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

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.ImmoniumIon
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable

public class ImmoniumIon
extends Ion

Represents an immonium ion.

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 ALANINE
          Subtype int for an alanine immonium ion.
static int ARGININE
          Subtype int for an arginine immonium ion.
static int ASPARAGINE
          Subtype int for an asparagine immonium ion.
static int ASPARTIC_ACID
          Subtype int for an aspartic acid immonium ion.
static int CYSTEINE
          Subtype int for a cysteine immonium ion.
static int GLUTAMIC_ACID
          Subtype int for a glutamic acid immonium ion.
static int GLUTAMINE
          Subtype int for a glutamine immonium ion.
static int GLYCINE
          Subtype int for a glycine immonium ion.
static int HISTIDINE
          Subtype int for an histidine immonium ion.
static int ISOLEUCINE
          Subtype int for an isoleucine immonium ion.
static int LEUCINE
          Subtype int for a leucine immonium ion.
static int LYSINE
          Subtype int for a lysine immonium ion.
static int METHIONINE
          Subtype int for a methionine immonium ion.
static int PHENYLALANINE
          Subtype int for a phenylananine immonium ion.
static int PROLINE
          Subtype int for a proline immonium ion.
static int SELENOCYSTEINE
          Subtype int for a selenocysteine immonium ion.
static int SERINE
          Subtype int for a serine immonium ion.
static int THREONINE
          Subtype int for a threonine immonium ion.
static int TRYPTOPHAN
          Subtype int for a tryptophan immonium ion.
static int TYROSINE
          Subtype int for a tyrosine immonium ion.
static int VALINE
          Subtype int for a valine immonium ion.
 
Fields inherited from class com.compomics.util.experiment.biology.Ion
theoreticMass, type
 
Constructor Summary
ImmoniumIon(char residue)
          Constructor for an immonium ion.
ImmoniumIon(int subType)
          Constructor for an immonium ion.
 
Method Summary
 java.lang.String getName()
          Returns the name of the ion.
 java.util.ArrayList<NeutralLoss> getNeutralLosses()
          Returns the possible neutral losses of this ion type.
static java.util.ArrayList<java.lang.Integer> getPossibleSubtypes()
          Returns an arraylist of possible subtypes.
 CvTerm getPrideCvTerm()
          Returns the pride cv term adapted to the fragment ion.
static char getResidue(int subtype)
          Returns the amino acid of the immonium ion based on the subtype index.
 int getSubType()
          Returns the ion subtype.
static int getSubtype(char residue)
          Returns the subtype identifier based on the amino acid one letter symbol.
 java.lang.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

ALANINE

public static final int ALANINE
Subtype int for an alanine immonium ion.

See Also:
Constant Field Values

ARGININE

public static final int ARGININE
Subtype int for an arginine immonium ion.

See Also:
Constant Field Values

ASPARAGINE

public static final int ASPARAGINE
Subtype int for an asparagine immonium ion.

See Also:
Constant Field Values

ASPARTIC_ACID

public static final int ASPARTIC_ACID
Subtype int for an aspartic acid immonium ion.

See Also:
Constant Field Values

CYSTEINE

public static final int CYSTEINE
Subtype int for a cysteine immonium ion.

See Also:
Constant Field Values

GLUTAMIC_ACID

public static final int GLUTAMIC_ACID
Subtype int for a glutamic acid immonium ion.

See Also:
Constant Field Values

GLUTAMINE

public static final int GLUTAMINE
Subtype int for a glutamine immonium ion.

See Also:
Constant Field Values

GLYCINE

public static final int GLYCINE
Subtype int for a glycine immonium ion.

See Also:
Constant Field Values

HISTIDINE

public static final int HISTIDINE
Subtype int for an histidine immonium ion.

See Also:
Constant Field Values

ISOLEUCINE

public static final int ISOLEUCINE
Subtype int for an isoleucine immonium ion.

See Also:
Constant Field Values

LEUCINE

public static final int LEUCINE
Subtype int for a leucine immonium ion.

See Also:
Constant Field Values

LYSINE

public static final int LYSINE
Subtype int for a lysine immonium ion.

See Also:
Constant Field Values

METHIONINE

public static final int METHIONINE
Subtype int for a methionine immonium ion.

See Also:
Constant Field Values

PHENYLALANINE

public static final int PHENYLALANINE
Subtype int for a phenylananine immonium ion.

See Also:
Constant Field Values

PROLINE

public static final int PROLINE
Subtype int for a proline immonium ion.

See Also:
Constant Field Values

SELENOCYSTEINE

public static final int SELENOCYSTEINE
Subtype int for a selenocysteine immonium ion.

See Also:
Constant Field Values

SERINE

public static final int SERINE
Subtype int for a serine immonium ion.

See Also:
Constant Field Values

THREONINE

public static final int THREONINE
Subtype int for a threonine immonium ion.

See Also:
Constant Field Values

TRYPTOPHAN

public static final int TRYPTOPHAN
Subtype int for a tryptophan immonium ion.

See Also:
Constant Field Values

TYROSINE

public static final int TYROSINE
Subtype int for a tyrosine immonium ion.

See Also:
Constant Field Values

VALINE

public static final int VALINE
Subtype int for a valine immonium ion.

See Also:
Constant Field Values
Constructor Detail

ImmoniumIon

public ImmoniumIon(char residue)
Constructor for an immonium ion.

Parameters:
residue - the type of immonium ion as char

ImmoniumIon

public ImmoniumIon(int subType)
Constructor for an immonium ion.

Parameters:
subType - the type of immonium ion as integer as indexed by the static fields
Method Detail

getResidue

public static char getResidue(int subtype)
Returns the amino acid of the immonium ion based on the subtype index.

Parameters:
subtype - the subtype index from the static fields
Returns:
the one letter code of the amino acid

getSubtype

public static int getSubtype(char residue)
Returns the subtype identifier based on the amino acid one letter symbol.

Parameters:
residue - the amino acid as char
Returns:
the subtype as indexed by the static fields. -1 if not found.

getName

public java.lang.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 java.lang.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 java.util.ArrayList<java.lang.Integer> getPossibleSubtypes()
Returns an arraylist of possible subtypes.

Returns:
an arraylist of possible subtypes

getNeutralLosses

public java.util.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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