org.proteios.core
Class BioMaterial<D extends BioMaterialData>

java.lang.Object
  org.proteios.core.BasicItem<D>
      org.proteios.core.OwnedItem<D>
          org.proteios.core.SharedItem<D>
              org.proteios.core.CommonItem<D>
                  org.proteios.core.AnnotatedItem<D>
                      org.proteios.core.BioMaterial<D>

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Removable, Shareable

Direct Known Subclasses:

BioSource, MeasuredBioMaterial

public abstract class BioMaterial<D extends BioMaterialData>
extends AnnotatedItem<D>

This is the base class for for the four types of biomaterials: BioSource, Sample, Extract and LabeledExtract.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2009-04-09 08:48:11 +0200 (Thu, 09 Apr 2009) $

Field Summary

static int	MAX_EXTERNAL_ID_LENGTH The maximum length of the external id that can be stored in the database.
static int	MAX_STORAGE_LOCATION_LENGTH The maximum length of the storage location info that can be stored in the database.

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

void	addFile(File file) Add a File
String	getExternalId() Get the external id of the biomaterial.
Set<File>	getFiles()
String	getStorageLocation() Get the storage location of the biomaterial.
void	setExternalId(String externalId) Set the external id of the biomaterial.
void	setFiles(Set<File> files) Set the File files set.
void	setStorageLocation(String storageLocation) Set the storage location of the biomaterial.

Methods inherited from class org.proteios.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved

Methods inherited from class org.proteios.core.SharedItem

getItemKey, getProjectKey, isShared, setItemKey, setProjectKey

Methods inherited from class org.proteios.core.OwnedItem

getOwner, setOwner

Methods inherited from class org.proteios.core.BasicItem

checkPermission, equals, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.proteios.core.Identifiable

getId, getType, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Field Detail

MAX_EXTERNAL_ID_LENGTH

public static final int MAX_EXTERNAL_ID_LENGTH

The maximum length of the external id that can be stored in the database.

See Also:

setExternalId(String), Constant Field Values

MAX_STORAGE_LOCATION_LENGTH

public static final int MAX_STORAGE_LOCATION_LENGTH

The maximum length of the storage location info that can be stored in the database.

See Also:

setStorageLocation(String), Constant Field Values

Method Detail

getExternalId

public String getExternalId()

Get the external id of the biomaterial. This value can be used to link with information in external databases. It is not used by the Proteios core and it doesn't have to be unique.

Returns:

The external id for the biomaterial

setExternalId

public void setExternalId(String externalId)
                   throws PermissionDeniedException,
                          InvalidDataException

Set the external id of the biomaterial. The value may be null but must not be longer than the value specified by the MAX_EXTERNAL_ID_LENGTH constant.

Parameters:

externalId - The new value for the external id

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the string is too long

addFile

public void addFile(File file)

Add a File

Parameters:

file - The File to add to the Set

getFiles

public Set<File> getFiles()
                   throws ItemNotFoundException,
                          BaseException

Returns:

Returns the files.

Throws:

ItemNotFoundException

BaseException

setFiles

public void setFiles(Set<File> files)

Set the File files set.

Parameters:

files - The new Set item.

getStorageLocation

public String getStorageLocation()

Get the storage location of the biomaterial.

Returns:

The storage location for the biomaterial

setStorageLocation

public void setStorageLocation(String storageLocation)
                        throws PermissionDeniedException,
                               InvalidDataException

Set the storage location of the biomaterial. The value may be null but must not be longer than the value specified by the MAX_STORAGE_LOCATION_LENGTH constant.

Parameters:

storageLocation - The new value for the storage location.

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the string is too long