com.compomics.util.experiment.biology.ions
Class Glycon

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.Ion
          extended by com.compomics.util.experiment.biology.ions.Glycon
All Implemented Interfaces:
Serializable, Cloneable

public class Glycon
extends Ion

This class will models a glycon fragment.

Author:
Marc Vaudel
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.Ion
Ion.IonType
 
Field Summary
static int DEUTEROACETYLATED_MASS
          Final index for deuteroacetylated masses.
static int DEUTEROMETHYLATED_MASS
          Final index for deuteromethylated masses.
static int PERACETYLATED_MASS
          Final index for peracetylated masses.
static int PERMETHYLATED_MASS
          Final index for permethylated masses.
static int UNDERIVATED_MASS
          Final index for underivated masses.
 
Fields inherited from class com.compomics.util.experiment.biology.Ion
theoreticMass, type
 
Constructor Summary
Glycon(String name, String longName)
          Constructor for a glycon.
 
Method Summary
 void addMass(int massType, double value)
          Add a mass for this glycon.
 double getMass(int aType)
          Get the glycon mass.
 String getName()
          Returns the name of the ion.
 ArrayList<NeutralLoss> getNeutralLosses()
          Returns the possible neutral losses of this ion type.
static ArrayList<Integer> getPossibleSubtypes()
          Returns an arraylist of possible subtypes.
 CvTerm getPrideCvTerm()
          Returns the pride cv term adapted to the fragment ion.
 int getSubType()
          Returns the ion subtype.
 String getSubTypeAsString()
          Returns the subtype as string.
 boolean isSameAs(Ion anotherIon)
          Returns a boolean indicating whether the ion is the same as another ion.
 
Methods inherited from class com.compomics.util.experiment.biology.Ion
getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getType, getTypeAsString, getTypeAsString, setTheoreticMass
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

UNDERIVATED_MASS

public static final int UNDERIVATED_MASS
Final index for underivated masses.

See Also:
Constant Field Values

PERMETHYLATED_MASS

public static final int PERMETHYLATED_MASS
Final index for permethylated masses.

See Also:
Constant Field Values

DEUTEROMETHYLATED_MASS

public static final int DEUTEROMETHYLATED_MASS
Final index for deuteromethylated masses.

See Also:
Constant Field Values

PERACETYLATED_MASS

public static final int PERACETYLATED_MASS
Final index for peracetylated masses.

See Also:
Constant Field Values

DEUTEROACETYLATED_MASS

public static final int DEUTEROACETYLATED_MASS
Final index for deuteroacetylated masses.

See Also:
Constant Field Values
Constructor Detail

Glycon

public Glycon(String name,
              String longName)
Constructor for a glycon.

Parameters:
name - The name of the glycon
longName - A shortened name for the glycon
Method Detail

addMass

public void addMass(int massType,
                    double value)
Add a mass for this glycon.

Parameters:
massType - mass type indexed according to the static field
value - Value of the mass

getMass

public double getMass(int aType)
Get the glycon mass.

Parameters:
aType - Type of mass requested indexed according to static int.
Returns:
the requested mass

getName

public String getName()
Description copied from class: Ion
Returns the name of the ion. The name should be short enough to be displayed on a spectrum.

Specified by:
getName in class Ion
Returns:
the name of the ion

getPrideCvTerm

public CvTerm getPrideCvTerm()
Description copied from class: Ion
Returns the pride cv term adapted to the fragment ion. null if none corresponding.

Specified by:
getPrideCvTerm in class Ion
Returns:
the pride cv term adapted to the fragment ion. null if none corresponding

getSubType

public int getSubType()
Description copied from class: Ion
Returns the ion subtype.

Specified by:
getSubType in class Ion
Returns:
the ion subtype as integer

getSubTypeAsString

public String getSubTypeAsString()
Description copied from class: Ion
Returns the subtype as string.

Specified by:
getSubTypeAsString in class Ion
Returns:
the subtype as string

getPossibleSubtypes

public static ArrayList<Integer> getPossibleSubtypes()
Returns an arraylist of possible subtypes.

Returns:
an arraylist of possible subtypes

getNeutralLosses

public ArrayList<NeutralLoss> getNeutralLosses()
Description copied from class: Ion
Returns the possible neutral losses of this ion type. An empty list if none.

Specified by:
getNeutralLosses in class Ion
Returns:
the possible neutral losses of this ion type

isSameAs

public boolean isSameAs(Ion anotherIon)
Description copied from class: Ion
Returns a boolean indicating whether the ion is the same as another ion.

Specified by:
isSameAs in class Ion
Parameters:
anotherIon - the other ion
Returns:
a boolean indicating whether the ion is the same as another ion


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