org.proteios.core
Class ObservedModification

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.Modification<ObservedModificationData>
                      org.proteios.core.ObservedModification

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Ownable, Removable, Shareable

public class ObservedModification
extends Modification<ObservedModificationData>

This class represent observedModifications.

Version:

2.0

Author:

Fredrik

Field Summary

static Item

TYPE The type of item represented by this class.

Fields inherited from class org.proteios.core.Modification

MAX_CVID_LENGTH, MAX_DIFF_FORMULA_LENGTH

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

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

Methods inherited from class org.proteios.core.Modification

getAverageDeltaMass, getAverageMass, getCvId, getDiffFormula, getMonoisotopicDeltaMass, getMonoisotopicMass, getPosition, isSubstitutionModification, setAverageDeltaMass, setAverageMass, setCvId, setDiffFormula, setMonoisotopicDeltaMass, setMonoisotopicMass, setPosition, setSubstitutionModification

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_OBSERVEDMODIFICATION, getType()

Method Detail

getById

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

Get an ObservedModification 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 ObservedModification item

Throws:

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

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

BaseException - If there is another error

getQuery

public static ItemQuery<ObservedModification> getQuery()

Get a query that returns observedModification 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 observedModification

Specified by:

isUsed in class BasicItem<ObservedModificationData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getModifiedAminoAcid

public char getModifiedAminoAcid()

Returns:

Returns the modifiedAminoAcid.

setModifiedAminoAcid

public void setModifiedAminoAcid(char modifiedAminoAcid)

Parameters:

modifiedAminoAcid - The modifiedAminoAcid to set.