apollo.dataadapter
Class CurationState

java.lang.Object
  apollo.dataadapter.CurationState

public class CurationState
extends java.lang.Object

Constructor Summary

CurationState(int i)

Method Summary

void	addAnnotationEditor(AnnotationEditor ae, boolean forwardStrand)
void	emptyNameAdapter()
AnnotationEditor	getAnnotationEditor(boolean forwardStrand)
java.lang.String	getCurationName()
CurationSet	getCurationSet()
ApolloDataAdapterI	getDataAdapter()
ApolloNameAdapterI	getNameAdapter(AnnotatedFeatureI af) A style/property scheme can be used by multiple curations (which is often the case) BUT the name adapters proscribed by its feature properties are curation specific in that they require the curations transaction manager, as the TM is checked for past ids in making new temp ids.
PropertyScheme	getPropertyScheme()
TransactionManager	getTransactionManager() Get the TransactionManager used by the embed curationSet.
boolean	haveAnnots() Returns true if curSet have >0 annotations
boolean	haveSequence() Whether curationSet has ref sequence (formerly in ApolloFrame)
void	setCurationName(java.lang.String spStr)
void	setCurationSet(CurationSet cs) CurationHolder goes through compDatHolder and sets CurationState cur set
void	setDataAdapter(ApolloDataAdapterI da)

Methods inherited from class java.lang.Object

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

Constructor Detail

CurationState

public CurationState(int i)

Method Detail

setCurationName

public void setCurationName(java.lang.String spStr)

getCurationName

public java.lang.String getCurationName()

setCurationSet

public void setCurationSet(CurationSet cs)

CurationHolder goes through compDatHolder and sets CurationState cur set

getCurationSet

public CurationSet getCurationSet()

setDataAdapter

public void setDataAdapter(ApolloDataAdapterI da)

getDataAdapter

public ApolloDataAdapterI getDataAdapter()

getPropertyScheme

public PropertyScheme getPropertyScheme()

emptyNameAdapter

public void emptyNameAdapter()

getNameAdapter

public ApolloNameAdapterI getNameAdapter(AnnotatedFeatureI af)

A style/property scheme can be used by multiple curations (which is often the case) BUT the name adapters proscribed by its feature properties are curation specific in that they require the curations transaction manager, as the TM is checked for past ids in making new temp ids. So CurationState holds the name adapters for the curation associated with its feat props. af can be a Transcript or Exon as well as an top annot, as it queries for biotype which gives the type of the top level annot for exon & trans.

getTransactionManager

public TransactionManager getTransactionManager()

Get the TransactionManager used by the embed curationSet. This method call is delegated to CurationSet.getTransactionManager.

Returns:

addAnnotationEditor

public void addAnnotationEditor(AnnotationEditor ae,
                                boolean forwardStrand)

getAnnotationEditor

public AnnotationEditor getAnnotationEditor(boolean forwardStrand)

haveSequence

public boolean haveSequence()

Whether curationSet has ref sequence (formerly in ApolloFrame)

haveAnnots

public boolean haveAnnots()

Returns true if curSet have >0 annotations