public class RelatedIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
---|---|
static RelatedIon |
RELATED_C_1
Related ion for C.
|
static RelatedIon |
RELATED_C_2
Related ion for C.
|
static RelatedIon |
RELATED_D_1
Related ion for D.
|
static RelatedIon |
RELATED_E_1
Related ion for E.
|
static RelatedIon |
RELATED_F_1
Related ion for F.
|
static RelatedIon |
RELATED_H_1
Related ion for H (C4H5N2).
|
static RelatedIon |
RELATED_H_2
Related ion for H.
|
static RelatedIon |
RELATED_K_1
Related ion for K.
|
static RelatedIon |
RELATED_K_2
Related ion for K.
|
static RelatedIon |
RELATED_K_3
Related ion for K.
|
static RelatedIon |
RELATED_M_1
Related ion for M (C2H4S).
|
static RelatedIon |
RELATED_N_1
Related ion for N.
|
static RelatedIon |
RELATED_Q_1
Related ion for Q.
|
static RelatedIon |
RELATED_Q_2
Related ion for Q.
|
static RelatedIon |
RELATED_R_1
Related ion for R.
|
static RelatedIon |
RELATED_R_2
Related ion for R.
|
static RelatedIon |
RELATED_R_3
Related ion for R.
|
static RelatedIon |
RELATED_R_4
Related ion for R (C5H10N2O).
|
static RelatedIon |
RELATED_W_1
Related ion for W (C9H7N).
|
static RelatedIon |
RELATED_Y_1
Related ion for Y (C7H7O).
|
atomChain, theoreticMass, type
Constructor and Description |
---|
RelatedIon(AminoAcid aminoAcidTarget,
AtomChain atomChain,
int subType)
Constructor for a related ion.
|
RelatedIon(AminoAcid aminoAcidTarget,
AtomChain atomChain,
int subType,
boolean save)
Constructor for a related ion.
|
Modifier and Type | Method and Description |
---|---|
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.
|
static ArrayList<RelatedIon> |
getRelatedIons(AminoAcid aminoAcidTarget)
Returns the list of related ions for the given amino acid.
|
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.
|
boolean |
isSameAs(RelatedIon anotherRelatedIon)
Compares the current related ion with another one based on their
composition.
|
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, getParameterKey, getUrParam
public static final RelatedIon RELATED_R_1
public static final RelatedIon RELATED_R_2
public static final RelatedIon RELATED_R_3
public static final RelatedIon RELATED_R_4
public static final RelatedIon RELATED_N_1
public static final RelatedIon RELATED_D_1
public static final RelatedIon RELATED_C_1
public static final RelatedIon RELATED_C_2
public static final RelatedIon RELATED_E_1
public static final RelatedIon RELATED_Q_1
public static final RelatedIon RELATED_Q_2
public static final RelatedIon RELATED_H_1
public static final RelatedIon RELATED_H_2
public static final RelatedIon RELATED_K_1
public static final RelatedIon RELATED_K_2
public static final RelatedIon RELATED_K_3
public static final RelatedIon RELATED_M_1
public static final RelatedIon RELATED_F_1
public static final RelatedIon RELATED_W_1
public static final RelatedIon RELATED_Y_1
public RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType)
aminoAcidTarget
- the amino acid targetatomChain
- the atomic composition of this ionsubType
- the ion subtypepublic RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType, boolean save)
aminoAcidTarget
- the amino acid targetatomChain
- the atomic composition of this ionsubType
- the ion subtypesave
- if true the related ion will be saved in the static map for
later reusepublic static ArrayList<RelatedIon> getRelatedIons(AminoAcid aminoAcidTarget)
aminoAcidTarget
- the amino acid targetpublic String getName()
Ion
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public boolean isSameAs(RelatedIon anotherRelatedIon)
anotherRelatedIon
- the other related ionpublic int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static ArrayList<Integer> getPossibleSubtypes()
public ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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