SampleDAO (SeqWare 1.1.2 API)

All Known Implementing Classes:

SampleDAOHibernate
```
public interface SampleDAO
```
SampleDAO interface.

Version:

$Id: $Id

Author:

boconnor

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 sampleId)` 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 registration)` 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.

- Method Detail
  - 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)
```
    delete.
    
    Parameters:
    sample - a Sample object.
  - listComplete
```
List<Sample> listComplete()
```
    listComplete.
    
    Returns:
    a List object.
  - listIncomplete
```
List<Sample> listIncomplete()
```
    listIncomplete.
    
    Returns:
    a List object.
  - findByName
```
Sample findByName(String name)
```
    findByName.
    
    Parameters:
    name - a String object.
    
    Returns:
    a Sample object.
  - matchName
```
List<Sample> matchName(String name)
```
    findByName.
    
    Parameters:
    name - a String object.
    
    Returns:
    a Sample object.
  - findByTitle
```
Sample findByTitle(String title)
```
    findByTitle.
    
    Parameters:
    title - a String object.
    
    Returns:
    a Sample object.
  - findByID
```
Sample findByID(Integer sampleId)
```
    findByID.
    
    Parameters:
    sampleId - a Integer object.
    
    Returns:
    a Sample object.
  - 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 sampleId,
                  String metaType)
```
    getFiles.
    
    Parameters:
    sampleId - a Integer object.
    metaType - a String object.
    
    Returns:
    a List object.
  - isHasFile
```
boolean isHasFile(Integer sampleId,
                String metaType)
```
    isHasFile.
    
    Parameters:
    sampleId - a Integer object.
    metaType - a String object.
    
    Returns:
    a boolean.
  - getCountFiles
```
Map<Integer,Integer> getCountFiles(Integer expId)
```
    getCountFiles.
    
    Parameters:
    expId - a Integer object.
    
    Returns:
    a Map object.
  - getCountFiles
```
Map<Integer,Integer> getCountFiles(Integer expId,
                                 String metaType)
```
    getCountFiles.
    
    Parameters:
    expId - a Integer object.
    metaType - a String object.
    
    Returns:
    a Map object.
  - findBySWAccession
```
Sample findBySWAccession(Integer swAccession)
```
    findBySWAccession.
    
    Parameters:
    swAccession - a Integer object.
    
    Returns:
    a Sample 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 sample)
```
    getRootSample.
    
    Parameters:
    sample - a Sample object.
    
    Returns:
    a Sample object.
  - list
```
List<Sample> list()
```
    list.
    
    Returns:
    a List object.

Interface SampleDAO

Method Summary

Method Detail

insert

insert

update

update

delete

listComplete

listIncomplete

findByName

matchName

findByTitle

findByID

listSample

getFiles

isHasFile

getFiles

isHasFile

getCountFiles

getCountFiles

findBySWAccession

updateDetached

updateDetached

findByOwnerID

findByCriteria

getRootSamples

getRootSample

list