com.compomics.util.experiment.biology
Class PTM

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.PTM
All Implemented Interfaces:
Serializable, Cloneable

public class PTM
extends ExperimentObject

This class models a post-translational modification. Created by IntelliJ IDEA. User: Marc Date: Jun 22, 2010 Time: 8:02:00 PM

See Also:
Serialized Form

Field Summary
static int MODC
          modification at the C terminus of a protein
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 MODCAA
          modification at the C terminus of a protein 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 MODNP
          modification at the N terminus of a peptide
static int MODNPAA
          modification at the N terminus of a peptide at particular amino acids
static int MODNAA
          modification at the N terminus of a protein at particular amino acids
static int MODAA
          modification at particular amino acids
 
Constructor Summary
PTM()
          Constructor for the modification
PTM(int type, String name, double mass, ArrayList<String> residuesArray)
          Constructor for a reference modification
PTM(int type, String name, String shortName, double mass, ArrayList<String> residuesArray)
          Constructor for a reference modification
 
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
 ArrayList<ReporterIon> getReporterIons()
          Returns the reporter ions possibly encountered with this modification
 ArrayList<String> getResidues()
          getter for the residues affected by this modification
 String getShortName()
          getter for the short modification name
 int getType()
          getter for the modification type
 boolean isSameAs(PTM anotherPTM)
          Compares two PTMs
 void setName(String name)
          Sets the ptm name
 void setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
          Sets the neutral losses possibly encountered with 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

MODAA

public static final int MODAA
modification at particular amino acids

See Also:
Constant Field Values

MODN

public static final int MODN
modification at the N terminus of a protein

See Also:
Constant Field Values

MODNAA

public static final int MODNAA
modification at the N terminus of a protein at particular amino acids

See Also:
Constant Field Values

MODC

public static final int MODC
modification at the C terminus of a protein

See Also:
Constant Field Values

MODCAA

public static final int MODCAA
modification at the C terminus of a protein at particular amino acids

See Also:
Constant Field Values

MODNP

public static final int MODNP
modification at the N terminus of a peptide

See Also:
Constant Field Values

MODNPAA

public static final int MODNPAA
modification at the N terminus of a peptide at particular amino acids

See Also:
Constant Field Values

MODCP

public static final int MODCP
modification at the C terminus of a peptide

See Also:
Constant Field Values

MODCPAA

public static final int MODCPAA
modification at the C terminus of a peptide at particular amino acids

See Also:
Constant Field Values

MODMAX

public static final int MODMAX
the max number of modification types

See Also:
Constant Field Values
Constructor Detail

PTM

public PTM()
Constructor for the modification


PTM

public PTM(int type,
           String name,
           double mass,
           ArrayList<String> residuesArray)
Constructor for a reference modification

Parameters:
type - Type of modification according to static attributes
name - Name of the modification
mass - Mass difference produced by the modification
residuesArray - Residue array affected by this modification

PTM

public PTM(int type,
           String name,
           String shortName,
           double mass,
           ArrayList<String> residuesArray)
Constructor for a reference modification

Parameters:
type - Type of modification according to static attributes
name - Name of the modification
shortName - Short name of the modification
mass - Mass difference produced by the modification
residuesArray - Residue array affected by this modification
Method Detail

getType

public int getType()
getter for the modification type

Returns:
the modification type

getName

public String getName()
getter for the modification name

Returns:
the modification name

setName

public void setName(String name)
Sets the ptm name

Parameters:
name - the ptm name

getShortName

public String getShortName()
getter for the short modification name

Returns:
the short modification name

setShortName

public void setShortName(String shortName)
Sets the short ptm name

Parameters:
shortName - the ptm name

getMass

public double getMass()
getter for the mass difference induced by this modification

Returns:
the mass difference induced by the modification

getResidues

public ArrayList<String> getResidues()
getter for the residues affected by this modification

Returns:
an array containing potentially modified residues

isSameAs

public boolean isSameAs(PTM anotherPTM)
Compares two PTMs

Parameters:
anotherPTM - another PTM
Returns:
true if the given PTM is the same as the current ptm

getNeutralLosses

public ArrayList<NeutralLoss> getNeutralLosses()
Returns the neutral losses possibly encountered with this modification

Returns:
the neutral losses possibly encountered with this modification

setNeutralLosses

public void setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification

Parameters:
neutralLosses - the neutral losses possibly encountered with this modification

addNeutralLoss

public void addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss

Parameters:
neutralLoss - the new neutral loss

getReporterIons

public ArrayList<ReporterIon> getReporterIons()
Returns the reporter ions possibly encountered with this modification

Returns:
the reporter ions possibly encountered with this modification

setReporterIons

public void setReporterIons(ArrayList<ReporterIon> reporterIons)
Sets the reporter ions possibly encountered with this modification

Parameters:
reporterIons - the reporter ions possibly encountered with this modification

addReporterIon

public void addReporterIon(ReporterIon reporterIon)
Adds a reporter ion

Parameters:
reporterIon - the reporter ion to add


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