org.proteios.core
Class DigestParameter

java.lang.Object
  org.proteios.core.BasicItem<D>
      org.proteios.core.OwnedItem<D>
          org.proteios.core.SharedItem<D>
              org.proteios.core.CommonItem<DigestParameterData>
                  org.proteios.core.DigestParameter

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Ownable, Removable, Shareable

public class DigestParameter
extends CommonItem<DigestParameterData>

This class represent spectrumsearch.

Version:

2.0

Author:

Fredrik

Last modified

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

Field Summary

static int	MAX_NAME_LENGTH The maximum length of the name string that can be stored in the database.
static int	MAX_SPECIFICITY_LENGTH The maximum length of the specificity string that can be stored in the database.
static Item	TYPE The type of item represented by this class.

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH

Method Summary

Set<Annotatable>	getAnnotatableParents() Always null.
int	getMaxNumMissedCleavages()
String	getName() Get the Name of this DigestParameter.
static ItemQuery<DigestParameter>	getQuery() Get a query that returns spectrumsearchset items.
String	getSpecificity() Get the description of this DigestParameter.
SpectrumSearch	getSpectrumSearch() Get the SpectrumSearch this digestParameter is associated with.
Item	getType() Get the type of item represented by the object.
boolean	isUsed() Check that: no item has been created from this peaklistset
void	setMaxNumMissedCleavages(int maxNumMissedCleavages)
void	setName(String name) Set the name for this DigrestParameter item.
void	setSpecificity(String specificity) Set the specificity for this DigrestParameter item.
void	setSpectrumSearch(SpectrumSearch spectrumSearch) Set the SpectrumSearch this DigestParameter is associated with.

Methods inherited from class org.proteios.core.CommonItem

getDescription, isRemoved, setDescription, 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_SPECTRUMSEARCH, getType()

MAX_NAME_LENGTH

public static final int MAX_NAME_LENGTH

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

See Also:

setName(String), Constant Field Values

MAX_SPECIFICITY_LENGTH

public static final int MAX_SPECIFICITY_LENGTH

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

See Also:

setSpecificity(String), Constant Field Values

Method Detail

getQuery

public static ItemQuery<DigestParameter> getQuery()

Get a query that returns spectrumsearchset 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 item has been created from this peaklistset

Specified by:

isUsed in class BasicItem<DigestParameterData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getSpectrumSearch

public SpectrumSearch getSpectrumSearch()
                                 throws BaseException

Get the SpectrumSearch this digestParameter is associated with.

Returns:

The SpectrumSearch item or null if not known

Throws:

BaseException - If there is another error

setSpectrumSearch

public void setSpectrumSearch(SpectrumSearch spectrumSearch)
                       throws BaseException

Set the SpectrumSearch this DigestParameter is associated with.

Parameters:

spectrumSearch - The new SpectrumSearch item

Throws:

BaseException - If there is another error

getMaxNumMissedCleavages

public int getMaxNumMissedCleavages()

Returns:

Returns the maxNumMissedCleavages.

setMaxNumMissedCleavages

public void setMaxNumMissedCleavages(int maxNumMissedCleavages)

Parameters:

maxNumMissedCleavages - The maxNumMissedCleavages to set.

getName

public String getName()

Get the Name of this DigestParameter.

Specified by:

getName in interface Nameable

Overrides:

getName in class CommonItem<DigestParameterData>

Returns:

the name of this digest parameter

setName

public void setName(String name)
             throws InvalidDataException

Set the name for this DigrestParameter item. The value may be null but must not be longer than the value specified by the MAX_NAME_LENGTH constant.

Specified by:

setName in interface Nameable

Overrides:

setName in class CommonItem<DigestParameterData>

Parameters:

name - The new name for this item

Throws:

InvalidDataException - If the name is longer than MAX_NAME_LENGTH

getSpecificity

public String getSpecificity()

Get the description of this DigestParameter.

Returns:

the description of this digest parameter

setSpecificity

public void setSpecificity(String specificity)
                    throws InvalidDataException

Set the specificity for this DigrestParameter item. The value may be null but must not be longer than the value specified by the MAX_SPECIFICITY_LENGTH constant.

Parameters:

specificity - The new specificity for this item

Throws:

InvalidDataException - If the specificity is longer than MAX_SPECIFICITY_LENGTH