org.proteios.core
Class Peptide

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<PeptideData>
                          org.proteios.core.Peptide

All Implemented Interfaces:

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

public class Peptide
extends PolyPeptide<PeptideData>

This class represent peptide.

Version:

2.0

Author:

Fredrik

Field Summary

static int	MAX_POSTSEQUENCE_LENGTH The maximum length of the postSequence string that can be stored in the database.
static int	MAX_PRESEQUENCE_LENGTH The maximum length of the preSequence string that can be stored in the database.
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 Peptide	getById(DbControl dc, int id) Get an Peptide item when you know the id.
int	getEndPosition()
String	getPostSequence() Get the sequence before this peptide.
String	getPreSequence() Get the sequence before this peptide.
static ItemQuery<Peptide>	getQuery() Get a query that returns protein items.
int	getStartPosition()
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no Sample has been created from this protein
void	setEndPosition(int endPosition)
void	setPostSequence(String postSequence) Set the postSequence for this SearchResult item.
void	setPreSequence(String preSequence) Set the preSequence for this SearchResult item.
void	setStartPosition(int startPosition)

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_PEPTIDE, getType()

MAX_PRESEQUENCE_LENGTH

public static final int MAX_PRESEQUENCE_LENGTH

The maximum length of the preSequence string that can be stored in the database.

See Also:

setPreSequence(String), Constant Field Values

MAX_POSTSEQUENCE_LENGTH

public static final int MAX_POSTSEQUENCE_LENGTH

The maximum length of the postSequence string that can be stored in the database.

See Also:

setPostSequence(String), Constant Field Values

Method Detail

getById

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

Get an Peptide 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 Peptide 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<Peptide> 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<PeptideData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getPreSequence

public String getPreSequence()

Get the sequence before this peptide.

Returns:

the pre sequence

setPreSequence

public void setPreSequence(String preSequence)
                    throws InvalidDataException

Set the preSequence for this SearchResult item. The value may be null but must not be longer than the value specified by the MAX_PRESEQUENCE_LENGTH constant.

Parameters:

preSequence - The new preSequence for this item

Throws:

InvalidDataException - If the preSequence is longer than MAX_PRESEQUENCE_LENGTH

getPostSequence

public String getPostSequence()

Get the sequence before this peptide.

Returns:

the post sequence

setPostSequence

public void setPostSequence(String postSequence)
                     throws InvalidDataException

Set the postSequence for this SearchResult item. The value may be null but must not be longer than the value specified by the MAX_POSTSEQUENCE_LENGTH constant.

Parameters:

postSequence - The new postSequence for this item

Throws:

InvalidDataException - If the postSequence is longer than MAX_POSTSEQUENCE_LENGTH

getStartPosition

public int getStartPosition()

Returns:

Returns the startPosition.

setStartPosition

public void setStartPosition(int startPosition)

Parameters:

startPosition - The startPosition to set.

getEndPosition

public int getEndPosition()

Returns:

Returns the endPosition.

setEndPosition

public void setEndPosition(int endPosition)

Parameters:

endPosition - The endPosition to set.