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:
java.io.Serializable, java.lang.Cloneable

public class PTM
extends ExperimentObject

This class models a post-translational modification.

Author:
Marc Vaudel
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 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, java.lang.String name, double mass, AminoAcidPattern aminoAcidPattern)
          Constructor for a reference modification.
PTM(int type, java.lang.String name, double mass, java.util.ArrayList<java.lang.String> residuesArray)
          Deprecated. use amino acid pattern instead
PTM(int type, java.lang.String name, java.lang.String shortName, double mass, AminoAcidPattern aminoAcidPattern)
          Constructor for a reference modification.
PTM(int type, java.lang.String name, java.lang.String shortName, double mass, java.util.ArrayList<java.lang.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.
 java.lang.String getName()
          Getter for the modification name.
 java.util.ArrayList<NeutralLoss> getNeutralLosses()
          Returns the neutral losses possibly encountered with this modification.
 AminoAcidPattern getPattern()
          Returns the amino acid pattern targeted by this modification.
 java.util.ArrayList<ReporterIon> getReporterIons()
          Returns the reporter ions possibly encountered with this modification.
 java.util.ArrayList<java.lang.String> getResidues()
          Deprecated. use amino acid pattern instead
 java.lang.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(java.lang.String name)
          Sets the ptm name.
 void setNeutralLosses(java.util.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(java.util.ArrayList<ReporterIon> reporterIons)
          Sets the reporter ions possibly encountered with this modification.
 void setShortName(java.lang.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,
           java.lang.String name,
           double mass,
           java.util.ArrayList<java.lang.String> residuesArray)
Deprecated. use amino acid pattern instead

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,
           java.lang.String name,
           java.lang.String shortName,
           double mass,
           java.util.ArrayList<java.lang.String> residuesArray)
Deprecated. use amino acid pattern instead

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

PTM

public PTM(int type,
           java.lang.String name,
           double mass,
           AminoAcidPattern aminoAcidPattern)
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
aminoAcidPattern - Residue pattern affected by this modification

PTM

public PTM(int type,
           java.lang.String name,
           java.lang.String shortName,
           double mass,
           AminoAcidPattern aminoAcidPattern)
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
aminoAcidPattern - Residue pattern affected by this modification
Method Detail

getType

public int getType()
Getter for the modification type.

Returns:
the modification type

getName

public java.lang.String getName()
Getter for the modification name.

Returns:
the modification name

setName

public void setName(java.lang.String name)
Sets the ptm name.

Parameters:
name - the ptm name

getShortName

public java.lang.String getShortName()
Getter for the short modification name.

Returns:
the short modification name

setShortName

public void setShortName(java.lang.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 java.util.ArrayList<java.lang.String> getResidues()
Deprecated. use amino acid pattern instead

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 java.util.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(java.util.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 java.util.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(java.util.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

getPattern

public AminoAcidPattern getPattern()
Returns the amino acid pattern targeted by this modification.

Returns:
the amino acid pattern targeted by this modification

setPattern

public void setPattern(AminoAcidPattern pattern)
Sets the amino acid pattern targeted by this modification.

Parameters:
pattern - the amino acid pattern targeted by this modification

isStandardSearch

public 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.

Returns:
a boolean indicating whether a modification can be searched with standard search engines


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