org.proteios.core
Class Protein

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.PolyPeptide<ProteinData>
                          org.proteios.core.Protein

All Implemented Interfaces:

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

public class Protein
extends PolyPeptide<ProteinData>

This class represent proteins.

Version:

2.0

Author:

Fredrik

Last modified

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

Field Summary

static Item

TYPE The type of item represented by this class.

Fields inherited from class org.proteios.core.PolyPeptide

MAX_ACCESSION_NUMBER_LENGTH, MAX_LSID_LENGTH, MAX_SEQUENCE_LENGTH

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

Set<Annotatable>	getAnnotatableParents() Always null.
static Protein	getById(DbControl dc, int id) Get an Protein item when you know the id.
static ItemQuery<Protein>	getQuery() Get a query that returns protein items.
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no Sample has been created from this protein

Methods inherited from class org.proteios.core.PolyPeptide

addObservedModification, getAccessionNumber, getLsid, getObservedModifications, getSearchResult, getSequence, setAccessionNumber, setLsid, setObservedModifications, setSearchResult, setSequence

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, 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, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.PROTEIOS_PROTEIN, getType()

Method Detail

getById

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

Get an Protein 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 Protein item

Throws:

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

PermissionDeniedException - If the logged in user doesn't have read permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<Protein> getQuery()

Get a query that returns protein items.

Returns:

An ItemQuery object.

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

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Always null.

Throws:

BaseException

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no Sample has been created from this protein

Specified by:

isUsed in class BasicItem<ProteinData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException