SampleService (SeqWare 1.1.2 API)

All Known Implementing Classes:

SampleServiceImpl
```
public interface SampleService
```
SampleService interface.

Version:

$Id: $Id

Author:

boconnor

Field Summary

Fields
Modifier and Type Field and Description

static String NAME
Constant NAME="sampleService"

Fields
Modifier and Type	Field and Description
`static String`	`NAME` Constant `NAME="sampleService"`

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 id)` 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`	`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.

- Field Detail
  - NAME
```
static final String NAME
```
    Constant NAME="sampleService"
    
    See Also:
    Constant Field Values
- Method Detail
  - setSampleDAO
```
void setSampleDAO(SampleDAO sampleDAO)
```
    setSampleDAO.
    
    Parameters:
    sampleDAO - a SampleDAO object.
  - insert
```
Integer insert(Sample sample)
```
    insert.
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Integer object.
  - insert
```
Integer insert(Registration registration,
             Sample sample)
```
    insert.
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
    
    Returns:
    a Integer object.
  - update
```
void update(Sample sample)
```
    update.
    
    Parameters:
    sample - a Sample object.
  - update
```
void update(Registration registration,
          Sample sample)
```
    update.
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
  - delete
```
void delete(Sample sample,
          boolean deleteRealFiles)
```
    delete.
    
    Parameters:
    sample -
    deleteRealFiles -
  - findByName
```
Sample findByName(String name)
```
    findByName.
    
    Parameters:
    name - a String object.
    
    Returns:
    a Sample object.
  - matchName
```
List<Sample> matchName(String name)
```
  - findByTitle
```
Sample findByTitle(String title)
```
    findByTitle.
    
    Parameters:
    title - a String object.
    
    Returns:
    a Sample object.
  - findByID
```
Sample findByID(Integer id)
```
    findByID.
    
    Parameters:
    id - a Integer object.
    
    Returns:
    a Sample object.
  - findBySWAccession
```
Sample findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Sample object.
  - listComplete
```
List<Sample> listComplete()
```
    listComplete.
    
    Returns:
    a List object.
  - listIncomplete
```
List<Sample> listIncomplete()
```
    listIncomplete.
    
    Returns:
    a List object.
  - hasNameBeenUsed
```
boolean hasNameBeenUsed(String oldName,
                      String newName)
```
    hasNameBeenUsed.
    
    Parameters:
    oldName - a String object.
    newName - a String object.
    
    Returns:
    a boolean.
  - listSample
```
List<Sample> listSample(Registration registration)
```
    listSample.
    
    Parameters:
    registration - a Registration object.
    
    Returns:
    a List object.
  - getFiles
```
List<File> getFiles(Integer sampleId)
```
    getFiles.
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a List object.
  - isHasFile
```
boolean isHasFile(Integer sampleId)
```
    isHasFile.
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a boolean.
  - getFiles
```
List<File> getFiles(Integer studyId,
                  String metaType)
```
    getFiles.
    
    Parameters:
    studyId - a Integer object.
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
boolean isHasFile(Integer studyId,
                String metaType)
```
    isHasFile.
    
    Parameters:
    studyId - a Integer object.
    metaType - a String object.
    
    Returns:
    a boolean.
  - setWithHasFile
```
SortedSet<Sample> setWithHasFile(Integer expId,
                               SortedSet<Sample> list)
```
    setWithHasFile.
    
    Parameters:
    expId - a Integer object.
    list - a SortedSet object.
    
    Returns:
    a SortedSet object.
  - listWithHasFile
```
SortedSet<Sample> listWithHasFile(Integer expId,
                                SortedSet<Sample> list,
                                String metaType)
```
    listWithHasFile.
    
    Parameters:
    expId - a Integer object.
    list - a SortedSet object.
    metaType - a String object.
    
    Returns:
    a SortedSet object.
  - updateDetached
```
Sample updateDetached(Sample sample)
```
    updateDetached.
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Sample object.
  - updateDetached
```
Sample updateDetached(Registration registration,
                    Sample sample)
```
    updateDetached.
    
    Parameters:
    registration - a Registration object.
    sample - a Sample object.
    
    Returns:
    a Sample object.
  - findByOwnerID
```
List<Sample> findByOwnerID(Integer registrationId)
```
    findByOwnerID.
    
    Parameters:
    registrationId - a Integer object.
    
    Returns:
    a List object.
  - findByCriteria
```
List<Sample> findByCriteria(String criteria,
                          boolean isCaseSens)
```
    findByCriteria.
    
    Parameters:
    criteria - a String object.
    isCaseSens - a boolean.
    
    Returns:
    a List object.
  - getRootSamples
```
List<Sample> getRootSamples(Study study)
```
    getRootSamples.
    
    Parameters:
    study - a Study object.
    
    Returns:
    a List object.
  - getRootSample
```
Sample getRootSample(Sample childSample)
```
    getRootSample.
    
    Parameters:
    childSample - a Sample object.
    
    Returns:
    a Sample object.
  - list
```
List<Sample> list()
```
    list.
    
    Returns:
    a List object.

Interface SampleService

Field Summary

Method Summary

Field Detail

NAME

Method Detail

setSampleDAO

insert

insert

update

update

delete

findByName

matchName

findByTitle

findByID

findBySWAccession

listComplete

listIncomplete

hasNameBeenUsed

listSample

getFiles

isHasFile

getFiles

isHasFile

setWithHasFile

listWithHasFile

updateDetached

updateDetached

findByOwnerID

findByCriteria

getRootSamples

getRootSample

list