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 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
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, String[] residuesArray)
          Constructor for a reference modification
 
Method Summary
 double getMass()
          getter for the mass difference induced by this modification
 String getName()
          getter for the modification name
 String[] getResiduesArray()
          getter for the residues affected by this modification
 int getType()
          getter for the modification type
 void setName(String name)
          Sets the ptm name
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, 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

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,
           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
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

getMass

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

Returns:
the mass difference induced by the modification

getResiduesArray

public String[] getResiduesArray()
getter for the residues affected by this modification

Returns:
an array containing potentially modified residues


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