edu.asu.cri.MirkE.dataStructures
Class DataSet

java.lang.Object
  edu.asu.cri.MirkE.dataStructures.DataSet

public class DataSet

extends java.lang.Object

DataSet - a JDBC database / Hibernate backed data store provides a HQL searchable collection of DataPoints TODO - for now, this is really a MultiWellPlateDataSet; need to refactor the DataSet from MultiWellPlateDataSet so this can be used for other applications

Version:

0.3.0, 17 january, 2005

Author:

Scott Menor

Constructor Summary

DataSet()
default constructor - create a hsqldb database in memory and initialize the tables for Hibernate based object persistance

Method Summary

java.lang.String	columnNumberToColumnLabel(int columnNumber)
void	computePlateDimensions() Determine and set the numberOfRows and numberOfColumns of the plate // TODO - refactor this out into another class (probably a subclass of DataSet -> MultiwellPlateDataSet)
void	delete(java.lang.Object object) remove an Object from the DataSet
java.util.List	find(java.lang.String query) execute a database query on the DataSet
java.util.Set	getCategoryNames()
net.sf.hibernate.cfg.Configuration	getConfiguration() get the Hibernate configuration
java.sql.Connection	getConnection() return the SQL database connection
DataPointCategoryFactory	getDataPointCategoryFactory()
java.util.Vector	getMeasuredPlateRowColumnVector()
int	getNumberOfColumns()
int	getNumberOfRows()
ObservableFactory	getObservableFactory()
java.util.Set	getObservables()
java.util.Set	getPlateIdentifiers()
net.sf.hibernate.Session	getSession()
net.sf.hibernate.SessionFactory	getSessionFactory() get the Hibernate sessionFactory
java.lang.String	rowNumberToLabel(int rowNumber)
void	save(java.lang.Object object) save an Object to the DataSet
void	setConfiguration(net.sf.hibernate.cfg.Configuration configuration) set the Hibernate configuration
void	setConnection(java.sql.Connection connection) set the SQL database connection
void	setSessionFactory(net.sf.hibernate.SessionFactory sessionFactory) set the Hibernate sessionFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

DataSet

public DataSet()
        throws MirkESystemException

default constructor - create a hsqldb database in memory and initialize the tables for Hibernate based object persistance

Throws:

MirkEApplicationException

MirkESystemException

Method Detail

getObservableFactory

public ObservableFactory getObservableFactory()

Returns:

observableFactory

getDataPointCategoryFactory

public DataPointCategoryFactory getDataPointCategoryFactory()

Returns:

dataPointCategoryFactory

getConnection

public java.sql.Connection getConnection()

return the SQL database connection

Returns:

connection

setConnection

public void setConnection(java.sql.Connection connection)

set the SQL database connection

Parameters:

connection -

getConfiguration

public net.sf.hibernate.cfg.Configuration getConfiguration()

get the Hibernate configuration

Returns:

configuration

setConfiguration

public void setConfiguration(net.sf.hibernate.cfg.Configuration configuration)

set the Hibernate configuration

Parameters:

configuration -

getSessionFactory

public net.sf.hibernate.SessionFactory getSessionFactory()

get the Hibernate sessionFactory

Returns:

sessionFactory

setSessionFactory

public void setSessionFactory(net.sf.hibernate.SessionFactory sessionFactory)

set the Hibernate sessionFactory

Parameters:

sessionFactory -

getSession

public net.sf.hibernate.Session getSession()
                                    throws MirkEApplicationException

Returns:

a new Hibernate Session

Throws:

MirkEApplicationException

save

public void save(java.lang.Object object)
          throws MirkEApplicationException

save an Object to the DataSet

Parameters:

object -

Throws:

MirkEApplicationException

delete

public void delete(java.lang.Object object)

remove an Object from the DataSet

Parameters:

object -

getObservables

public java.util.Set getObservables()
                             throws MirkEApplicationException

Returns:

A set of all Observables known to the DataSet

Throws:

MirkEApplicationException

getPlateIdentifiers

public java.util.Set getPlateIdentifiers()
                                  throws MirkEApplicationException

Returns:

plateIdentifiers

Throws:

MirkEApplicationException

getCategoryNames

public java.util.Set getCategoryNames()
                               throws MirkEApplicationException

Returns:

categoryNames Set of all category names known to this DataSet. Cagetories represent a collection of one or more DataPoint(s) with a common property ('growth control'; 'media control'; 'strain 1'; etc).

Throws:

MirkEApplicationException

rowNumberToLabel

public java.lang.String rowNumberToLabel(int rowNumber)

Parameters:

rowNumber - of a row in a multiwell plate

Returns:

label corresponding to a row in a multiwell plate ('A', 'B', 'C', 'D', etc)

columnNumberToColumnLabel

public java.lang.String columnNumberToColumnLabel(int columnNumber)

Parameters:

columnNumber - of a column in a multiwell plate

Returns:

label corresponding to a column in a multiwell plate ('1', '2', '3', '4', etc)

getNumberOfRows

public int getNumberOfRows()

Returns:

numberOfRows in a multiwell plate persisted in this DataSet

getNumberOfColumns

public int getNumberOfColumns()

Returns:

numberOfColumns in a multiwell plate persisted in this DataSet

computePlateDimensions

public void computePlateDimensions()
                            throws MirkEApplicationException

Determine and set the numberOfRows and numberOfColumns of the plate // TODO - refactor this out into another class (probably a subclass of DataSet -> MultiwellPlateDataSet)

Throws:

MirkEApplicationException

getMeasuredPlateRowColumnVector

public java.util.Vector getMeasuredPlateRowColumnVector()
                                                 throws MirkEApplicationException

Returns:

measuredPlateRowColumnVector

Throws:

MirkEApplicationException

find

public java.util.List find(java.lang.String query)
                    throws MirkEApplicationException

execute a database query on the DataSet

Parameters:

query - HQL query

Returns:

list

Throws:

MirkEApplicationException