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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Ion
com.compomics.util.experiment.biology.ions.Glycon
public class Glycon
This class will models a glycon fragment.
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 |
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 |
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theoreticMass, type |
Constructor Summary | |
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Glycon(String name,
String longName)
Constructor for a glycon. |
Method Summary | |
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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 |
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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 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
Constructor Detail |
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public Glycon(String name, String longName)
name
- The name of the glyconlongName
- A shortened name for the glyconMethod Detail |
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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
getName
in class 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
public boolean isSameAs(Ion anotherIon)
Ion
isSameAs
in class Ion
anotherIon
- the other ion
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