org.proteios.core
Class Modification<D extends ModificationData>

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<D>

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Ownable, Removable, Shareable

Direct Known Subclasses:

ObservedModification, SearchModification

public abstract class Modification<D extends ModificationData>
extends CommonItem<D>

This is the base class for for the two types of Modifications: ObservedModification and SearchModification.

Version:

2.0

Author:

Fredrik

Field Summary

static int	MAX_CVID_LENGTH The maximum length of the CV ID that can be saved in the database.
static int	MAX_DIFF_FORMULA_LENGTH The maximum length of the formula that can be stored in the database.

Fields inherited from interface org.proteios.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Method Summary

float	getAverageDeltaMass()
float	getAverageMass()
String	getCvId() Get the controlled vocabulary ID of the modification.
String	getDiffFormula() Get the differential chemical formula of the modification.
double	getMonoisotopicDeltaMass()
double	getMonoisotopicMass()
int	getPosition()
boolean	isSubstitutionModification()
void	setAverageDeltaMass(float averageDeltaMass)
void	setAverageMass(float averageMass)
void	setCvId(String cvId) Set the CV ID of the Modification.
void	setDiffFormula(String diffFormula) Set the differential chemical formula of the Modification.
void	setMonoisotopicDeltaMass(double monoisotopicDeltaMass)
void	setMonoisotopicMass(double monoisotopicMass)
void	setPosition(int position)
void	setSubstitutionModification(boolean substitutionModification)

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, isUsed, 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, getType, getVersion

Methods inherited from interface org.proteios.core.AccessControlled

checkPermission, hasPermission

Methods inherited from interface org.proteios.core.Ownable

getOwner, setOwner

Field Detail

MAX_DIFF_FORMULA_LENGTH

public static final int MAX_DIFF_FORMULA_LENGTH

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

See Also:

setDiffFormula(String), Constant Field Values

MAX_CVID_LENGTH

public static final int MAX_CVID_LENGTH

The maximum length of the CV ID that can be saved in the database.

See Also:

Constant Field Values

Method Detail

isSubstitutionModification

public boolean isSubstitutionModification()

Returns:

Returns the substitutionModififcation flag

setSubstitutionModification

public void setSubstitutionModification(boolean substitutionModification)

Parameters:

substitutionModification - Whether the modification is an amino acid substitution.

getPosition

public int getPosition()

Returns:

Returns the position index.

setPosition

public void setPosition(int position)

Parameters:

position - The position index to set.

getAverageMass

public float getAverageMass()

Returns:

Returns the average mass.

setAverageMass

public void setAverageMass(float averageMass)

Parameters:

averageMass - The averageMass index to set.

getAverageDeltaMass

public float getAverageDeltaMass()

Returns:

Returns the average delta mass.

setAverageDeltaMass

public void setAverageDeltaMass(float averageDeltaMass)

Parameters:

averageDeltaMass - The averageDeltaMass index to set.

getMonoisotopicMass

public double getMonoisotopicMass()

Returns:

Returns the monoisotopic mass.

setMonoisotopicMass

public void setMonoisotopicMass(double monoisotopicMass)

Parameters:

monoisotopicMass - The monoisotopicMass index to set.

getMonoisotopicDeltaMass

public double getMonoisotopicDeltaMass()

Returns:

Returns the monoisotopic delta mass.

setMonoisotopicDeltaMass

public void setMonoisotopicDeltaMass(double monoisotopicDeltaMass)

Parameters:

monoisotopicDeltaMass - The monoisotopicDeltaMass index to set.

getDiffFormula

public String getDiffFormula()

Get the differential chemical formula of the modification.

Returns:

The formula for the modification

setDiffFormula

public void setDiffFormula(String diffFormula)
                    throws PermissionDeniedException,
                           InvalidDataException

Set the differential chemical formula of the Modification. The value may be null but must not be longer than the value specified by the MAX_DIFF_FORMULA_LENGTH constant.

Parameters:

diffFormula - String The new value for the formula

Throws:

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

InvalidDataException - If the string is too long

getCvId

public String getCvId()

Get the controlled vocabulary ID of the modification.

Returns:

The CV ID for the modification

setCvId

public void setCvId(String cvId)
             throws PermissionDeniedException,
                    InvalidDataException

Set the CV ID of the Modification. The value may be null but must not be longer than the value specified by the MAX_CVID_LENGTH constant.

Parameters:

cvId - The new CV ID

Throws:

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

InvalidDataException - If the string is too long