SampleDAOHibernate (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.SampleDAOHibernate

All Implemented Interfaces:

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

Version:

$Id: $Id

Author:

boconnor

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

Constructor Summary

Constructors
Constructor and Description

SampleDAOHibernate()
Constructor for SampleDAOHibernate.

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

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`delete(Sample sample)` delete.
`List<Sample>`	`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`Sample`	`findByID(Integer id)` findByID.
`Sample`	`findByName(String name)` findByName.
`List<Sample>`	`findByOwnerID(Integer registrationId)` findByOwnerID.
`Sample`	`findBySWAccession(Integer swAccession)` findBySWAccession.
`Sample`	`findByTitle(String title)` findByTitle.
`Map<Integer,Integer>`	`getCountFiles(Integer expId)` getCountFiles.
`Map<Integer,Integer>`	`getCountFiles(Integer expId, String metaType)` getCountFiles.
`List<File>`	`getFiles(Integer sampleId)` getFiles.
`List<File>`	`getFiles(Integer sampleId, String metaType)` getFiles.
`Sample`	`getRootSample(Sample sample)` getRootSample.
`List<Sample>`	`getRootSamples(Study study)` getRootSamples.
`Integer`	`insert(Registration registration, Sample sample)` insert.
`Integer`	`insert(Sample sample)` insert.
`boolean`	`isHasFile(Integer sampleId)` isHasFile.
`boolean`	`isHasFile(Integer sampleId, String metaType)` isHasFile.
`List<Sample>`	`list()` list.
`List<Sample>`	`listComplete()` listComplete.
`List<Sample>`	`listIncomplete()` listIncomplete.
`List<Sample>`	`listSample(Registration registaration)` listSample.
`List<Sample>`	`matchName(String name)` findByName.
`void`	`update(Registration registration, Sample sample)` update.
`void`	`update(Sample sample)` update.
`Sample`	`updateDetached(Registration registration, Sample sample)` updateDetached.
`Sample`	`updateDetached(Sample sample)` 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
  - SampleDAOHibernate
```
public SampleDAOHibernate()
```
    Constructor for SampleDAOHibernate.
- Method Detail
  - insert
```
public Integer insert(Sample sample)
```
    insert.
    Inserts an instance of Sample into the database.
    
    Specified by:
    
    insert in interface SampleDAO
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Integer object.
  - update
```
public void update(Sample sample)
```
    update.
    Updates an instance of Sample in the database.
    
    Specified by:
    
    update in interface SampleDAO
    
    Parameters:
    sample - a Sample object.
  - delete
```
public void delete(Sample sample)
```
    delete.
    This deletion will result in just the sample being deleted but the 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 SampleDAO
    
    Parameters:
    sample - a Sample object.
  - getFiles
```
public List<File> getFiles(Integer sampleId)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface SampleDAO
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer sampleId)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface SampleDAO
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a boolean.
  - getFiles
```
public List<File> getFiles(Integer sampleId,
                  String metaType)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface SampleDAO
    
    Parameters:
    sampleId - a Integer object.
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer sampleId,
                String metaType)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface SampleDAO
    
    Parameters:
    sampleId - a Integer object.
    metaType - a String object.
    
    Returns:
    a boolean.
  - getCountFiles
```
public Map<Integer,Integer> getCountFiles(Integer expId)
```
    getCountFiles.
    
    Specified by:
    
    getCountFiles in interface SampleDAO
    
    Parameters:
    expId - a Integer object.
    
    Returns:
    a Map object.
  - getCountFiles
```
public Map<Integer,Integer> getCountFiles(Integer expId,
                                 String metaType)
```
    getCountFiles.
    
    Specified by:
    
    getCountFiles in interface SampleDAO
    
    Parameters:
    expId - a Integer object.
    metaType - a String object.
    
    Returns:
    a Map object.
  - findByTitle
```
public Sample findByTitle(String title)
```
    findByTitle.
    Finds an instance of Sample in the database by the Experiment name.
    
    Specified by:
    
    findByTitle in interface SampleDAO
    
    Parameters:
    title - a String object.
    
    Returns:
    a Sample object.
  - findByName
```
public Sample findByName(String name)
```
    findByName.
    Finds an instance of Sample in the database by the Sample emailAddress.
    
    Specified by:
    
    findByName in interface SampleDAO
    
    Parameters:
    name - a String object.
    
    Returns:
    a Sample object.
  - matchName
```
public List<Sample> matchName(String name)
```
    findByName.
    Finds an instance of Sample in the database by the Sample emailAddress.
    
    Specified by:
    
    matchName in interface SampleDAO
    
    Parameters:
    name - a String object.
    
    Returns:
    a Sample object.
  - findByID
```
public Sample findByID(Integer id)
```
    findByID.
    Finds an instance of Sample in the database by the Sample ID.
    
    Specified by:
    
    findByID in interface SampleDAO
    
    Parameters:
    id -
    
    Returns:
    a Sample object.
  - findBySWAccession
```
public Sample findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Specified by:
    
    findBySWAccession in interface SampleDAO
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Sample object.
  - findByOwnerID
```
public List<Sample> findByOwnerID(Integer registrationId)
```
    findByOwnerID.
    
    Specified by:
    
    findByOwnerID in interface SampleDAO
    
    Parameters:
    registrationId - a Integer object.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<Sample> findByCriteria(String criteria,
                          boolean isCaseSens)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface SampleDAO
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - listComplete
```
public List<Sample> listComplete()
```
    listComplete.
    
    Specified by:
    
    listComplete in interface SampleDAO
    
    Returns:
    a List object.
  - listIncomplete
```
public List<Sample> listIncomplete()
```
    listIncomplete.
    
    Specified by:
    
    listIncomplete in interface SampleDAO
    
    Returns:
    a List object.
  - listSample
```
public List<Sample> listSample(Registration registaration)
```
    listSample.
    
    Specified by:
    
    listSample in interface SampleDAO
    
    Parameters:
    registaration -
    
    Returns:
    a List object.
  - getRootSamples
```
public List<Sample> getRootSamples(Study study)
```
    getRootSamples.
    
    Specified by:
    
    getRootSamples in interface SampleDAO
    
    Parameters:
    study - a Study object.
    
    Returns:
    a List object.
  - getRootSample
```
public Sample getRootSample(Sample sample)
```
    getRootSample.
    
    Specified by:
    
    getRootSample in interface SampleDAO
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Sample object.
  - updateDetached
```
public Sample updateDetached(Sample sample)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface SampleDAO
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Sample object.
  - list
```
public List<Sample> list()
```
    list.
    
    Specified by:
    
    list in interface SampleDAO
    
    Returns:
    a List object.
  - update
```
public void update(Registration registration,
          Sample sample)
```
    update.
    
    Specified by:
    
    update in interface SampleDAO
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
  - insert
```
public Integer insert(Registration registration,
             Sample sample)
```
    insert.
    
    Specified by:
    
    insert in interface SampleDAO
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
    
    Returns:
    a Integer object.
  - updateDetached
```
public Sample updateDetached(Registration registration,
                    Sample sample)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface SampleDAO
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
    
    Returns:
    a Sample object.

Class SampleDAOHibernate

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

SampleDAOHibernate

Method Detail

insert

update

delete

getFiles

isHasFile

getFiles

isHasFile

getCountFiles

getCountFiles

findByTitle

findByName

matchName

findByID

findBySWAccession

findByOwnerID

findByCriteria

listComplete

listIncomplete

listSample

getRootSamples

getRootSample

updateDetached

list

update

insert

updateDetached