'SPECIESNAME'.
setSPECIESNAME(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Sets the value of field 'SPECIESNAME'.
setSpeciesName(String) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Sets the value of field 'speciesName'.
setState(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'state'.
setStatus(String) - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Sets the value of field 'status'.
setStructuralInference(StructuralInference) - Method in class edu.cornell.med.icb.trac.article.xml.Construct
Sets the value of field 'structuralInference'.
setStructuralInferenceData(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setStructuralInferenceState(Set<String>) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setSubmittedBy(String) - Method in class edu.cornell.med.icb.trac.article.xml.Note
Sets the value of field 'submittedBy'.
setSubstrate(int, Substrate) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
setSubstrate(Substrate[]) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
setSubstrate(List<Substrate>) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Sets the value of '_substrateList' by copying the given Vector.
setSubstrateAsReference(List<Substrate>) - Method in class edu.cornell.med.icb.trac.article.xml.Transport
Deprecated.  
setSubstrateBinding(boolean) - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Sets the value of field 'substrateBinding'.
setSwissProtID(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Sets the value of field 'swissProtID'.
setSynonym(String) - Method in class edu.cornell.med.icb.trac.article.xml.IdType
Sets the value of field 'synonym'.
setSynonym(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.SynonymsItem
Sets the value of field 'synonym'.
setSynonyms(Synonyms) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Sets the value of field 'synonyms'.
setSynonymsItem(int, SynonymsItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
setSynonymsItem(SynonymsItem[]) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
setSynonymsItem(List<SynonymsItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Sets the value of '_items' by copying the given Vector.
setSynonymsItemAsReference(List<SynonymsItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Deprecated.  
setTag(String) - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Sets the value of field 'tag'.
setTitle(Title) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'title'.
setTitle(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'title'.
setTRACAbstract(TRACAbstract) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSetItem
Sets the value of field 'TRACAbstract'.
setTRACAbstractMap(Map<Long, TRACAbstract>) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setTRACAbstractSetFilename(String) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setTRACAbstractSetItem(int, TRACAbstractSetItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
setTRACAbstractSetItem(TRACAbstractSetItem[]) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
setTRACAbstractSetItem(List<TRACAbstractSetItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Sets the value of '_items' by copying the given Vector.
setTRACAbstractSetItemAsReference(List<TRACAbstractSetItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Deprecated.  
setTransport(Transport) - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Sets the value of field 'transport'.
setTransportData(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setTransporter(Transporter) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TransportersItem
Sets the value of field 'transporter'.
setTransporterName(String) - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Sets the value of field 'transporterName'.
setTransporterName(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.JmolViewerPage
 
setTransporterName(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.QueryPage
 
setTransporterName(String) - Method in interface edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramComponent
 
setTRANSPORTERNAME(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLERItem
Sets the value of field 'TRANSPORTERNAME'.
setTRANSPORTERNAME(String) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextTypeItem
Sets the value of field 'TRANSPORTERNAME'.
setTransporters(Transporters) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'transporters'.
setTransportersItem(int, TransportersItem) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
setTransportersItem(TransportersItem[]) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
setTransportersItem(List<TransportersItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Sets the value of '_items' by copying the given Vector.
setTransportersItemAsReference(List<TransportersItem>) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Deprecated.  
setTransportInhibition(int, TransportInhibition) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
setTransportInhibition(TransportInhibition[]) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
setTransportInhibition(List<TransportInhibition>) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Sets the value of '_transportInhibitionList' by copying the given Vector.
setTransportInhibitionAsReference(List<TransportInhibition>) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Deprecated.  
setTransportState(Set<String>) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
setTreeModel(ITreeModel) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Sets the treeModel.
setTreeModelBinding(IBinding) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Sets the treeModelBinding.
setTreeRowObject(TreeRowObject) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
setTreeSessionState(Object) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
Sets the treeSessionState.
setTreeViewBinding(IBinding) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
Sets the treeViewBinding.
setType(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setUnalteredIonNames(String) - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
Sets the value of field 'unalteredIonNames'.
setUniprotName(String) - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Sets the value of field 'uniprotName'.
setUnit(String) - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
Sets the value of field 'unit'.
setUnit(String) - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Sets the value of field 'unit'.
setUnit(String) - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Sets the value of field 'unit'.
setUpdating(boolean) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Indicate whether or not this is a new user registration or a current user attempting to update their registration information.
setUptake(Uptake) - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
Sets the value of field 'uptake'.
setUptakeIonDependence(UptakeIonDependence) - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
Sets the value of field 'uptakeIonDependence'.
setUser(User) - Method in class edu.cornell.med.icb.trac.tapestry.user.RegisterPage
Set the user object of the person trying to log in.
setUser(User) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
Store the currently logged in user.
setUser(int, User) - Method in class edu.cornell.med.icb.trac.user.UserSet
 
setUser(User[]) - Method in class edu.cornell.med.icb.trac.user.UserSet
 
setUser(List<User>) - Method in class edu.cornell.med.icb.trac.user.UserSet
Sets the value of '_userList' by copying the given Vector.
setUserAsReference(List<User>) - Method in class edu.cornell.med.icb.trac.user.UserSet
Deprecated.  
setUsername(String) - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
Sets the value of field 'username'.
setUsername(String) - Method in class edu.cornell.med.icb.trac.tapestry.user.LoginPage
Set the username of the person trying to login.
setUsername(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'username'.
setValue(String) - Method in class edu.cornell.med.icb.trac.article.xml.Ki
Sets the value of field 'value'.
setValue(String) - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Sets the value of field 'value'.
setVmax(Vmax) - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Sets the value of field 'vmax'.
setWtRes(String) - Method in class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
setWtResidue(String) - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
Sets the value of field 'wtResidue'.
setWtResidue(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
setYear(String) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ArticleList0Page
 
setYear(String) - Method in class edu.cornell.med.icb.trac.tapestry.Visit
 
setYear(int) - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Sets the value of field 'year'.
setZip(String) - Method in class edu.cornell.med.icb.trac.user.User
Sets the value of field 'zip'.
SimpleMutant - Class in edu.cornell.med.icb.trac.rbdg
 
SimpleMutant() - Constructor for class edu.cornell.med.icb.trac.rbdg.SimpleMutant
 
SOURCE - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
SOURCE_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.EffectTypeComponent
 
species - Variable in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
 
SPECIES_NAMES - Static variable in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
speciesName - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
STATUS_MODEL - Static variable in class edu.cornell.med.icb.trac.article.ArticleManager
 
statusFinished - Static variable in class edu.cornell.med.icb.trac.article.ArticleManager
string for "finished" status.
statusInProgress - Static variable in class edu.cornell.med.icb.trac.article.ArticleManager
string for "in progress" status.
statusMutationsEntered - Static variable in class edu.cornell.med.icb.trac.article.ArticleManager
string for "mutations entered" status.
statusNotAnnotated - Static variable in class edu.cornell.med.icb.trac.article.ArticleManager
string for "not annotated" status.
store(T) - Method in class edu.cornell.med.icb.trac.AbstractManager
Store the given object into the datastore.
store(T) - Method in interface edu.cornell.med.icb.trac.jdo.PersistenceManager
Store the given object into the datastore.
storeSesion() - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeView
 
StructuralInference - Class in edu.cornell.med.icb.trac.article.xml
Class StructuralInference.
StructuralInference() - Constructor for class edu.cornell.med.icb.trac.article.xml.StructuralInference
 
StructuralInferenceDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class StructuralInferenceDescriptor.
StructuralInferenceDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.StructuralInferenceDescriptor
 
structuralInferenceOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
StructuralInferencePage - Class in edu.cornell.med.icb.trac.tapestry.pages
Logic for Annotating an Article.
StructuralInferencePage() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.StructuralInferencePage
 
Substrate - Class in edu.cornell.med.icb.trac.article.xml
Class Substrate.
Substrate() - Constructor for class edu.cornell.med.icb.trac.article.xml.Substrate
 
SubstrateComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
SubstrateComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.SubstrateComponent
 
SubstrateDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class SubstrateDescriptor.
SubstrateDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.SubstrateDescriptor
 
substrateOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
Synonyms - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class Synonyms.
Synonyms() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
SynonymsDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class SynonymsDescriptor.
SynonymsDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsDescriptor
 
SynonymsItem - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class SynonymsItem.
SynonymsItem() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.SynonymsItem
 
SynonymsItemDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class SynonymsItemDescriptor.
SynonymsItemDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.SynonymsItemDescriptor
 

T

tag - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
TextfilePropertySelectionModel - Class in edu.cornell.med.icb.trac.tapestry.form
 
TextfilePropertySelectionModel(String) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
Creates a new property selection model based on the constructs in an article object.
Title - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class Title.
Title() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
 
TitleDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TitleDescriptor.
TitleDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TitleDescriptor
 
tm50 - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
toString() - Method in class edu.cornell.med.icb.trac.tapestry.model.ConstructTreeNode
 
TRACAbstract - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Comment describing your root element
TRACAbstract() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
TRACAbstractDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TRACAbstractDescriptor.
TRACAbstractDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractDescriptor
 
TRACAbstractSet - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class TRACAbstractSet.
TRACAbstractSet() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
TRACAbstractSetDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TRACAbstractSetDescriptor.
TRACAbstractSetDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetDescriptor
 
TRACAbstractSetItem - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class TRACAbstractSetItem.
TRACAbstractSetItem() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSetItem
 
TRACAbstractSetItemDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TRACAbstractSetItemDescriptor.
TRACAbstractSetItemDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TRACAbstractSetItemDescriptor
 
TRACConfiguration - Class in edu.cornell.med.icb.trac
Helper class to load configuration property information for the TRAC application.
TRACStringPropertySelectionModel - Class in edu.cornell.med.icb.trac.tapestry.form
Created by IntelliJ IDEA.
TRACStringPropertySelectionModel(String[]) - Constructor for class edu.cornell.med.icb.trac.tapestry.form.TRACStringPropertySelectionModel
Standard constructor.
TRACTransporterDir - Static variable in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
 
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.BackgroundPropertySelectionModel
Returns the option corresponding to a value.
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.CastorTypePropertySelectionModel
Returns the option corresponding to a value.
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.DynamicStringPropertySelectionModel
 
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.ExpressionSystemPropertySelectionModel
Returns the option corresponding to a value.
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.ResiduePropertySelectionModel
Returns the option corresponding to a value.
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.TextfilePropertySelectionModel
Returns the option corresponding to a value.
translateValue(String) - Method in class edu.cornell.med.icb.trac.tapestry.form.TRACStringPropertySelectionModel
 
Transport - Class in edu.cornell.med.icb.trac.article.xml
Class Transport.
Transport() - Constructor for class edu.cornell.med.icb.trac.article.xml.Transport
 
TRANSPORT - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
TransportComponent - Class in edu.cornell.med.icb.trac.tapestry.pages
Created by IntelliJ IDEA.
TransportComponent() - Constructor for class edu.cornell.med.icb.trac.tapestry.pages.TransportComponent
 
TransportDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class TransportDescriptor.
TransportDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.TransportDescriptor
 
Transporter - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class Transporter.
Transporter() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
 
Transporter - Class in edu.cornell.med.icb.trac.transporter.xml
Comment describing your root element
Transporter() - Constructor for class edu.cornell.med.icb.trac.transporter.xml.Transporter
 
TRANSPORTER_DIRECTORY_PREFIX - Static variable in class edu.cornell.med.icb.trac.transporter.TransporterUtils
Base location of transporter files relative to the classpath.
TRANSPORTER_NAMES - Static variable in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
TRANSPORTER_NAMES_BYSPECIES - Static variable in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
TRANSPORTER_SYNONYMS - Static variable in class edu.cornell.med.icb.trac.transporter.TransporterUtils
 
TransporterDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TransporterDescriptor.
TransporterDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransporterDescriptor
 
TransporterDescriptor - Class in edu.cornell.med.icb.trac.transporter.xml.descriptors
Class TransporterDescriptor.
TransporterDescriptor() - Constructor for class edu.cornell.med.icb.trac.transporter.xml.descriptors.TransporterDescriptor
 
transporterName - Variable in class edu.cornell.med.icb.trac.tapestry.rbdg.AbstractSequenceDiagramAsset
 
Transporters - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class Transporters.
Transporters() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
TransportersDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TransportersDescriptor.
TransportersDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersDescriptor
 
TransportersItem - Class in edu.cornell.med.icb.trac.TRACAbstract.xml
Class TransportersItem.
TransportersItem() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.TransportersItem
 
TransportersItemDescriptor - Class in edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors
Class TransportersItemDescriptor.
TransportersItemDescriptor() - Constructor for class edu.cornell.med.icb.trac.TRACAbstract.xml.descriptors.TransportersItemDescriptor
 
transporterSpeciesDelimiter - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.BasicInfoComponent
 
TransporterUtils - Class in edu.cornell.med.icb.trac.transporter
Created by IntelliJ IDEA.
TransportInhibition - Class in edu.cornell.med.icb.trac.article.xml
Class TransportInhibition.
TransportInhibition() - Constructor for class edu.cornell.med.icb.trac.article.xml.TransportInhibition
 
TransportInhibitionDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class TransportInhibitionDescriptor.
TransportInhibitionDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.TransportInhibitionDescriptor
 
transportOC(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.pages.ConstructTreePage
 
trigger(IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.rbdg.SequenceDiagramArea
Invoked by the direct service to have the component perform the appropriate action.

U

unmarshal(Reader) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Reads an XML article from a given input source into a new Article.
unmarshal(Reader, Article) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Reads an XML article from a given input source into an existing article object.
unmarshal(String) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
 
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Article
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Binding
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.BindingSite
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Bmax
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Construct
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.ConstructId
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Expression
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.History
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Id
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.IsBackground
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.IsMutant
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Kd
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Ki
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Kinetics
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Km
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Ligand
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Mutation
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Note
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Phenotype
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Protection
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Reactivity
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Saturation
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.SCAM
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Substrate
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Transport
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Uptake
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.article.xml.Vmax
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.transporter.xml.Indices
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.transporter.xml.Residue
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.user.User
Method unmarshal.
unmarshal(Reader) - Static method in class edu.cornell.med.icb.trac.user.UserSet
Method unmarshal.
unmarshal(Reader) - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Reads an XML object from a given input source into a new object.
unmarshal(Reader, T) - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Reads an XML object from a given input source into an existing object.
Uptake - Class in edu.cornell.med.icb.trac.article.xml
Class Uptake.
Uptake() - Constructor for class edu.cornell.med.icb.trac.article.xml.Uptake
 
UptakeDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class UptakeDescriptor.
UptakeDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeDescriptor
 
UptakeIonDependence - Class in edu.cornell.med.icb.trac.article.xml
Class UptakeIonDependence.
UptakeIonDependence() - Constructor for class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
 
UptakeIonDependenceDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class UptakeIonDependenceDescriptor.
UptakeIonDependenceDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.UptakeIonDependenceDescriptor
 
usage(Options) - Method in class edu.cornell.med.icb.trac.AbstractManager
Print usage message for main method.
User - Class in edu.cornell.med.icb.trac.user
A user that has been registered with the TRAC system
User() - Constructor for class edu.cornell.med.icb.trac.user.User
 
UserDescriptor - Class in edu.cornell.med.icb.trac.user.descriptors
Class UserDescriptor.
UserDescriptor() - Constructor for class edu.cornell.med.icb.trac.user.descriptors.UserDescriptor
 
UserManager - Class in edu.cornell.med.icb.trac.user
Manage operations on users.
UserSet - Class in edu.cornell.med.icb.trac.user
Class UserSet.
UserSet() - Constructor for class edu.cornell.med.icb.trac.user.UserSet
 
UserSetDescriptor - Class in edu.cornell.med.icb.trac.user.descriptors
Class UserSetDescriptor.
UserSetDescriptor() - Constructor for class edu.cornell.med.icb.trac.user.descriptors.UserSetDescriptor
 
UserUtils - Class in edu.cornell.med.icb.trac.user
Utilities to assist in dealing with users and passwords.

V

validate(T) - Method in class edu.cornell.med.icb.trac.AbstractManager
 
validate(Article) - Method in class edu.cornell.med.icb.trac.article.ArticleManager
Checks the validity of the current article and throws a runtime exception if the article is not in a valid state.
validate() - Method in class edu.cornell.med.icb.trac.article.xml.AnnotationStatus
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Article
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.ArticleSet
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Binding
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.BindingInhibition
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.BindingIonDependence
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSite
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.BindingSiteInferenceNote
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Bmax
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Construct
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.ConstructId
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.CreatedBy
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.EffectType
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Expression
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.History
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Id
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IdType
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.InferenceNoteType
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.InhibitionType
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.InterInferenceNote
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IntermolecularInteraction
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IntraInferenceNote
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IntramolecularInteraction
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IonDependenceType
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IsBackground
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.IsMutant
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Kd
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Ki
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Kinetics
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Km
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.LastmodifiedBy
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Ligand
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Mutation
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Note
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Pharmacology
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Phenotype
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Protection
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Reactivity
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.RecordType
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Saturation
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.SCAM
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.SCAMReagent
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.StructuralInference
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Substrate
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Transport
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.TransportInhibition
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Uptake
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.UptakeIonDependence
 
validate() - Method in class edu.cornell.med.icb.trac.article.xml.Vmax
 
validate(T) - Method in interface edu.cornell.med.icb.trac.jdo.PersistenceManager
Checks the validity of the object and throws a runtime exception if it is not in a valid state.
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.AbstractText
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Authors
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.COUPLER
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.MarkedTextType
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Synonyms
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Title
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstract
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.TRACAbstractSet
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporter
 
validate() - Method in class edu.cornell.med.icb.trac.TRACAbstract.xml.Transporters
 
validate() - Method in class edu.cornell.med.icb.trac.transporter.xml.Indices
 
validate() - Method in class edu.cornell.med.icb.trac.transporter.xml.Residue
 
validate() - Method in class edu.cornell.med.icb.trac.transporter.xml.Transporter
 
validate() - Method in class edu.cornell.med.icb.trac.user.User
 
validate(User) - Method in class edu.cornell.med.icb.trac.user.UserManager
Checks the validity of the user and throws a runtime exception if the user is not in a valid state.
validate() - Method in class edu.cornell.med.icb.trac.user.UserSet
 
validate(T) - Method in interface edu.cornell.med.icb.trac.xml.Exportable
Checks the validity of the object and throws a runtime exception if it is not in a valid state.
validateEmailAddress(String) - Static method in class edu.cornell.med.icb.trac.user.UserUtils
Validate that this address conforms to the syntax rules of RFC 822.
Visit - Class in edu.cornell.med.icb.trac.tapestry
The Visit object of a tapestry application holds information about the session of a single user.
Visit() - Constructor for class edu.cornell.med.icb.trac.tapestry.Visit
Create a new Visit object.
Vmax - Class in edu.cornell.med.icb.trac.article.xml
Class Vmax.
Vmax() - Constructor for class edu.cornell.med.icb.trac.article.xml.Vmax
 
VMAX - Static variable in class edu.cornell.med.icb.trac.tapestry.pages.ConstructDataTableComponent
 
VMAX_MODEL - Static variable in class edu.cornell.med.icb.trac.tapestry.form.EffectTypePropertySelectionModels
 
VmaxDescriptor - Class in edu.cornell.med.icb.trac.article.xml.descriptors
Class VmaxDescriptor.
VmaxDescriptor() - Constructor for class edu.cornell.med.icb.trac.article.xml.descriptors.VmaxDescriptor
 

W

walkTree(Object, Object, int, ITreeModel, IMarkupWriter, IRequestCycle) - Method in class edu.cornell.med.icb.trac.tapestry.model.components.ConstructTreeDataView
 
WEB_ALIGNMENT_DIRECTORY - Static variable in class edu.cornell.med.icb.trac.alignment.IndexCalculator
 
writeConstraint(Construct) - Static method in class edu.cornell.med.icb.trac.constraints.ConstraintsGenerator
Writes a CHARMM and MODELLER NOE type constraint for this construct.
writeImage(List<SimpleMutant>, String, ImageFormatType, String) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Write an sequence diagram based on the list of mutants to the specified stream.
writeImage(List<SimpleMutant>, String, ImageFormatType, File) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Write an sequence diagram based on the list of mutants to the specified stream.
writeImage(List<SimpleMutant>, String, ImageFormatType, OutputStream) - Method in class edu.cornell.med.icb.trac.rbdg.ConstructRetriever
Write an sequence diagram based on the list of mutants to the specified stream.

X

xmlFilename - Static variable in class edu.cornell.med.icb.trac.constraints.ConstraintsGenerator
 

A B C D E F G H I J K L M N P Q R S T U V W X
TRAC

Copyright © 2006-2008 Institute for Computational Biomedicine, All Rights Reserved.