public class Glycan extends Ion
Ion.IonType
Modifier and Type | Field and Description |
---|---|
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.
|
atomChain, theoreticMass, type
Constructor and Description |
---|
Glycan(String name,
String longName)
Constructor for a glycan.
|
Modifier and Type | Method and Description |
---|---|
void |
addMass(int massType,
double value)
Add a mass for this glycan.
|
double |
getMass(int aType)
Get the glycan 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.
|
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, getParameterKey, getUrParam
public static final int UNDERIVATED_MASS
public static final int PERMETHYLATED_MASS
public static final int DEUTEROMETHYLATED_MASS
public static final int PERACETYLATED_MASS
public static final int DEUTEROACETYLATED_MASS
public void addMass(int massType, double value)
massType
- mass type indexed according to the static fieldvalue
- Value of the masspublic double getMass(int aType)
aType
- Type of mass requested indexed according to static int.public String getName()
Ion
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 ArrayList<Integer> getPossibleSubtypes()
public ArrayList<NeutralLoss> getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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