Uses of Package
phenote.datamodel

Packages that use phenote.datamodel

phenote.charactertemplate
phenote.config
phenote.dataadapter	Generalized methods for creating customized Data Adapters
phenote.dataadapter.annotation
phenote.dataadapter.birn
phenote.dataadapter.delimited
phenote.dataadapter.fly
phenote.dataadapter.nexus
phenote.dataadapter.phenosyntax
phenote.dataadapter.phenoxml
phenote.dataadapter.worm
phenote.datamodel
phenote.edit
phenote.gui
phenote.gui.field
phenote.gui.selection
phenote.matrix.model
phenote.servlet
phenote.util

Classes in phenote.datamodel used by phenote.charactertemplate

CharacterI
CharacterIs are the building blocks of phenotypes.

CharField

Classes in phenote.datamodel used by phenote.config

AnnotationMappingDriver

CharField

CharFieldEnum
so this class has evolved - this was actually doing the setting of field values at one point - but now that we've gone to a generic datamodel, the datamodel is now determined by the configuration - and not restricted to CharFieldEnums - you can have a field that is not in CharFieldEnum - which leads to the question should we get rid of this class? and the answer at the moment is maybe not - as you can still use this in data adapters to get at predefined strings for definied fields - to make sure data adapters are using the same string for the pub of entity field.

Ontology
Ontology represents at this point the contents of a single obo file (which can be more than one ontology) an ontology wraps an obo edit OBOSession - at this point there is one OBOSession per obo file - that may change in the future

Classes in phenote.datamodel used by phenote.dataadapter

CharacterI
CharacterIs are the building blocks of phenotypes.

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

CharField

CharFieldValue
At the moment char field values can be Strings, OBOClasses, and dates, and possibly more coming.

Comparison
for making relations between statements

OntologyException

Classes in phenote.datamodel used by phenote.dataadapter.annotation

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.dataadapter.birn

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.dataadapter.delimited

CharacterI
CharacterIs are the building blocks of phenotypes.

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.dataadapter.fly

CharacterI
CharacterIs are the building blocks of phenotypes.

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.dataadapter.nexus

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.dataadapter.phenosyntax

CharacterI
CharacterIs are the building blocks of phenotypes.

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.dataadapter.phenoxml

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

PhenotypeCharacterI

PhenotypeCharacterI.PhenotypeCharacterFactory

Classes in phenote.datamodel used by phenote.dataadapter.worm

CharacterI
CharacterIs are the building blocks of phenotypes.

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

Classes in phenote.datamodel used by phenote.datamodel

AbstractCharacter

AnnotationMappingDriver

BasicAnnotationMappingDriver
Maps ENTITY to subject and QUALITY to object but is this proper? shouldnt genotype be subject?

CharacterEx

CharacterI
CharacterIs are the building blocks of phenotypes.

CharacterIFactory
Makes instances of CharacterI, according to mode set - OBOAnnotation or Character

CharacterListI
holds a list of Characters - rename phenotype? i dont think so - can have multiple genotypes in it - transfreable allows it to be plopped on the clipboard hmmm isnt this just a List?

CharField

CharFieldEnum
so this class has evolved - this was actually doing the setting of field values at one point - but now that we've gone to a generic datamodel, the datamodel is now determined by the configuration - and not restricted to CharFieldEnums - you can have a field that is not in CharFieldEnum - which leads to the question should we get rid of this class? and the answer at the moment is maybe not - as you can still use this in data adapters to get at predefined strings for definied fields - to make sure data adapters are using the same string for the pub of entity field.

CharFieldException

CharFieldManager
Manages all of the ontologies.

CharFieldValue
At the moment char field values can be Strings, OBOClasses, and dates, and possibly more coming.

Comparison
for making relations between statements

DefaultMappingDriver

OboUtil
changing this from static to non-static so can build post comp object from multiple rel-diffs

Ontology
Ontology represents at this point the contents of a single obo file (which can be more than one ontology) an ontology wraps an obo edit OBOSession - at this point there is one OBOSession per obo file - that may change in the future

OntologyException

PhenotypeCharacterI

RelationshipEnumeration
Created by IntelliJ IDEA.

TermNotFoundException
unclear to me if we really need both ontology ex and termo not found ex

Classes in phenote.datamodel used by phenote.edit

CharacterI
CharacterIs are the building blocks of phenotypes.

CharField

CharFieldValue
At the moment char field values can be Strings, OBOClasses, and dates, and possibly more coming.

Comparison
for making relations between statements

Classes in phenote.datamodel used by phenote.gui

CharacterI
CharacterIs are the building blocks of phenotypes.

Ontology
Ontology represents at this point the contents of a single obo file (which can be more than one ontology) an ontology wraps an obo edit OBOSession - at this point there is one OBOSession per obo file - that may change in the future

Classes in phenote.datamodel used by phenote.gui.field

CharacterI
CharacterIs are the building blocks of phenotypes.

CharField

CharFieldEnum
so this class has evolved - this was actually doing the setting of field values at one point - but now that we've gone to a generic datamodel, the datamodel is now determined by the configuration - and not restricted to CharFieldEnums - you can have a field that is not in CharFieldEnum - which leads to the question should we get rid of this class? and the answer at the moment is maybe not - as you can still use this in data adapters to get at predefined strings for definied fields - to make sure data adapters are using the same string for the pub of entity field.

CharFieldValue
At the moment char field values can be Strings, OBOClasses, and dates, and possibly more coming.

Ontology
Ontology represents at this point the contents of a single obo file (which can be more than one ontology) an ontology wraps an obo edit OBOSession - at this point there is one OBOSession per obo file - that may change in the future

Classes in phenote.datamodel used by phenote.gui.selection

CharacterI
CharacterIs are the building blocks of phenotypes.

Classes in phenote.datamodel used by phenote.matrix.model

CharacterI
CharacterIs are the building blocks of phenotypes.

CharFieldException

Classes in phenote.datamodel used by phenote.servlet

Ontology
Ontology represents at this point the contents of a single obo file (which can be more than one ontology) an ontology wraps an obo edit OBOSession - at this point there is one OBOSession per obo file - that may change in the future

Classes in phenote.datamodel used by phenote.util

OntologyException