net.sf.basedb.core
Class BioMaterialList

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.OwnedItem<D>
          net.sf.basedb.core.SharedItem<D>
              net.sf.basedb.core.CommonItem<BioMaterialListData>
                  net.sf.basedb.core.BioMaterialList

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Ownable, Removable, Shareable

public class BioMaterialList
extends CommonItem<BioMaterialListData>

This class represents a list of biomaterials.

Version:

2.10

Author:

Nicklas

Last modified

$Date: 2009-06-25 15:11:37 +0200 (Thu, 25 Jun 2009) $

Field Summary

static int	MAX_EXTERNAL_ID_LENGTH The maximum length of the external id variable that can be stored in the database.
static Item	TYPE The type of item represented by this class.

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

BioMaterialList(BioMaterialListData listData)

Method Summary

boolean	add(BioMaterial bioMaterial) Add a biomaterial to this list.
int	add(Iterator<? extends BioMaterial> it) Add multiple biomaterials to this list in one go.
int	addAll(BioMaterialList list) Add all items from another biomaterial list to this list.
int	addIfPresentIn(int minCount, int maxCount, Collection<BioMaterialList> lists) Add items that are present in the specified number of lists to this list.
int	addIntersection(Collection<BioMaterialList> lists) Add items that are present in ALL OF the given lists to this list.
private int	addMembers(Set<BioMaterialData> items) Add members to this list.
int	addUnion(Collection<BioMaterialList> lists) Add items that are present in at least ONE OF the given lists to this list.
private void	checkMemberType(Collection<BioMaterialList> lists) Checks that the lists have the same member type as this list.
private void	checkMemberType(Item otherType) Checks if the other type is the same type as the member type of this list.
private static Set<BioMaterialData>	count(Collection<BioMaterialList> lists, int minCount, int maxCount) Count the number of times each item is present in the given lists and return those items that are found in >=minCount and <=maxCount lists.
ItemQuery<? extends BioMaterial>	getAllBioMaterials() Get a query that returns all biomaterials that can possibly be members of this list.
static BioMaterialList	getById(DbControl dc, int id) Get a BioMaterialList item when you know the id.
String	getExternalId() Get the external id for this list.
ItemQuery<? extends BioMaterial>	getMemberBioMaterials() Get a query that returns all biomaterials that are members of this list.
Item	getMemberType() Get the item type of members on this list.
static BioMaterialList	getNew(DbControl dc, Item memberType) Create a new BioMaterialList item.
static ItemQuery<BioMaterialList>	getQuery() Get a query that returns biomaterial lists.
int	getSize() Get the number of members in this list.
Item	getType() Get the type of item represented by the object.
private static Set<BioMaterialData>	intersection(Collection<BioMaterialList> lists) Create a set with the intersection of the items in the given lists.
void	remove(BioMaterial bioMaterial) Remove a biomaterial from the list.
int	removeAll(BioMaterialList list) Remove all items from this list that are present in the other list.
int	removeIfPresentIn(int minCount, int maxCount, Collection<BioMaterialList> lists) Remove items that are present in the specified number of lists from this list.
int	removeIntersection(Collection<BioMaterialList> lists) Remove items that are present in ALL OF the given lists from this list.
private int	removeMembers(Set<BioMaterialData> items) Remove members from this list
int	removeUnion(Collection<BioMaterialList> lists) Remove items that are present in at least ONE OF the given lists from this list.
int	retainAll(BioMaterialList list) Remove all items from this list that are NOT present in the other list.
int	retainIfPresentIn(int minCount, int maxCount, Collection<BioMaterialList> lists) Retain items that are present in the specified number of lists in this list.
int	retainIntersection(Collection<BioMaterialList> lists) Retain items that are present in ALL OF the given lists in this list.
private int	retainMembers(Set<BioMaterialData> items) Keep only specified members in this list
int	retainUnion(Collection<BioMaterialList> lists) Retain items that are present in at least ONE OF the given lists in this list.
void	setExternalId(String externalId) Set the external id for this list.
private void	setMemberType(Item memberType)
private static Set<BioMaterialData>	union(Collection<BioMaterialList> lists) Create a set with the union of the items in the given lists.

Methods inherited from class net.sf.basedb.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable

Methods inherited from class net.sf.basedb.core.SharedItem

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey, toTransferable

Methods inherited from class net.sf.basedb.core.OwnedItem

getOwner, isOwner, setOwner, takeOwnership, toTransferable

Methods inherited from class net.sf.basedb.core.BasicItem

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, setProjectDefaults, toString, toTransferable, validate

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Ownable

getOwner, isOwner, setOwner, takeOwnership

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.BIOMATERIALLIST, getType()

MAX_EXTERNAL_ID_LENGTH

public static final int MAX_EXTERNAL_ID_LENGTH

The maximum length of the external id variable that can be stored in the database. Check the length against this value before calling the setExternalId(String) method to avoid exceptions.

See Also:

Constant Field Values

Constructor Detail

BioMaterialList

BioMaterialList(BioMaterialListData listData)

Method Detail

getNew

public static BioMaterialList getNew(DbControl dc,
                                     Item memberType)
                              throws BaseException

Create a new BioMaterialList item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

memberType - The item type of members in this list

Returns:

The new BioMaterialList item

Throws:

BaseException - If there is an error

getById

public static BioMaterialList getById(DbControl dc,
                                      int id)
                               throws ItemNotFoundException,
                                      PermissionDeniedException,
                                      BaseException

Get a BioMaterialList item when you know the id.

Parameters:

dc - The DbControl which will be used for permission checking and database access.

id - The id of the item to load

Returns:

The BioMaterialList item

Throws:

ItemNotFoundException - If an item with the specified id is not found

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<BioMaterialList> getQuery()

Get a query that returns biomaterial lists.

Returns:

An ItemQuery object

intersection

private static Set<BioMaterialData> intersection(Collection<BioMaterialList> lists)

Create a set with the intersection of the items in the given lists.

Returns:

A set with items. The set is always a new set, modifications to it will not affect anything else

union

private static Set<BioMaterialData> union(Collection<BioMaterialList> lists)

Create a set with the union of the items in the given lists.

Returns:

A set with items. The set is always a new set, modifications to it will not affect anything else

count

private static Set<BioMaterialData> count(Collection<BioMaterialList> lists,
                                          int minCount,
                                          int maxCount)

Count the number of times each item is present in the given lists and return those items that are found in >=minCount and <=maxCount lists.

NOTE!

• 'minCount=1' and 'maxCount=number of lists' is the same as union(Collection)
• 'minCount=maxCount=number of lists' is the same as intersection(Collection).

Parameters:

lists - The lists to look in

minCount - The minimum number of list an item is required to be present in

maxCount - The maximum number of lists an item is allowed to the present in

Returns:

A set with items. It is always a new set, modifications to it will not affect anything else

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Returns:

A value indicating the type of item

getExternalId

public String getExternalId()

Get the external id for this list.

Returns:

A string with the external id of this item, or null

setExternalId

public void setExternalId(String externalId)
                   throws PermissionDeniedException,
                          InvalidDataException

Set the external id for this list. Null is allowed, but the value must not be longer than the value specified by the MAX_EXTERNAL_ID_LENGTH constant. The value doesn't have to be unique.

Parameters:

externalId - The new external id for this item

Throws:

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

InvalidDataException - If the new value is longer than MAX_EXTERNAL_ID_LENGTH

getSize

public int getSize()

Get the number of members in this list.

getMemberType

public Item getMemberType()

Get the item type of members on this list.

Returns:

An Item object

setMemberType

private void setMemberType(Item memberType)

checkMemberType

private void checkMemberType(Item otherType)

Checks if the other type is the same type as the member type of this list.

checkMemberType

private void checkMemberType(Collection<BioMaterialList> lists)

Checks that the lists have the same member type as this list.

add

public boolean add(BioMaterial bioMaterial)
            throws PermissionDeniedException,
                   InvalidDataException

Add a biomaterial to this list.

Parameters:

bioMaterial - The biomaterial to add to the list

Returns:

TRUE if the biomaterial was added, FALSE if it already existed in this list

Throws:

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

InvalidDataException - If the biomaterial is null or not of the correct member type

add

public int add(Iterator<? extends BioMaterial> it)
        throws PermissionDeniedException,
               InvalidDataException

Add multiple biomaterials to this list in one go.

Parameters:

it - An iterator that returns all biomaterials to be added, null items are ignored

Returns:

The numer of added biomaterials

Throws:

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

InvalidDataException - If the iterator returns a biomaterial of a different type than getMemberType()

remove

public void remove(BioMaterial bioMaterial)
            throws PermissionDeniedException,
                   InvalidDataException

Remove a biomaterial from the list.

Parameters:

bioMaterial - The biomaterial to remove.

Throws:

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

InvalidDataException - If the biomaterial is null

getMemberBioMaterials

public ItemQuery<? extends BioMaterial> getMemberBioMaterials()
                                                       throws BaseException

Get a query that returns all biomaterials that are members of this list.

Returns:

An ItemQuery object

Throws:

BaseException - If the query could not be created and configured.

getAllBioMaterials

public ItemQuery<? extends BioMaterial> getAllBioMaterials()
                                                    throws BaseException

Get a query that returns all biomaterials that can possibly be members of this list. NOTE! This is just a convenience function that calls BioSource.getQuery(), etc. depending on the member type of the list.

Returns:

An ItemQuery object

Throws:

BaseException - If the query could not be created and configured

See Also:

ListUtil.getQuery(Item)

addMembers

private int addMembers(Set<BioMaterialData> items)

Add members to this list.

Parameters:

items - The items to add

Returns:

The number of new items

removeMembers

private int removeMembers(Set<BioMaterialData> items)

Remove members from this list

Parameters:

items - The items to remove

Returns:

The number of removed items

retainMembers

private int retainMembers(Set<BioMaterialData> items)

Keep only specified members in this list

Parameters:

items - The items to keep

Returns:

The number of removed items

addAll

public int addAll(BioMaterialList list)

Add all items from another biomaterial list to this list. The new list is the union of the existing list and the added list. The other list must have the same member type as this list.

Parameters:

list - The list to add items from

Returns:

The number of items added (not including items that already was in this list)

addUnion

public int addUnion(Collection<BioMaterialList> lists)

Add items that are present in at least ONE OF the given lists to this list. Eg. the added items is the union from the given lists.

Parameters:

lists - The lists to add items from

Returns:

The number of items added (not including items that already was in this list)

addIfPresentIn

public int addIfPresentIn(int minCount,
                          int maxCount,
                          Collection<BioMaterialList> lists)

Add items that are present in the specified number of lists to this list.

• Delegate to addUnion(Collection) if minCount <= 1 && maxCount >= size(lists)
• Delegate to addIntersection(Collection) if minCount = size(lists) && maxCount >= size(lists).
• If minCount > size(lists) || minCount > maxCount no items will be added.

Parameters:

lists - The lists to add items from

minCount - The minimum number of lists an item is required to be present in

maxCount - The maximum number of lists an item is allowed to be present in

Returns:

The number of items added (not including items that already was in this list)

addIntersection

public int addIntersection(Collection<BioMaterialList> lists)

Add items that are present in ALL OF the given lists to this list. Eg. the added items is the intersection from the given lists.

Parameters:

lists - The lists to add items from

Returns:

The number of items added (not including items that already was in this list)

removeAll

public int removeAll(BioMaterialList list)

Remove all items from this list that are present in the other list.

Parameters:

list - The list that contains the items to remove

Returns:

The number of items removed from this list

removeUnion

public int removeUnion(Collection<BioMaterialList> lists)

Remove items that are present in at least ONE OF the given lists from this list. Eg. the removed items is the union from the given lists.

Parameters:

lists - The lists that contains the items to remove

Returns:

The number of items removed from this list

removeIfPresentIn

public int removeIfPresentIn(int minCount,
                             int maxCount,
                             Collection<BioMaterialList> lists)

Remove items that are present in the specified number of lists from this list.

• Delegate to removeUnion(Collection) if minCount <= 1 && maxCount >= size(lists)
• Delegate to removeIntersection(Collection) if minCount = size(lists) && maxCount >= size(lists).
• If minCount > size(lists) || minCount > maxCount no items will be removed.

Parameters:

lists - The lists with the items

minCount - The minimum number of lists an item is required to be present in

maxCount - The maximum number of lists an item is allowed to be present in

Returns:

The number of items removed

removeIntersection

public int removeIntersection(Collection<BioMaterialList> lists)

Remove items that are present in ALL OF the given lists from this list. Eg. the removed items is the intersection from the given lists.

Parameters:

lists - The lists that contains the items to remove

Returns:

The number of items removed from this list

retainAll

public int retainAll(BioMaterialList list)

Remove all items from this list that are NOT present in the other list. The new list is the intersection of the existing list and the other list. NOTE! If the other list is null or empty, all items will be removed from this list.

Parameters:

list - The list that contains the items to be retained

Returns:

The number of items removed from this list

retainUnion

public int retainUnion(Collection<BioMaterialList> lists)

Retain items that are present in at least ONE OF the given lists in this list. Eg. items that are not found in any of the given lists are removed from this list.

Parameters:

lists - The lists that contains the items to retain

Returns:

The number of items removed from this list

retainIntersection

public int retainIntersection(Collection<BioMaterialList> lists)

Retain items that are present in ALL OF the given lists in this list. Eg. items that are not found in all lists of the given lists are removed from this list.

Parameters:

lists - The lists that contains the items to retain

Returns:

The number of items removed from this list

retainIfPresentIn

public int retainIfPresentIn(int minCount,
                             int maxCount,
                             Collection<BioMaterialList> lists)

Retain items that are present in the specified number of lists in this list.

• Delegate to retainUnion(Collection) if minCount <= 1 && maxCount >= size(lists)
• Delegate to retainIntersection(Collection) if minCount = size(lists) && maxCount >= size(lists).
• If minCount > size(lists) || minCount > maxCount no items will be removed.

Parameters:

lists - The lists with the items

minCount - The minimum number of lists an item is required to be present in

maxCount - The maximum number of lists an item is allowed to be present in

Returns:

The number of items removed