phenote.config
Class OntologyConfig

java.lang.Object
  phenote.config.OntologyConfig

public class OntologyConfig
extends java.lang.Object

May not even have ontology file (free text eg genotype) rename FieldConfig?

Field Summary

java.lang.String

ontologyFile just the filename - no path/url

Constructor Summary

OntologyConfig(phenote.config.xml.FieldDocument.Field field, FieldConfig fc)
PASE! Ontology stuff in field itself (field only has one ontology) - this is getting phased out replaced by field with single ontology element this also doesnt have Ontology xml bean - phase out now??

OntologyConfig(phenote.config.xml.OntologyDocument.Ontology o, FieldConfig fc)
confusing - this is xml bean Ontology NOT datamodel Ontology - this is reading in from xml config - if ontology doesnt have name use fieldName (single ontols just use field name)

OntologyConfig(java.lang.String name, java.lang.String displayName, FieldConfig fc)

Method Summary

java.lang.String	getFile()
java.net.URL	getLoadUrl()
java.net.URL	getLocalUrl()
java.lang.String	getName()
java.lang.String	getNamespace()
phenote.config.xml.OnTheFlySlimTermDocument.OnTheFlySlimTerm[]	getOnTheFlySlimTerms()
(package private) phenote.config.xml.OntologyDocument.Ontology	getOntologyBean()
java.net.URL	getReposUrl()
java.lang.String	getSlim()
long	getUpdateDate()
boolean	hasLoadUrl()
(package private) boolean	hasName()
boolean	hasNamespace()
boolean	hasOnTheFlySlim()
boolean	hasOntology()
boolean	hasReposUrl()
boolean	hasSlim()
boolean	isPostCompRel()
(package private) static OntologyConfig	makePostCompRelCfg(java.lang.String file, FieldConfig fc)
(package private) void	mergeWithOldConfig(FieldConfig oldFC) make ontology xml bean and add to field xml bean for writeback
void	setFile(java.lang.String file) File can be url(repos) or filename (from cache/jar/app), if url sets reposUrlString and ontologyFile with end of url
void	setLoadUrl(java.net.URL u) The actual url used to load ontology - this may be file: or http: so if from file cache this is different than repository url
void	setLocalUrl(java.net.URL u)
void	setName(java.lang.String name)
void	setNamespace(java.lang.String n)
void	setOntFileFromTermDefs(java.lang.String name, phenote.config.xml.OntologyFileDocument.OntologyFile[] ontologyList) look for ontology in ontology list with name, and set OntConfig state from that ontology
(package private) void	setOntologyFile(java.lang.String file)
void	setSlim(java.lang.String s)
void	setUpdateDate(long date)
boolean	sortById()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ontologyFile

public java.lang.String ontologyFile

just the filename - no path/url

Constructor Detail

OntologyConfig

OntologyConfig(phenote.config.xml.OntologyDocument.Ontology o,
               FieldConfig fc)

confusing - this is xml bean Ontology NOT datamodel Ontology - this is reading in from xml config - if ontology doesnt have name use fieldName (single ontols just use field name)

OntologyConfig

public OntologyConfig(java.lang.String name,
                      java.lang.String displayName,
                      FieldConfig fc)

OntologyConfig

OntologyConfig(phenote.config.xml.FieldDocument.Field field,
               FieldConfig fc)

PASE! Ontology stuff in field itself (field only has one ontology) - this is getting phased out replaced by field with single ontology element this also doesnt have Ontology xml bean - phase out now??

Method Detail

getOntologyBean

phenote.config.xml.OntologyDocument.Ontology getOntologyBean()

makePostCompRelCfg

static OntologyConfig makePostCompRelCfg(java.lang.String file,
                                         FieldConfig fc)

setFile

public void setFile(java.lang.String file)

File can be url(repos) or filename (from cache/jar/app), if url sets reposUrlString and ontologyFile with end of url

isPostCompRel

public boolean isPostCompRel()

hasName

boolean hasName()

setName

public void setName(java.lang.String name)

getName

public java.lang.String getName()

setOntologyFile

void setOntologyFile(java.lang.String file)

getFile

public java.lang.String getFile()

getReposUrl

public java.net.URL getReposUrl()
                         throws java.net.MalformedURLException

Throws:

java.net.MalformedURLException

hasReposUrl

public boolean hasReposUrl()

hasOntology

public boolean hasOntology()

hasNamespace

public boolean hasNamespace()

getNamespace

public java.lang.String getNamespace()

setNamespace

public void setNamespace(java.lang.String n)

hasSlim

public boolean hasSlim()

getSlim

public java.lang.String getSlim()

setSlim

public void setSlim(java.lang.String s)

setLoadUrl

public void setLoadUrl(java.net.URL u)

The actual url used to load ontology - this may be file: or http: so if from file cache this is different than repository url

setLocalUrl

public void setLocalUrl(java.net.URL u)

getLocalUrl

public java.net.URL getLocalUrl()

getLoadUrl

public java.net.URL getLoadUrl()

hasLoadUrl

public boolean hasLoadUrl()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

mergeWithOldConfig

void mergeWithOldConfig(FieldConfig oldFC)

make ontology xml bean and add to field xml bean for writeback

sortById

public boolean sortById()

setOntFileFromTermDefs

public void setOntFileFromTermDefs(java.lang.String name,
                                   phenote.config.xml.OntologyFileDocument.OntologyFile[] ontologyList)

look for ontology in ontology list with name, and set OntConfig state from that ontology

hasOnTheFlySlim

public boolean hasOnTheFlySlim()

getOnTheFlySlimTerms

public phenote.config.xml.OnTheFlySlimTermDocument.OnTheFlySlimTerm[] getOnTheFlySlimTerms()

setUpdateDate

public void setUpdateDate(long date)

getUpdateDate

public long getUpdateDate()