apollo.editor
Class Transaction

java.lang.Object
  apollo.editor.Transaction

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

AddTransaction, CompoundTransaction, DeleteTransaction, UpdateTransaction

public class Transaction
extends java.lang.Object
implements java.io.Serializable

Class for keeping track of transactions (changes to annotations or annotation subparts (transactions, exons)). Built and talked to by AnnotationChangeEvents and also by GAMEAdapter as it reads in old transactions. this class is in dire need of some spring cleaning!

See Also:

Serialized Form

Field Summary

protected java.lang.String	author
protected java.util.Date	date
protected static org.apache.log4j.Logger	logger
static int	NEW
protected java.util.Hashtable	newProperties
static int	OLD
protected java.util.Hashtable	oldProperties

Constructor Summary

Transaction()

Transaction(FeatureChangeEvent ace)

Method Summary

void	addProperty(java.lang.String name, java.lang.String value, int oldOrNew) Add a new value to the Vector for this property name.
AnnotationChangeEvent	generateAnnotationChangeEvent(java.lang.Object source) different source than trans.
AnnotationChangeEvent	generateUndoChangeEvent(java.lang.Object source)
java.lang.String	getAuthor()
java.lang.String	getClassString()
java.util.Date	getDate()
SeqFeatureI	getDeletedFeature()
java.util.List	getLeafTransactions() Return all descendant leaves of this transaction.
java.lang.String	getNewId()
AnnotatedFeatureI	getNewSplitFeature() If split compound transaction, this returns the new split off feature.
java.lang.Object	getNewSubpartValue()
TransactionClass	getObjectClass()
Comment	getOldComment() Convenience method for getting old comment
java.lang.String	getOldId()
java.lang.String	getOldString()
java.lang.Object	getOldSubpartValue() Get the previous value.
TransactionOperation	getOperation()
protected java.lang.String	getOperationString()
SeqFeatureI	getParentFeature()
SeqFeatureI	getParentFeatureClone()
CompoundTransaction	getParentTransaction() If this is a child of a compound transactions, return compound transaction parent return null if have no parent.
java.lang.String	getProperty(java.lang.String name, int oldOrNew) Return a single property for name.
int	getRank()
SeqFeatureI	getSeqFeature() Get the touched SeqFeatureI object.
SeqFeatureI	getSeqFeatureClone() Return a clone of the touched SeqFeatureI object; it should reflect the state of the SeqFeatureI when the transaction actually ocurred.
TransactionSubpart	getSubpart()
int	getSubpartRank()
java.lang.String	getSubpartString()
Transaction	getTransaction(int i) Default return null.
boolean	hasKids() returns true for comp trans if actually has kid trans
boolean	hasParentTransaction()
boolean	isAdd()
boolean	isAddPeptide()
boolean	isCompound() default false.
boolean	isDelete()
boolean	isMerge()
boolean	isSplit()
boolean	isUpdate()
boolean	isUpdateParent()
java.lang.String	oneLineSummary() Short (one-line) summary of the object; concise alternative to toString()
void	setAuthor(java.lang.String name)
void	setDate(java.util.Date date)
void	setDate(java.lang.String date)
void	setNewId(java.lang.String newId)
void	setNewSubpartValue(java.lang.Object obj) Set the subpart value for this Transaction object.
void	setObjectClass(java.lang.String objectClass)
void	setOldId(java.lang.String id) feature id needs to be explictly set if id changes (type change)
void	setOldSubpartValue(java.lang.Object preValue) Set the previouse value for this UpdateTransaction.
void	setOperation(java.lang.String operation)
void	setOperation(TransactionOperation operation)
void	setParentFeature(SeqFeatureI parent)
void	setRank(int rank)
void	setSeqFeature(SeqFeatureI feature) Set the touched SeqFeatureI object.
void	setSource(java.lang.Object src)
void	setSubpart(TransactionSubpart transactionSubpart)
void	setSubpartRank(int rank)
int	size() overridded by CompositeTransaction.
boolean	subpartIsString()
java.lang.String	toString()
java.lang.String	toString(java.lang.String indent) Returns a String of XML representing this transaction.
void	updateClonedTranscriptIdsAndNames(Transaction t, boolean updateAllIds, boolean updateAllParentIds) Traverses a transaction and updates the ids/names of any cloned Transcript objects it finds.

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

date

protected java.util.Date date

author

protected java.lang.String author

oldProperties

protected java.util.Hashtable oldProperties

newProperties

protected java.util.Hashtable newProperties

OLD

public static int OLD

NEW

public static int NEW

Constructor Detail

Transaction

public Transaction(FeatureChangeEvent ace)

Transaction

public Transaction()

Method Detail

setDate

public void setDate(java.lang.String date)

setDate

public void setDate(java.util.Date date)

getDate

public java.util.Date getDate()

setAuthor

public void setAuthor(java.lang.String name)

getAuthor

public java.lang.String getAuthor()

isUpdate

public boolean isUpdate()

isAdd

public boolean isAdd()

isAddPeptide

public boolean isAddPeptide()

isDelete

public boolean isDelete()

isCompound

public boolean isCompound()

default false. CompoundTransactions overrides with true.

isSplit

public boolean isSplit()

isMerge

public boolean isMerge()

isUpdateParent

public boolean isUpdateParent()

getNewSplitFeature

public AnnotatedFeatureI getNewSplitFeature()

If split compound transaction, this returns the new split off feature. getSeqFeature() returns the feature split off from.

getDeletedFeature

public SeqFeatureI getDeletedFeature()

setSubpart

public void setSubpart(TransactionSubpart transactionSubpart)

getSubpart

public TransactionSubpart getSubpart()

generateAnnotationChangeEvent

public AnnotationChangeEvent generateAnnotationChangeEvent(java.lang.Object source)

different source than trans. should trans even have a source? does it need it?

generateUndoChangeEvent

public AnnotationChangeEvent generateUndoChangeEvent(java.lang.Object source)

setSeqFeature

public void setSeqFeature(SeqFeatureI feature)

Set the touched SeqFeatureI object.

Parameters:

feature -

getSeqFeature

public SeqFeatureI getSeqFeature()

Get the touched SeqFeatureI object.

Returns:

getSeqFeatureClone

public SeqFeatureI getSeqFeatureClone()

Return a clone of the touched SeqFeatureI object; it should reflect the state of the SeqFeatureI when the transaction actually ocurred. Will return null unless Config.getSaveClonedFeaturesInTransactions() was set to true when the transaction was created.

setParentFeature

public void setParentFeature(SeqFeatureI parent)

getParentFeature

public SeqFeatureI getParentFeature()

getParentFeatureClone

public SeqFeatureI getParentFeatureClone()

setSource

public void setSource(java.lang.Object src)

setOldSubpartValue

public void setOldSubpartValue(java.lang.Object preValue)

Set the previouse value for this UpdateTransaction.

Parameters:

preValue - old value

getOldSubpartValue

public java.lang.Object getOldSubpartValue()

Get the previous value. This value is the one before update carried out. Or the value that was deleted.

Returns:

getOldComment

public Comment getOldComment()

Convenience method for getting old comment

getOldString

public java.lang.String getOldString()

setOldId

public void setOldId(java.lang.String id)

feature id needs to be explictly set if id changes (type change)

getOldId

public java.lang.String getOldId()

setNewId

public void setNewId(java.lang.String newId)

getNewId

public java.lang.String getNewId()

setRank

public void setRank(int rank)

getRank

public int getRank()

setSubpartRank

public void setSubpartRank(int rank)

getSubpartRank

public int getSubpartRank()

setNewSubpartValue

public void setNewSubpartValue(java.lang.Object obj)

Set the subpart value for this Transaction object. A subpart value is an object that is touched by this Transaction object. For example, a Comment object is updated, added or deleted. This Comment object should be the subpartValue. So for adds the added subpart is the subpart value(prevalue is null). For updates the new value is the subpart value, the old is the prevalue. For deletes previously deleted value was subpart value and prevalue was null. This seemed inconsistent to me and i changed it to prevaule having deleted value and subpart value being null. What this really means is subpartValue is really the post or new value. If this change is ok then this should be renamed getNewSubpartValue for clarity.

Parameters:

obj -

getNewSubpartValue

public java.lang.Object getNewSubpartValue()

Returns:

See Also:

setSubpartValue(Object).

subpartIsString

public boolean subpartIsString()

getSubpartString

public java.lang.String getSubpartString()

size

public int size()

overridded by CompositeTransaction. Number of child transactions.

hasKids

public boolean hasKids()

returns true for comp trans if actually has kid trans

getTransaction

public Transaction getTransaction(int i)

Default return null. Returns ith child transaction if composite.

getParentTransaction

public CompoundTransaction getParentTransaction()

If this is a child of a compound transactions, return compound transaction parent return null if have no parent.

hasParentTransaction

public boolean hasParentTransaction()

getLeafTransactions

public java.util.List getLeafTransactions()

Return all descendant leaves of this transaction. If not compound just return self as only item in list. CompoundTrans overrides and gets all leaves.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

oneLineSummary

public java.lang.String oneLineSummary()

Short (one-line) summary of the object; concise alternative to toString()

getOperationString

protected java.lang.String getOperationString()

getClassString

public java.lang.String getClassString()

setOperation

public void setOperation(TransactionOperation operation)

setOperation

public void setOperation(java.lang.String operation)

getOperation

public TransactionOperation getOperation()

setObjectClass

public void setObjectClass(java.lang.String objectClass)

getObjectClass

public TransactionClass getObjectClass()

addProperty

public void addProperty(java.lang.String name,
                        java.lang.String value,
                        int oldOrNew)

Add a new value to the Vector for this property name. Store in oldProperties or newProperties hash, as specified.

getProperty

public java.lang.String getProperty(java.lang.String name,
                                    int oldOrNew)

Return a single property for name. If there's more than one value, return the LAST one, not the first.

toString

public java.lang.String toString(java.lang.String indent)

Returns a String of XML representing this transaction. indent is a string of spaces. -> GAME adapter? this is old transactions -- delete

updateClonedTranscriptIdsAndNames

public void updateClonedTranscriptIdsAndNames(Transaction t,
                                              boolean updateAllIds,
                                              boolean updateAllParentIds)

Traverses a transaction and updates the ids/names of any cloned Transcript objects it finds. This is a workaround for the problem that the PureJDBCTransactionWriter can only manipulate objects with valid ids, but the AnnotationEditor frequently creates transactions in which the Transcripts (and other objects) have no valid id or name. In addition, the claimed order of ID and NAME udpate transactions does not always match the actual order, making it necessary in some cases to retroactively update the ids used in lookups to the current id of the feature in question.

Parameters:

updateAllIds - If false then only cloned feature ids/names that are either null or "no_name" will be updated. If true then all cloned seq feature ids and names will be updated (but not parent feature ids/names.)

updateAllParentIds - Same as updateAllIds, but applies only to cloned parent features.