ExperimentDAOHibernate (SeqWare 1.1.2 API)

java.lang.Object
- org.springframework.dao.support.DaoSupport
- - org.springframework.orm.hibernate3.support.HibernateDaoSupport
  - - net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate

All Implemented Interfaces:

ExperimentDAO, org.springframework.beans.factory.InitializingBean
```
public class ExperimentDAOHibernate
extends org.springframework.orm.hibernate3.support.HibernateDaoSupport
implements ExperimentDAO
```
ExperimentDAOHibernate class.

Version:

$Id: $Id

Author:

boconnor

Field Summary
- Fields inherited from class org.springframework.dao.support.DaoSupport
  logger

Constructor Summary

Constructors
Constructor and Description

ExperimentDAOHibernate()
Constructor for ExperimentDAOHibernate.

Constructors
Constructor and Description
`ExperimentDAOHibernate()` Constructor for ExperimentDAOHibernate.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`delete(Experiment experiment)` delete.
`List<Experiment>`	`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`Experiment`	`findByID(Integer expID)` findByID.
`List<Experiment>`	`findByOwnerID(Integer registrationID)` findByOwnerID.
`Experiment`	`findBySWAccession(Integer swAccession)` findBySWAccession.
`Experiment`	`findByTitle(String title)` findByTitle.
`List<File>`	`getFiles(Integer experimentId)` getFiles.
`List<File>`	`getFiles(Integer experimentId, String metaType)` getFiles.
`Integer`	`insert(Experiment experiment)` insert.
`Integer`	`insert(Registration registration, Experiment experiment)` insert.
`boolean`	`isHasFile(Integer experimentId)` isHasFile.
`boolean`	`isHasFile(Integer experimentId, String metaType)` isHasFile.
`List<Experiment>`	`list()` list.
`List<Experiment>`	`list(Registration registration)` list.
`List<Experiment>`	`list(Study study)` list.
`void`	`merge(Experiment experiment)` merge.
`void`	`update(Experiment experiment)` update.
`void`	`update(Registration registration, Experiment experiment)` update.
`Experiment`	`updateDetached(Experiment experiment)` updateDetached.
`Experiment`	`updateDetached(Registration registration, Experiment experiment)` updateDetached.

Methods inherited from class org.springframework.orm.hibernate3.support.HibernateDaoSupport
checkDaoConfig, convertHibernateAccessException, createHibernateTemplate, getHibernateTemplate, getSession, getSession, getSessionFactory, releaseSession, setHibernateTemplate, setSessionFactory

Methods inherited from class org.springframework.dao.support.DaoSupport
afterPropertiesSet, initDao

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ExperimentDAOHibernate
```
public ExperimentDAOHibernate()
```
    Constructor for ExperimentDAOHibernate.
- Method Detail
  - insert
```
public Integer insert(Experiment experiment)
```
    insert.
    
    Specified by:
    
    insert in interface ExperimentDAO
    
    Parameters:
    experiment -
    
    Returns:
    a Integer object.
  - update
```
public void update(Experiment experiment)
```
    update.
    
    Specified by:
    
    update in interface ExperimentDAO
    
    Parameters:
    experiment -
  - merge
```
public void merge(Experiment experiment)
```
    merge.
    
    Specified by:
    
    merge in interface ExperimentDAO
    
    Parameters:
    experiment - a Experiment object.
  - delete
```
public void delete(Experiment experiment)
```
    delete.
    This deletion will result in just the experiment being deleted but the samples and IUS will remain. This will potentially cause orphans which is not really at all good. A better solution is to never delete but just use a deletion attribute.
    
    Specified by:
    
    delete in interface ExperimentDAO
    
    Parameters:
    experiment -
  - list
```
public List<Experiment> list(Registration registration)
```
    list.
    
    Specified by:
    
    list in interface ExperimentDAO
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - list
```
public List<Experiment> list(Study study)
```
    list.
    
    Specified by:
    
    list in interface ExperimentDAO
    
    Parameters:
    study - a Study object.
    
    Returns:
    a List object.
  - getFiles
```
public List<File> getFiles(Integer experimentId)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface ExperimentDAO
    
    Parameters:
    experimentId - a Integer object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer experimentId)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface ExperimentDAO
    
    Parameters:
    experimentId - a Integer object.
    
    Returns:
    a boolean.
  - getFiles
```
public List<File> getFiles(Integer experimentId,
                  String metaType)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface ExperimentDAO
    
    Parameters:
    experimentId -
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer experimentId,
                String metaType)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface ExperimentDAO
    
    Parameters:
    experimentId -
    metaType - a String object.
    
    Returns:
    a boolean.
  - findByTitle
```
public Experiment findByTitle(String title)
```
    findByTitle.
    Finds an instance of Experiment in the database by the Experiment name.
    
    Specified by:
    
    findByTitle in interface ExperimentDAO
    
    Parameters:
    title - a String object.
    
    Returns:
    a Experiment object.
  - findByID
```
public Experiment findByID(Integer expID)
```
    findByID.
    Finds an instance of Experiment in the database by the Experiment ID.
    
    Specified by:
    
    findByID in interface ExperimentDAO
    
    Parameters:
    expID -
    
    Returns:
    a Experiment object.
  - findBySWAccession
```
public Experiment findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Specified by:
    
    findBySWAccession in interface ExperimentDAO
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Experiment object.
  - updateDetached
```
public Experiment updateDetached(Experiment experiment)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface ExperimentDAO
    
    Parameters:
    experiment - a Experiment object.
    
    Returns:
    a Experiment object.
  - findByOwnerID
```
public List<Experiment> findByOwnerID(Integer registrationID)
```
    findByOwnerID.
    
    Specified by:
    
    findByOwnerID in interface ExperimentDAO
    
    Parameters:
    registrationID - a Integer object.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<Experiment> findByCriteria(String criteria,
                              boolean isCaseSens)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface ExperimentDAO
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - list
```
public List<Experiment> list()
```
    list.
    
    Specified by:
    
    list in interface ExperimentDAO
    
    Returns:
    a List object.
  - update
```
public void update(Registration registration,
          Experiment experiment)
```
    update.
    
    Specified by:
    
    update in interface ExperimentDAO
    
    Parameters:
    registration - a Registration object.
    experiment - a Experiment object.
  - insert
```
public Integer insert(Registration registration,
             Experiment experiment)
```
    insert.
    
    Specified by:
    
    insert in interface ExperimentDAO
    
    Parameters:
    experiment -
    registration - a Registration object.
    
    Returns:
    a Integer object.
  - updateDetached
```
public Experiment updateDetached(Registration registration,
                        Experiment experiment)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface ExperimentDAO
    
    Parameters:
    registration - a Registration object.
    experiment - a Experiment object.
    
    Returns:
    a Experiment object.

Class ExperimentDAOHibernate

Field Summary

Fields inherited from class org.springframework.dao.support.DaoSupport

Constructor Summary

Method Summary

Methods inherited from class org.springframework.orm.hibernate3.support.HibernateDaoSupport

Methods inherited from class org.springframework.dao.support.DaoSupport

Methods inherited from class java.lang.Object

Constructor Detail

ExperimentDAOHibernate

Method Detail

insert

update

merge

delete

list

list

getFiles

isHasFile

getFiles

isHasFile

findByTitle

findByID

findBySWAccession

updateDetached

findByOwnerID

findByCriteria

list

update

insert

updateDetached