SampleServiceImpl (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.common.business.impl.SampleServiceImpl

All Implemented Interfaces:

SampleService
```
public class SampleServiceImpl
extends Object
implements SampleService
```
SampleServiceImpl class.

Version:

$Id: $Id

Author:

boconnor

Field Summary
- Fields inherited from interface net.sourceforge.seqware.common.business.SampleService
  NAME

Constructor Summary

Constructors
Constructor and Description

SampleServiceImpl()
Constructor for SampleServiceImpl.

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

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`delete(Sample sample, boolean deleteRealFiles)` delete.
`List<Sample>`	`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`Sample`	`findByID(Integer sampleId)` findByID.
`Sample`	`findByName(String name)` findByName.
`List<Sample>`	`findByOwnerID(Integer registrationId)` findByOwnerID.
`Sample`	`findBySWAccession(Integer swAccession)` findBySWAccession.
`Sample`	`findByTitle(String title)` findByTitle.
`List<File>`	`getFiles(Integer sampleId)` getFiles.
`List<File>`	`getFiles(Integer studyId, String metaType)` getFiles.
`Sample`	`getRootSample(Sample childSample)` getRootSample.
`List<Sample>`	`getRootSamples(Study study)` getRootSamples.
`boolean`	`hasNameBeenUsed(String oldName, String newName)` hasNameBeenUsed.
`Integer`	`insert(Registration registration, Sample sample)` insert.
`Integer`	`insert(Sample sample)` insert.
`boolean`	`isHasFile(Integer sampleId)` isHasFile.
`boolean`	`isHasFile(Integer studyId, String metaType)` isHasFile.
`List<Sample>`	`list()` list.
`List<Sample>`	`listComplete()` listComplete.
`List<Sample>`	`listIncomplete()` listIncomplete.
`List<Sample>`	`listSample(Registration registration)` listSample.
`SortedSet<Sample>`	`listWithHasFile(Integer expId, SortedSet<Sample> list, String metaType)` listWithHasFile.
`List<Sample>`	`matchName(String name)`
`void`	`setFileDAO(FileDAO fileDAO)` Sets a private member variable with an instance of an implementation of FileDAO.
`void`	`setSampleDAO(SampleDAO sampleDAO)` setSampleDAO.
`SortedSet<Sample>`	`setWithHasFile(Integer expId, SortedSet<Sample> list)` setWithHasFile.
`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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - SampleServiceImpl
```
public SampleServiceImpl()
```
    Constructor for SampleServiceImpl.
- Method Detail
  - setSampleDAO
```
public void setSampleDAO(SampleDAO sampleDAO)
```
    setSampleDAO.
    Sets a private member variable with an instance of an implementation of SampleDAO. This method is called by the Spring framework at run time.
    
    Specified by:
    
    setSampleDAO in interface SampleService
    
    Parameters:
    sampleDAO - a SampleDAO object.
    See Also:
    SampleDAO
  - setFileDAO
```
public void setFileDAO(FileDAO fileDAO)
```
    Sets a private member variable with an instance of an implementation of FileDAO. This method is called by the Spring framework at run time.
    
    Parameters:
    fileDAO - implementation of FileDAO
    See Also:
    FileDAO
  - insert
```
public Integer insert(Sample sample)
```
    insert.
    Inserts an instance of Sample into the database.
    
    Specified by:
    
    insert in interface SampleService
    
    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 SampleService
    
    Parameters:
    sample - a Sample object.
  - delete
```
public void delete(Sample sample,
          boolean deleteRealFiles)
```
    delete.
    Deletes an instance of Sample in the database.
    
    Specified by:
    
    delete in interface SampleService
    
    Parameters:
    sample -
    deleteRealFiles -
  - getFiles
```
public List<File> getFiles(Integer sampleId)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface SampleService
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer sampleId)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface SampleService
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a boolean.
  - getFiles
```
public List<File> getFiles(Integer studyId,
                  String metaType)
```
    getFiles.
    
    Specified by:
    
    getFiles in interface SampleService
    
    Parameters:
    studyId - a Integer object.
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
public boolean isHasFile(Integer studyId,
                String metaType)
```
    isHasFile.
    
    Specified by:
    
    isHasFile in interface SampleService
    
    Parameters:
    studyId - a Integer object.
    metaType - a String object.
    
    Returns:
    a boolean.
  - setWithHasFile
```
public SortedSet<Sample> setWithHasFile(Integer expId,
                               SortedSet<Sample> list)
```
    setWithHasFile.
    
    Specified by:
    
    setWithHasFile in interface SampleService
    
    Parameters:
    expId - a Integer object.
    list - a SortedSet object.
    
    Returns:
    a SortedSet object.
  - listWithHasFile
```
public SortedSet<Sample> listWithHasFile(Integer expId,
                                SortedSet<Sample> list,
                                String metaType)
```
    listWithHasFile.
    
    Specified by:
    
    listWithHasFile in interface SampleService
    
    Parameters:
    expId - a Integer object.
    list - a SortedSet object.
    metaType - a String object.
    
    Returns:
    a SortedSet object.
  - findByTitle
```
public Sample findByTitle(String title)
```
    findByTitle.
    
    Specified by:
    
    findByTitle in interface SampleService
    
    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, and copies the Sample properties to an instance of Sample.
    
    Specified by:
    
    findByName in interface SampleService
    
    Parameters:
    name - a String object.
    
    Returns:
    a Sample object.
  - matchName
```
public List<Sample> matchName(String name)
```
    Specified by:
    
    matchName in interface SampleService
  - findByID
```
public Sample findByID(Integer sampleId)
```
    findByID.
    
    Specified by:
    
    findByID in interface SampleService
    
    Parameters:
    sampleId -
    
    Returns:
    a Sample object.
  - findBySWAccession
```
public Sample findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Specified by:
    
    findBySWAccession in interface SampleService
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Sample object.
  - findByOwnerID
```
public List<Sample> findByOwnerID(Integer registrationId)
```
    findByOwnerID.
    
    Specified by:
    
    findByOwnerID in interface SampleService
    
    Parameters:
    registrationId - a Integer object.
    
    Returns:
    a List object.
  - findByCriteria
```
public List<Sample> findByCriteria(String criteria,
                          boolean isCaseSens)
```
    findByCriteria.
    
    Specified by:
    
    findByCriteria in interface SampleService
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - hasNameBeenUsed
```
public boolean hasNameBeenUsed(String oldName,
                      String newName)
```
    hasNameBeenUsed.
    Determines if an email address has already been used.
    
    Specified by:
    
    hasNameBeenUsed in interface SampleService
    
    Parameters:
    oldName - a String object.
    newName - a String object.
    
    Returns:
    a boolean.
  - listComplete
```
public List<Sample> listComplete()
```
    listComplete.
    
    Specified by:
    
    listComplete in interface SampleService
    
    Returns:
    a List object.
  - listIncomplete
```
public List<Sample> listIncomplete()
```
    listIncomplete.
    
    Specified by:
    
    listIncomplete in interface SampleService
    
    Returns:
    a List object.
  - listSample
```
public List<Sample> listSample(Registration registration)
```
    listSample.
    
    Specified by:
    
    listSample in interface SampleService
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - updateDetached
```
public Sample updateDetached(Sample sample)
```
    updateDetached.
    
    Specified by:
    
    updateDetached in interface SampleService
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Sample object.
  - getRootSamples
```
public List<Sample> getRootSamples(Study study)
```
    getRootSamples.
    
    Specified by:
    
    getRootSamples in interface SampleService
    
    Parameters:
    study - a Study object.
    
    Returns:
    a List object.
  - getRootSample
```
public Sample getRootSample(Sample childSample)
```
    getRootSample.
    
    Specified by:
    
    getRootSample in interface SampleService
    
    Parameters:
    childSample - a Sample object.
    
    Returns:
    a Sample object.
  - list
```
public List<Sample> list()
```
    list.
    
    Specified by:
    
    list in interface SampleService
    
    Returns:
    a List object.
  - update
```
public void update(Registration registration,
          Sample sample)
```
    update.
    
    Specified by:
    
    update in interface SampleService
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
  - insert
```
public Integer insert(Registration registration,
             Sample sample)
```
    insert.
    
    Specified by:
    
    insert in interface SampleService
    
    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 SampleService
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
    
    Returns:
    a Sample object.

Class SampleServiceImpl

Field Summary

Fields inherited from interface net.sourceforge.seqware.common.business.SampleService

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SampleServiceImpl

Method Detail

setSampleDAO

setFileDAO

insert

update

delete

getFiles

isHasFile

getFiles

isHasFile

setWithHasFile

listWithHasFile

findByTitle

findByName

matchName

findByID

findBySWAccession

findByOwnerID

findByCriteria

hasNameBeenUsed

listComplete

listIncomplete

listSample

updateDetached

getRootSamples

getRootSample

list

update

insert

updateDetached