apollo.editor
Class TransactionManager

java.lang.Object
  apollo.editor.TransactionManager

All Implemented Interfaces:

AnnotationChangeListener, java.io.Serializable, java.util.EventListener

public class TransactionManager
extends java.lang.Object
implements AnnotationChangeListener, java.io.Serializable

Author:

wgm rename TransactionList?

See Also:

Serialized Form

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

TransactionManager()
Default constructor.

Method Summary

void	addTransaction(Transaction trans)
void	clear()
void	coalesce() Coalesce all Transaction instances in this TransactionManager.
void	emptyTransactions() Remove all transactions in the memory.
boolean	featureHasBeenEdited(SeqFeatureI feat) convenience function.
protected java.util.List	generateTransaction(AnnotationChangeEvent e) Generate a Transaction based on a specified AnnotationChangeEvent.
java.lang.String	getAuthor()
java.util.List	getFlattenedTransactions() Flattens out transactions.
Transaction	getTransaction(int i)
java.util.List	getTransactions() Get the list of Transaction instances managed by this object.
boolean	handleAnnotationChangeEvent(AnnotationChangeEvent evt) Implements the method from AnnotationChangeListener.
boolean	hasTransactions()
boolean	isCoalescedDone() Check if coalescing is done.
int	numberOfTransactions()
Transaction	popTransaction()
void	replaceIdUpdatesWithDelAndAdd() Change all id update transactions to delete and add.
void	setAnnotationChangeListener(AnnotationChangeListener acl) For firing annot change events from undos
void	setAuthor(java.lang.String author)
void	setCurationState(CurationState cs)
void	setTransactions(java.util.List list) Set a list of Transactions for this TransactionManager.
int	size()
void	undo(java.lang.Object source) direct undo - to replace undo via ACE

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

TransactionManager

public TransactionManager()

Default constructor.

Method Detail

setAuthor

public void setAuthor(java.lang.String author)

getAuthor

public java.lang.String getAuthor()

addTransaction

public void addTransaction(Transaction trans)

coalesce

public void coalesce()

Coalesce all Transaction instances in this TransactionManager. This method should be called for a TransactionManager instance whose needCoalesce is false before Transaction instances are saved. This presently has the side effect of flattening unflattened transactions.

generateTransaction

protected java.util.List generateTransaction(AnnotationChangeEvent e)

Generate a Transaction based on a specified AnnotationChangeEvent. The generated Transaction should be one of subclasses to Transaction. old way - annotation change event does not have transaction - have to create a transaction from the annotation change event new way - annotation change event just holds the transaction - just get it and we're done

Parameters:

e -

getFlattenedTransactions

public java.util.List getFlattenedTransactions()

Flattens out transactions. Compound transactions are reduced to their children. children still have

replaceIdUpdatesWithDelAndAdd

public void replaceIdUpdatesWithDelAndAdd()

Change all id update transactions to delete and add. Current rice/fly chado trigger for creating new ids only, doesnt give new ids for id updates scott may have ammended this - check this out - no scott hasnt ammended this yet but its not urgent. this will modify flattened list of trans(if there is an id update), which will invalidate the unflattened list, for now that means just setting the unflattened = flattened, which i think will be ok. in other words once we've flattened i dont think theres any need to go back to unflattened

handleAnnotationChangeEvent

public boolean handleAnnotationChangeEvent(AnnotationChangeEvent evt)

Implements the method from AnnotationChangeListener. Basically, this method just delegates to addTransaction(AnnotationChangeEvent).

Specified by:

handleAnnotationChangeEvent in interface AnnotationChangeListener

Returns:

always return true for the time being

setTransactions

public void setTransactions(java.util.List list)

Set a list of Transactions for this TransactionManager. This method should be called during opening a new file to load saved Transaction instances.

Parameters:

list -

getTransactions

public java.util.List getTransactions()

Get the list of Transaction instances managed by this object. A new List object (cloned) is returned. why are we cloning the list? taking out clone for now - dont think we need it.

Returns:

undo

public void undo(java.lang.Object source)

direct undo - to replace undo via ACE

popTransaction

public Transaction popTransaction()

setAnnotationChangeListener

public void setAnnotationChangeListener(AnnotationChangeListener acl)

For firing annot change events from undos

hasTransactions

public boolean hasTransactions()

numberOfTransactions

public int numberOfTransactions()

size

public int size()

getTransaction

public Transaction getTransaction(int i)

isCoalescedDone

public boolean isCoalescedDone()

Check if coalescing is done.

Returns:

emptyTransactions

public void emptyTransactions()

Remove all transactions in the memory. This method should be called after Transactions are saved to the database to keep the data synchronization.

clear

public void clear()

featureHasBeenEdited

public boolean featureHasBeenEdited(SeqFeatureI feat)

convenience function. returns true if feat has been edited or a descendant of feat has been edited. (looks through compound trans as well)

setCurationState

public void setCurationState(CurationState cs)