com.compomics.util.experiment.identification.matches
Class ModificationMatch

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.identification.matches.ModificationMatch
All Implemented Interfaces:
Serializable, Cloneable

public class ModificationMatch
extends ExperimentObject

This class models the match between theoretic ptm and identification results.

Author:
Marc Vaudel
See Also:
Serialized Form

Constructor Summary
ModificationMatch(String theoreticPtm, boolean variable, int modifiedSite)
          Constructor for a modification match.
 
Method Summary
 int getModificationSite()
          Getter for the modification site, 1 is the first amino acid.
 String getTheoreticPtm()
          Getter for the theoretic PTM name.
 boolean isConfident()
          Returns a boolean indicating whether the modification is confidently localized on the sequence.
 boolean isInferred()
          Returns a boolean indicating whether the modification is inferred from another peptide.
 boolean isVariable()
          Returns a boolean indicating if the modification is variable.
 void setConfident(boolean confident)
          Sets whether the modification is confidently localized on the sequence.
 void setInferred(boolean inferred)
          Sets whether the modification is inferred from another peptide.
 void setModificationSite(int site)
          Setter for the modification site, 1 is the first amino acid.
 void setTheoreticPtm(String ptm)
          Sets the theoretic PTM.
 
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
 

Constructor Detail

ModificationMatch

public ModificationMatch(String theoreticPtm,
                         boolean variable,
                         int modifiedSite)
Constructor for a modification match.

Parameters:
theoreticPtm - the theoretic PTM
variable - true for variable modifications, false otherwise
modifiedSite - the position of the modification in the sequence, 1 is the first residue
Method Detail

isVariable

public boolean isVariable()
Returns a boolean indicating if the modification is variable.

Returns:
a boolean indicating if the modification is variable

getTheoreticPtm

public String getTheoreticPtm()
Getter for the theoretic PTM name.

Returns:
the theoretic PTM name

setTheoreticPtm

public void setTheoreticPtm(String ptm)
Sets the theoretic PTM.

Parameters:
ptm - the theoretic PTM name

getModificationSite

public int getModificationSite()
Getter for the modification site, 1 is the first amino acid.

Returns:
the index of the modification in the sequence

setModificationSite

public void setModificationSite(int site)
Setter for the modification site, 1 is the first amino acid.

Parameters:
site - the index of the modification in the sequence

isConfident

public boolean isConfident()
Returns a boolean indicating whether the modification is confidently localized on the sequence.

Returns:
a boolean indicating whether the modification is confidently localized on the sequence

setConfident

public void setConfident(boolean confident)
Sets whether the modification is confidently localized on the sequence.

Parameters:
confident - a boolean indicating whether the modification is confidently localized on the sequence

isInferred

public boolean isInferred()
Returns a boolean indicating whether the modification is inferred from another peptide.

Returns:
a boolean indicating whether the modification is inferred from another peptide

setInferred

public void setInferred(boolean inferred)
Sets whether the modification is inferred from another peptide.

Parameters:
inferred - a boolean indicating whether the modification is inferred from another peptide


Copyright © 2012. All Rights Reserved.