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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Ion
com.compomics.util.experiment.biology.ions.PeptideFragmentIon
public class PeptideFragmentIon
This class models a peptide fragment ion.
Nested Class Summary |
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Nested classes/interfaces inherited from class com.compomics.util.experiment.biology.Ion |
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Ion.IonType |
Field Summary | |
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static int |
A_ION
Identifier for an a ion. |
static int |
B_ION
Identifier for a b ion. |
static int |
C_ION
Identifier for a c ion. |
static int |
X_ION
Identifier for an x ion. |
static int |
Y_ION
Identifier for a y ion. |
static int |
Z_ION
Identifier for a z ion. |
Fields inherited from class com.compomics.util.experiment.biology.Ion |
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theoreticMass, type |
Constructor Summary | |
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PeptideFragmentIon(int fragmentType)
Constructor for a generic ion without neutral losses. |
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PeptideFragmentIon(int fragmentType,
ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion. |
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PeptideFragmentIon(int fragmentType,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Constructor. |
Method Summary | |
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String |
getName()
Returns the name of the ion. |
String |
getNameWithNumber()
Returns the name with number. |
ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the possible neutral losses of this ion type. |
int |
getNumber()
Returns the number of the fragment in the sequence. |
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. |
static String |
getSubTypeAsString(int subType)
Returns the type of fragment ion as a letter. |
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 |
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getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, setTheoreticMass |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int A_ION
public static final int B_ION
public static final int C_ION
public static final int X_ION
public static final int Y_ION
public static final int Z_ION
Constructor Detail |
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public PeptideFragmentIon(int fragmentType, int number, double mass, ArrayList<NeutralLoss> neutralLosses)
fragmentType
- the type of peptide fragment ion as indexed by the
static fieldsnumber
- the number of the fragment ionmass
- the mass of the fragment ionneutralLosses
- the neutral losses of the ionpublic PeptideFragmentIon(int fragmentType, ArrayList<NeutralLoss> neutralLosses)
fragmentType
- the type of peptide fragment ion as indexed by the
static fieldsneutralLosses
- the neutral losses of the ionpublic PeptideFragmentIon(int fragmentType)
fragmentType
- the type of peptide fragment ion as indexed by the
static fieldsMethod Detail |
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public int getNumber()
public ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
public String getName()
Ion
getName
in class Ion
public String getNameWithNumber()
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static String getSubTypeAsString(int subType)
subType
- the subtype
public static ArrayList<Integer> getPossibleSubtypes()
public boolean isSameAs(Ion anotherIon)
Ion
isSameAs
in class Ion
anotherIon
- the other ion
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