|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.PTM
public class PTM
This class models a post-translational modification.
Field Summary | |
---|---|
static int |
MODAA
Modification at particular amino acids. |
static int |
MODC
Modification at the C terminus of a protein. |
static int |
MODCAA
Modification at the C terminus of a protein at particular amino acids. |
static int |
MODCP
Modification at the C terminus of a peptide. |
static int |
MODCPAA
Modification at the C terminus of a peptide at particular amino acids. |
static int |
MODMAX
The max number of modification types. |
static int |
MODN
Modification at the N terminus of a protein. |
static int |
MODNAA
Modification at the N terminus of a protein at particular amino acids. |
static int |
MODNP
Modification at the N terminus of a peptide. |
static int |
MODNPAA
Modification at the N terminus of a peptide at particular amino acids. |
Constructor Summary | |
---|---|
PTM()
Constructor for the modification. |
|
PTM(int type,
String name,
double mass,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification. |
|
PTM(int type,
String name,
double mass,
ArrayList<String> residuesArray)
Deprecated. use amino acid pattern instead |
|
PTM(int type,
String name,
String shortName,
double mass,
AminoAcidPattern aminoAcidPattern)
Constructor for a reference modification. |
|
PTM(int type,
String name,
String shortName,
double mass,
ArrayList<String> residuesArray)
Deprecated. use amino acid pattern instead |
Method Summary | |
---|---|
void |
addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss. |
void |
addReporterIon(ReporterIon reporterIon)
Adds a reporter ion. |
double |
getMass()
Getter for the mass difference induced by this modification. |
String |
getName()
Getter for the modification name. |
ArrayList<NeutralLoss> |
getNeutralLosses()
Returns the neutral losses possibly encountered with this modification. |
AminoAcidPattern |
getPattern()
Returns the amino acid pattern targeted by this modification. |
ArrayList<ReporterIon> |
getReporterIons()
Returns the reporter ions possibly encountered with this modification. |
ArrayList<String> |
getResidues()
Deprecated. use amino acid pattern instead |
String |
getShortName()
Getter for the short modification name. |
int |
getType()
Getter for the modification type. |
boolean |
isSameAs(PTM anotherPTM)
Compares two PTMs. |
boolean |
isStandardSearch()
Indicates whether a modification can be searched with standard search engines, i.e., true if it targets a single amino acid position, false if it targets a complex pattern. |
void |
setName(String name)
Sets the PTM name. |
void |
setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification. |
void |
setPattern(AminoAcidPattern pattern)
Sets the amino acid pattern targeted by this modification. |
void |
setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification. |
void |
setShortName(String shortName)
Sets the short PTM name. |
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 |
---|
public static final int MODAA
public static final int MODN
public static final int MODNAA
public static final int MODC
public static final int MODCAA
public static final int MODNP
public static final int MODNPAA
public static final int MODCP
public static final int MODCPAA
public static final int MODMAX
Constructor Detail |
---|
public PTM()
public PTM(int type, String name, double mass, ArrayList<String> residuesArray)
type
- Type of modification according to static attributesname
- Name of the modificationmass
- Mass difference produced by the modificationresiduesArray
- Residue array affected by this modificationpublic PTM(int type, String name, String shortName, double mass, ArrayList<String> residuesArray)
type
- Type of modification according to static attributesname
- Name of the modificationshortName
- Short name of the modificationmass
- Mass difference produced by the modificationresiduesArray
- Residue array affected by this modificationpublic PTM(int type, String name, double mass, AminoAcidPattern aminoAcidPattern)
type
- Type of modification according to static attributesname
- Name of the modificationmass
- Mass difference produced by the modificationaminoAcidPattern
- Residue pattern affected by this modificationpublic PTM(int type, String name, String shortName, double mass, AminoAcidPattern aminoAcidPattern)
type
- Type of modification according to static attributesname
- Name of the modificationshortName
- Short name of the modificationmass
- Mass difference produced by the modificationaminoAcidPattern
- Residue pattern affected by this modificationMethod Detail |
---|
public int getType()
public String getName()
public void setName(String name)
name
- the PTM namepublic String getShortName()
public void setShortName(String shortName)
shortName
- the PTM namepublic double getMass()
public ArrayList<String> getResidues()
public boolean isSameAs(PTM anotherPTM)
anotherPTM
- another PTM
public ArrayList<NeutralLoss> getNeutralLosses()
public void setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
neutralLosses
- the neutral losses possibly encountered with this
modificationpublic void addNeutralLoss(NeutralLoss neutralLoss)
neutralLoss
- the new neutral losspublic ArrayList<ReporterIon> getReporterIons()
public void setReporterIons(ArrayList<ReporterIon> reporterIons)
reporterIons
- the reporter ions possibly encountered with this
modificationpublic void addReporterIon(ReporterIon reporterIon)
reporterIon
- the reporter ion to addpublic AminoAcidPattern getPattern()
public void setPattern(AminoAcidPattern pattern)
pattern
- the amino acid pattern targeted by this modificationpublic boolean isStandardSearch()
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |