org.proteios.core
Class SearchModification

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<SearchModificationData>
                      org.proteios.core.SearchModification

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Ownable, Removable, Shareable

public class SearchModification
extends Modification<SearchModificationData>

This class represent searchModifications.

Version:

2.0

Author:

Fredrik

Nested Class Summary

static class

SearchModification.TerminalSpecificity This enum is used to verify terminal specificities.

Field Summary

static int	MAX_AASPECIFICITY_LENGTH The maximum length of the amino acid specficity 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.Modification

MAX_CVID_LENGTH, MAX_DIFF_FORMULA_LENGTH

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

String	getAminoAcidSpecificity() Get the amino acid specificity of the modification.
Set<Annotatable>	getAnnotatableParents() Always null.
static ItemQuery<SearchModification>	getQuery() Get a query that returns searchModification items.
SpectrumSearch	getSpectrumSearch() Get the SpectrumSearch this SearchModification is associated with.
SearchModification.TerminalSpecificity	getTerminalSpecificity() The enum representation of the int value in the database is returned.
Item	getType() Get the type of item represented by the object.
boolean	isFixed()
boolean	isUsed() Check that: no Sample has been created from this searchModification
void	setAminoAcidSpecificity(String aminoAcidSpecificity) Set the amino acid specificities of the Modification.
void	setFixed(boolean fixed)
void	setSpectrumSearch(SpectrumSearch spectrumSearch) Set the SpectrumSearch this SearchModification is associated with.
void	setTerminalSpecificity(SearchModification.TerminalSpecificity terminalSpecificity) The terminalSpecificity is converted to the ordinal in the enum before it is sent to the data layer.

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_SEARCHMODIFICATION, getType()

MAX_AASPECIFICITY_LENGTH

public static final int MAX_AASPECIFICITY_LENGTH

The maximum length of the amino acid specficity that can be stored in the database.

See Also:

setAminoAcidSpecificity(String), Constant Field Values

Method Detail

getQuery

public static ItemQuery<SearchModification> getQuery()

Get a query that returns searchModification 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 searchModification

Specified by:

isUsed in class BasicItem<SearchModificationData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getSpectrumSearch

public SpectrumSearch getSpectrumSearch()
                                 throws BaseException

Get the SpectrumSearch this SearchModification 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 SearchModification is associated with.

Parameters:

spectrumSearch - The new SpectrumSearch item

Throws:

BaseException - If there is another error

getTerminalSpecificity

public SearchModification.TerminalSpecificity getTerminalSpecificity()

The enum representation of the int value in the database is returned. The String representation of the TerminalSpecificity can be obtained by toString().

Returns:

terminalSpecificity The terminal specificity

setTerminalSpecificity

public void setTerminalSpecificity(SearchModification.TerminalSpecificity terminalSpecificity)

The terminalSpecificity is converted to the ordinal in the enum before it is sent to the data layer.

Parameters:

terminalSpecificity - The terminalSpecificity to set.

isFixed

public boolean isFixed()

Returns:

Returns the fixed modififcation flag

setFixed

public void setFixed(boolean fixed)

Parameters:

fixed - Whether the modification is static.

getAminoAcidSpecificity

public String getAminoAcidSpecificity()

Get the amino acid specificity of the modification. Should be amino acid one letter codes

Returns:

The amino acid for the modification

setAminoAcidSpecificity

public void setAminoAcidSpecificity(String aminoAcidSpecificity)
                             throws PermissionDeniedException,
                                    InvalidDataException

Set the amino acid specificities of the Modification. The amino acids should be gven as single letter values. The value may be null but must not be longer than the value specified by the MAX_AASPECIFICITY_LENGTH constant.

Parameters:

aminoAcidSpecificity - The amino acid specificities

Throws:

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

InvalidDataException - If the string is too long